Contacts of the strand formed by residues 81 - 101 (chain A) in PDB entry 4EWS
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 SER 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 2.8 34.7 + - - +
80A LYS* 1.3 97.4 + - - +
82A ILE* 1.4 62.4 - - - +
83A ASP* 2.7 23.3 + - - -
126A ASN* 3.8 5.7 - - - +
127A THR 3.2 25.1 - - - -
128A GLN* 4.2 6.5 - - - -
223A ILE* 3.7 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.6 9.0 - - + -
74A VAL* 3.7 27.4 - - + -
75A GLU 3.9 2.0 - - - -
76A LEU* 3.9 12.6 - - + -
81A SER* 1.4 70.7 - - - +
83A ASP* 1.3 60.2 + - - +
84A VAL* 3.8 7.6 + - + +
125A ILE 3.4 4.2 - - - +
127A THR* 2.9 40.5 + - - +
129A LEU* 3.6 35.9 - - + -
223A ILE* 4.4 4.7 - - + -
228A LEU* 4.0 25.8 - - + -
501A 2OB 4.0 26.5 - - + -
505A PGE 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN 3.7 1.4 - - - +
74A VAL* 3.4 3.2 - - - -
75A GLU* 2.8 52.7 + - + +
77A VAL* 3.3 19.8 - - - +
80A LYS* 3.2 14.8 + - - -
81A SER* 2.7 27.4 + - - -
82A ILE* 1.3 71.8 - - - +
84A VAL* 1.3 61.4 + - - +
85A SER* 4.2 1.4 + - - -
124A GLN* 3.7 11.3 + - - +
125A ILE 3.6 3.4 - - - -
126A ASN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 5.3 1.8 - - - +
27A THR* 4.3 9.6 - - + -
72A SER* 5.9 0.2 - - - -
73A GLN 3.3 7.4 - - - +
74A VAL* 3.9 21.5 - - + -
82A ILE* 4.5 10.3 - - + +
83A ASP* 1.3 77.0 - - - +
85A SER* 1.3 59.7 + - - +
86A ILE* 3.6 19.9 + - + -
124A GLN* 3.4 5.1 - - - +
125A ILE* 2.7 47.7 + - + +
127A THR* 6.0 0.4 - - - +
501A 2OB 3.5 41.3 - - + -
505A PGE 5.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 3.2 6.1 - - - -
73A GLN* 2.8 44.6 + - - +
83A ASP 5.0 1.2 + - - -
84A VAL* 1.3 72.0 - - - +
86A ILE* 1.3 62.3 + - - +
87A GLN* 3.3 18.5 - - - +
123A LEU 3.4 7.9 - - - -
124A GLN* 2.6 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.3 2.9 - - + -
31A ILE* 3.8 24.9 - - + -
69A ILE* 3.4 41.1 - - + -
71A SER 3.6 2.2 - - - -
72A SER* 3.9 13.7 - - - -
84A VAL* 3.6 18.6 - - + +
85A SER* 1.3 74.8 - - - +
87A GLN* 1.3 64.5 + - - +
89A VAL* 4.4 13.2 - - + -
121A ILE 4.5 0.2 - - - +
122A ASP* 3.4 4.9 - - - +
123A LEU* 2.8 43.3 + - + +
125A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.4 19.2 + - - +
71A SER* 2.9 24.3 + - - +
73A GLN* 2.7 39.5 + - - +
85A SER* 3.3 26.5 - - - +
86A ILE* 1.3 77.6 - - - +
88A ASP* 1.3 78.4 + - - +
89A VAL 3.7 0.8 + - - -
122A ASP* 3.3 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 3.2 5.7 + - - +
70A ALA* 3.2 32.3 + - + +
87A GLN* 1.3 79.6 - - - +
89A VAL* 1.3 60.7 + - - +
90A SER* 3.4 5.2 + - - -
120A ALA* 5.6 6.7 - - + +
121A ILE 3.5 6.9 + - - +
122A ASP* 2.8 20.9 + - - +
148A HIS* 4.5 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 5.4 0.2 - - + -
35A PHE* 4.2 13.2 - - + -
67A LEU* 3.7 29.8 - - + -
68A SER 3.3 4.0 - - - -
69A ILE* 3.7 22.0 - - + +
86A ILE* 4.4 10.1 - - + -
87A GLN 3.7 0.4 - - - -
88A ASP* 1.3 68.0 - - - +
90A SER* 1.3 59.8 + - - +
91A VAL* 3.4 18.7 + - + +
120A ALA* 3.6 1.7 - - - -
121A ILE* 2.8 56.1 + - + +
123A LEU* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 3.6 18.0 + - - -
67A LEU* 3.4 6.1 - - - -
68A SER* 2.8 46.6 + - - -
88A ASP 3.4 4.5 + - - -
89A VAL* 1.3 68.2 - - - +
91A VAL* 1.4 58.5 + - - +
92A VAL* 4.9 4.7 - - - +
118A ASP* 4.9 4.7 + - - -
119A SER 3.7 5.5 + - - -
120A ALA* 4.7 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.8 24.9 - - + -
64A ILE* 3.8 23.6 - - + -
66A HIS 3.6 2.2 - - - +
67A LEU* 4.5 4.5 - - + -
89A VAL* 3.6 29.6 - - + +
90A SER* 1.4 72.6 - - - +
92A VAL* 1.3 68.7 + - - +
