Contacts of the strand formed by residues 81 - 109 (chain A) in PDB entry 5D8F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 4.0 25.8 - - - +
77A VAL* 3.3 6.3 - - - -
78A PHE 2.9 33.4 + - - +
79A LYS* 3.2 12.4 - - - -
80A GLY* 1.3 81.5 - - - +
82A LEU* 1.3 65.7 + - - +
83A THR* 3.2 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL 5.5 1.6 - - - +
10A ILE* 3.3 28.9 - - + +
11A LYS* 4.7 1.6 - - + -
12A PRO* 3.8 31.9 - - + -
50A ILE* 3.6 27.3 - - + +
51A ASN* 3.5 23.0 + - - +
75A ALA* 4.2 12.3 - - + -
76A SER 3.3 17.5 - - - +
77A VAL* 4.8 2.7 - - + +
80A GLY 4.2 0.4 + - - -
81A CYS* 1.3 73.2 - - - +
83A THR* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 5.2 0.9 - - + -
50A ILE* 4.8 2.7 - - - -
51A ASN* 3.3 17.7 + - + +
52A ILE 4.3 0.2 - - - -
53A SER* 3.5 28.0 - - - +
75A ALA* 3.4 4.7 - - - -
76A SER 2.9 36.3 + - - -
78A PHE* 3.5 21.1 + - + +
81A CYS* 3.2 14.2 + - - +
82A LEU* 1.3 76.3 + - - +
84A LEU* 1.3 74.3 + - - +
85A TYR* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.4 7.2 - - + -
17A LEU* 3.7 31.2 - - + -
19A LEU* 3.6 28.5 - - + -
21A PHE* 4.7 7.4 - - + -
43A VAL* 4.8 1.3 - - + -
50A ILE* 3.8 31.6 - - + -
51A ASN 2.7 14.4 + - - +
52A ILE* 3.3 18.7 - - + +
53A SER 3.0 26.3 + - - -
70A LEU* 4.2 22.7 - - + -
74A TYR 3.6 8.1 - - - +
75A ALA* 4.7 2.9 - - + -
83A THR* 1.3 76.6 - - - +
85A TYR* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.9 2.0 - - - -
53A SER* 4.2 26.9 - - - -
55A TRP* 5.4 10.1 - + - -
70A LEU* 4.2 5.3 - - - +
73A GLY* 3.1 6.1 - - - -
74A TYR* 2.9 76.7 + + + +
76A SER* 3.6 23.1 - - - -
77A VAL 4.4 3.5 + - - -
78A PHE* 3.1 34.2 - + - +
83A THR* 3.6 24.5 - - + -
84A LEU* 1.3 76.9 - - - +
86A THR* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 5.0 2.1 - - - +
53A SER 4.7 5.2 + - - -
54A VAL* 5.0 4.8 - - - +
58A VAL* 5.6 1.8 - - - +
70A LEU* 3.7 20.4 - - + +
74A TYR* 4.0 6.1 - - - -
85A TYR* 1.3 72.5 - - - +
87A GLY* 1.3 72.3 + - - +
88A ARG 3.9 0.7 + - - -
90A GLY* 3.9 21.8 - - - +
91A ASP* 4.1 5.6 - - - +
92A LEU* 3.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS 3.2 22.3 + - - -
74A TYR* 3.8 20.5 - - - -
85A TYR 3.6 3.6 + - - -
86A THR* 1.3 79.0 - - - +
88A ARG* 1.3 59.1 + - - -
90A GLY* 2.7 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 4.7 6.8 + - - +
86A THR 3.9 1.2 + - - -
87A GLY* 1.3 71.7 - - - -
89A GLY* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 5.4 0.7 + - - -
72A LYS* 3.2 28.2 + - - +
88A ARG* 1.3 73.1 - - - +
90A GLY* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.1 18.6 - - - -
72A LYS* 3.6 6.5 - - - +
86A THR* 3.9 11.8 - - - +
87A GLY 2.7 16.7 + - - +
88A ARG 3.2 0.2 - - - -
89A GLY* 1.3 82.6 + - - +
91A ASP* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG 3.4 1.3 - - - +
70A LEU* 3.4 7.2 - - - +
71A THR* 2.9 41.8 + - - +
86A THR* 4.1 6.0 - - - +
90A GLY* 1.3 77.3 - - - +
92A LEU* 1.3 78.7 + - - +
93A GLN* 3.7 18.5 + - + +
109B SER* 2.7 33.7 + - - -
110B HIS 3.2 10.2 - - - +
111B HIS* 4.5 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.0 9.6 - - + -
52A ILE* 4.4 6.3 - - + -
54A VAL* 3.7 31.0 - - + -
58A VAL* 3.9 13.0 - - + -
62A ILE* 4.6 12.3 - - + -
68A ILE* 3.7 17.7 - - + -
69A ARG 3.5 0.4 - - - -
70A LEU* 3.6 34.8 - - + -
86A THR* 3.8 15.7 - - + +
91A ASP* 1.3 78.7 + - - +
93A GLN* 1.3 62.0 + - - +
109B SER* 3.4 3.5 - - - -
110B HIS* 2.8 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.2 6.3 - - - +
69A ARG* 2.8 56.9 + - + +
71A THR* 5.4 5.1 + - - +
91A ASP* 3.7 23.9 + - + +
92A LEU* 1.3 76.2 - - - +
94A LYS* 1.3 63.6 + - - +
95A ILE* 3.3 5.4 + - + +
107B ASN* 3.6 47.3 + - - +
108B PHE 3.3 3.6 - - - +
109B SER* 4.2 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 2.9 23.6 + - + +
63A GLN* 5.1 1.5 - - - +
66A ASP* 2.6 39.9 + - + -
67A ILE 3.6 4.7 - - - +
68A ILE* 4.3 3.6 - - + +