93A PHE* 3.6 24.2 - - + -
117A ILE 3.7 0.5 - - - +
118A ASP* 4.0 0.5 - - - +
119A SER* 2.8 49.7 + - - +
121A ILE* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.5 3.3 - - - +
65A SER* 2.6 50.1 + - - +
66A HIS* 3.0 35.2 + - + +
90A SER* 4.9 2.7 - - - +
91A VAL* 1.3 79.6 - - - +
93A PHE* 1.3 62.1 + - - +
116A GLU* 4.2 20.6 - - + +
117A ILE 3.4 9.2 - - - +
118A ASP* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 5.0 4.7 - + - -
40A TYR* 4.2 11.0 - + - -
62A ILE* 4.0 26.5 - - + -
63A GLN 3.3 9.0 - - - +
64A ILE* 4.2 20.6 - - + -
91A VAL* 3.6 26.2 - - + -
92A VAL* 1.3 76.8 - - - +
94A LYS* 1.3 59.5 + - - +
115A PHE* 5.2 1.3 - - + -
116A GLU* 3.1 8.5 - - - +
117A ILE* 2.8 61.2 + - + +
119A SER* 3.3 25.4 - - - -
175A LEU* 5.8 3.6 - - + -
179A LEU* 3.6 42.4 - - + -
----------------------------------------------------------
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 ASN* 3.3 5.5 - - - +
62A ILE* 3.3 7.6 - - - +
63A GLN* 2.8 55.2 + - + +
64A ILE 5.7 1.7 + - - -
65A SER* 4.3 22.0 - - - +
92A VAL 4.3 0.2 + - - -
93A PHE* 1.3 75.0 - - - +
95A GLY* 1.3 60.1 + - - +
115A PHE* 3.4 16.3 - - - +
116A GLU* 4.7 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS 3.4 12.8 - - - -
61A ASN* 3.6 9.6 - - - -
94A LYS* 1.3 80.2 - - - +
96A THR* 1.3 62.7 + - - -
114A ASP* 3.4 8.5 - - - +
115A PHE* 3.0 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY 3.4 2.9 - - - +
60A HIS* 2.8 46.1 + - - +
61A ASN* 5.0 7.5 + - - +
95A GLY* 1.3 74.2 - - - -
97A LEU* 1.3 61.4 + - - +
98A LYS* 3.8 18.3 + - + -
112A SER* 3.2 27.1 - - - +
113A ILE 3.5 6.1 - - - +
114A ASP* 3.4 19.4 + - - +
115A PHE* 3.4 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.4 9.6 - - + -
58A GLY 3.4 17.9 - - - +
59A LEU* 3.9 21.1 - - + -
96A THR* 1.3 70.6 - - - +
98A LYS* 1.3 66.5 + - - +
99A TYR* 4.0 17.0 + - + -
111A GLN 4.1 0.5 - - - +
112A SER* 3.4 2.6 + - - -
113A ILE* 2.5 49.5 + - + +
115A PHE* 3.5 13.8 - - + -
152A LEU* 5.5 0.7 - - + -
154A LEU* 3.7 26.0 - - + -
162A TRP* 4.7 4.0 - - + -
163A ILE* 3.9 31.0 - - + -
166A LEU* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS 4.1 0.2 - - - +
57A TYR* 3.3 3.1 - - - +
58A GLY* 2.8 32.7 + - - -
60A HIS* 3.8 30.5 - - + +
96A THR* 4.0 11.4 - - + -
97A LEU* 1.3 78.2 - - - +
99A TYR* 1.3 61.8 + - - +
111A GLN 3.4 8.5 - - - +
112A SER* 3.7 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 4.4 3.4 - - + -
56A LYS 3.1 14.4 - - - +
57A TYR* 4.0 4.5 - - + -
97A LEU* 4.0 14.8 - - + -
98A LYS* 1.3 73.7 - - - +
100A GLY* 1.3 63.4 + - - +
101A TYR* 3.5 30.5 + + - -
110A ASP* 3.4 7.8 - - - +
111A GLN* 2.9 54.9 + - + +
113A ILE* 3.5 26.1 - - + +
158A ARG* 3.3 26.2 + - - -
160A PRO* 4.1 3.4 - - + +
162A TRP* 3.4 40.8 - + + -
163A ILE* 4.4 4.9 - - + -
506A CL 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.4 6.5 - - - -
56A LYS* 3.0 30.8 + - - +
99A TYR* 1.3 81.1 - - - +
101A TYR* 1.4 65.2 + - - -
102A THR* 3.3 7.1 + - - -
110A ASP* 3.3 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 21.1 - - + +
54A GLN 3.8 4.5 - - - +
55A VAL* 3.7 20.0 - - + -
99A TYR* 3.5 27.0 + + - -
100A GLY* 1.4 69.0 - - - -
102A THR* 1.3 64.4 - - - +
103A THR 3.6 1.6 - - - -
104A ALA* 3.4 32.1 - - + +
105A TRP* 3.8 6.2 + - - +
107A LEU* 4.0 36.8 - - + -
108A GLY 4.9 10.1 + - - +
109A ILE 5.2 4.5 - - - -
110A ASP* 4.3 4.2 + - - +
111A GLN* 5.3 4.9 - - + -
160A PRO* 3.5 16.8 - - - +
162A TRP* 3.2 30.6 + + - -
----------------------------------------------------------
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