93A GLN* 1.3 68.9 - - - +
95A ILE* 1.3 58.5 + - - +
96A GLY 3.7 13.2 - - - +
97A GLU* 3.2 28.9 - - - +
105B VAL* 3.3 27.9 - - + +
107B ASN* 3.5 2.4 - - - -
108B PHE* 2.8 37.9 + - + +
110B HIS* 3.5 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.2 28.7 - - + -
67A ILE* 2.7 38.3 + - + +
68A ILE 4.4 0.2 - - - +
69A ARG* 4.0 21.1 - - + +
93A GLN* 3.6 14.4 - - + +
94A LYS* 1.3 74.8 - - - +
96A GLY* 1.3 58.9 + - - +
200A PEG 4.7 9.0 - - - -
102B TYR* 4.1 3.6 + - - +
104B GLU* 3.8 8.0 - - - +
105B VAL* 3.0 29.8 + - - +
107B ASN* 3.4 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.6 2.9 - - - -
67A ILE* 2.9 35.5 + - - +
94A LYS* 3.6 8.4 - - - +
95A ILE* 1.3 81.7 - - - +
97A GLU* 1.3 66.0 + - - +
102B TYR* 3.5 17.7 - - - -
103B SER 3.8 5.8 - - - -
105B VAL* 4.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY 4.3 5.6 - - - -
66A ASP* 3.6 14.9 - - - +
94A LYS* 3.2 20.4 - - - +
96A GLY* 1.3 75.9 - - - +
98A PHE* 1.3 64.0 + - - +
99A CYS* 3.5 27.9 - - - -
102B TYR* 3.4 7.5 - - - -
103B SER* 2.8 46.3 + - - +
105B VAL* 3.6 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.7 10.3 - - + -
64A PRO 5.3 5.8 + - - +
65A GLY* 3.4 36.1 + - - -
66A ASP* 4.8 1.2 + - - +
67A ILE* 5.1 2.7 - - + -
97A GLU* 1.3 77.5 - - - +
99A CYS* 1.3 64.3 + - - +
100B MET* 4.3 36.6 - - + -
101B VAL* 3.4 3.8 - - - +
102B TYR* 3.6 46.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 3.5 36.3 - - - -
98A PHE* 1.3 76.8 - - - +
100A MET* 1.3 67.4 + - - +
101A VAL* 3.9 3.5 + - + -
100B MET* 3.4 6.0 - - - -
101B VAL* 2.8 38.6 + - + +
103B SER* 4.9 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A CYS* 1.3 77.0 - - - +
101A VAL* 1.3 67.7 + - - +
98B PHE* 4.2 28.0 - - + -
99B CYS 3.4 10.8 - - - +
100B MET* 4.8 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A CYS* 4.7 3.8 - - + +
100A MET* 1.3 80.1 - - - +
102A TYR* 1.3 67.1 + - - +
103A SER* 5.7 1.3 - - - -
98B PHE* 3.3 8.6 - - - -
99B CYS* 2.7 47.7 + - + +
101B VAL* 3.7 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 1.3 82.0 - - - +
103A SER* 1.3 63.0 + - - +
104A GLU* 3.6 31.8 - - + +
67B ILE* 4.0 25.7 - - + +
95B ILE* 3.6 18.5 + - - +
96B GLY* 3.7 5.8 - - - -
97B GLU 3.6 17.3 - - - -
98B PHE* 3.6 33.3 - + + -
200B PEG 4.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 5.7 1.1 - - - -
102A TYR* 1.3 80.5 - - - +
104A GLU* 1.3 71.6 + - - +
105A VAL* 3.5 4.2 + - - +
96B GLY* 3.7 0.2 - - - -
97B GLU* 2.8 49.9 + - - +
99B CYS* 4.3 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.6 27.8 - - + +
103A SER* 1.3 80.5 + - - +
105A VAL* 1.3 61.0 + - - +
106A PRO* 4.0 6.2 - - - +
95B ILE 3.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 3.6 11.9 - - - +
104A GLU* 1.3 78.5 - - - +
106A PRO* 1.3 61.6 - - + +
107A ASN 2.7 15.2 + - - -
108A PHE* 3.8 20.9 - - + +
94B LYS* 3.3 30.5 - - + +
95B ILE* 3.0 26.6 + - - +
96B GLY 3.9 15.7 - - - +
97B GLU* 4.0 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU 4.0 6.5 - - - +
105A VAL* 1.3 84.6 - - + +
107A ASN* 1.3 74.9 + - - +
108A PHE* 3.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL 2.7 13.3 + - - -
106A PRO* 1.3 77.4 - - - +
108A PHE* 1.3 58.8 + - - +
109A SER* 3.5 5.8 + - - -
69B ARG* 4.2 10.0 + - - +
93B GLN* 4.2 27.2 + - - +
94B LYS 3.7 5.4 - - - -
95B ILE* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 3.8 21.1 - - + -
106A PRO 4.6 0.7 - - - +
107A ASN* 1.3 71.7 - - - +
109A SER* 1.3 68.7 + - - +
110A HIS* 3.4 16.9 - + - -
112A HIS* 3.3 40.8 - + + -
61B LEU* 4.5 16.8 - - + -
93B GLN* 4.2 0.7 - - - -
94B LYS* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN 3.5 6.8 + - - -
108A PHE* 1.3 76.8 - - - +
110A HIS* 1.3 53.1 + - - +
111A HIS 3.2 15.9 + - - -
112A HIS* 2.3 45.1 + - - +
91B ASP* 2.5 35.9 + - - -
92B LEU 3.5 6.5 - - - -
93B GLN* 4.0 9.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il