Contacts of the strand formed by residues 82 - 95 (chain A) in PDB entry 5IXM
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 ALA 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 3.1 10.8 - - - +
69A ASP* 3.1 27.7 + - + +
72A TYR* 4.4 16.1 - - + +
73A THR 4.3 8.0 - - - +
79A ASP* 3.3 35.2 - - + +
80A LYS 4.1 0.9 - - - -
81A ASN* 1.3 77.9 - - - +
83A THR* 1.3 63.3 + - - +
84A ARG* 3.8 1.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
65A TRP* 3.5 32.8 - - + +
66A LEU 3.4 10.1 - - - +
67A PRO* 3.1 16.0 + - + +
81A ASN 5.0 1.0 + - - -
82A ALA* 1.3 75.4 - - - +
84A ARG* 1.3 67.9 + - - +
85A TRP* 3.8 19.9 + - + -
109A SER* 3.9 6.6 + - - -
110A ASP* 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.4 9.1 - - - +
45A GLN* 5.7 0.4 + - - -
64A ASP 4.5 0.2 - - - -
65A TRP* 3.7 0.5 - - - -
66A LEU* 2.8 46.7 + - + +
69A ASP* 2.9 29.4 + - + +
72A TYR* 3.1 32.0 - - - -
82A ALA* 5.2 0.9 - - - -
83A THR* 1.3 75.8 - - - +
85A TRP* 1.3 63.6 + - - +
109A SER* 3.5 2.9 - - - +
110A ASP* 2.5 42.6 + - - -
112A ALA 3.5 12.9 + - - -
113A TYR* 3.6 10.2 - - + +
116A ASP* 2.1 42.3 + - - +
117A LEU* 3.7 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 5.0 8.1 - - + -
64A ASP 3.1 11.7 - - - +
65A TRP* 4.7 11.2 - + + -
83A THR* 3.8 19.5 + - + -
84A ARG* 1.3 75.6 - - - +
86A LEU* 1.3 69.9 + - - +
87A TYR* 4.2 9.0 - - + -
107A ARG* 3.6 59.7 - - + -
108A VAL* 3.5 9.1 - - - -
109A SER* 3.0 54.7 + - - -
113A TYR* 3.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 4.6 3.8 - - + +
63A LEU* 3.3 11.2 - - - +
64A ASP* 2.9 43.2 + - + +
85A TRP* 1.3 75.8 - - - +
87A TYR* 1.3 74.4 + - - +
88A TYR* 4.1 13.9 - - + +
106A THR* 4.7 4.3 - - + -
107A ARG 3.5 5.2 - - - +
108A VAL* 3.6 12.6 - - + -
113A TYR* 3.3 28.7 - - + +
114A PHE* 3.5 34.3 - - + -
119A SER* 4.1 7.6 - - - +
121A TYR* 4.4 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.2 33.7 - - + +
62A ALA 3.3 14.4 - - - -
63A LEU* 4.6 15.7 - - + -
85A TRP* 4.2 10.5 - - + -
86A LEU* 1.3 76.3 - - - +
88A TYR* 1.3 68.5 + - - +
89A TRP* 3.8 26.0 - + + +
105A TYR* 3.6 33.0 - + - -
106A THR* 3.5 4.3 - - - +
107A ARG* 2.9 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.4 25.8 - - - -
61A MET* 3.2 4.5 - - - +
62A ALA* 2.9 44.2 + - + +
86A LEU* 4.1 6.7 - - + -
87A TYR* 1.3 81.8 - - - +
89A TRP* 1.3 64.6 + - - +
90A GLY* 3.5 19.1 - - - -
104A ASN* 4.5 13.6 + - - -
105A TYR 3.4 9.4 - - - -
106A THR* 3.2 24.5 - - - +
121A TYR* 3.4 53.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 2.8 30.7 + + - -
60A THR 3.5 3.4 - - - -
61A MET* 3.5 27.6 - - + +
87A TYR* 3.8 27.8 - + + +
88A TYR* 1.3 79.0 - - - +
90A GLY* 1.3 79.2 + - - +
91A HIS* 4.1 2.7 - + + +
103A ILE* 3.4 38.7 - - + +
104A ASN* 3.8 0.2 - - - -
105A TYR* 2.9 42.8 + + + +
133A PHE* 4.3 16.4 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
59A GLY* 3.1 3.4 - - - -
60A THR* 2.9 36.8 + - - +
88A TYR* 3.5 21.4 - - - -
89A TRP* 1.3 78.1 - - - +
91A HIS* 1.3 62.3 + - - +
103A ILE 3.2 7.4 - - - -
104A ASN* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 2.7 34.5 + + - +
56A PRO* 2.9 32.3 + - + +
57A GLY* 3.4 32.1 - - - -
58A SER 3.5 5.5 + - - -
89A TRP* 4.1 2.4 - + - +
90A GLY* 1.3 74.3 - - - +
92A SER* 1.3 76.1 + - - +
101A PHE* 3.8 26.8 - - + +
102A ASN* 3.4 4.0 - - - +
103A ILE* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 3.3 0.2 - - - -
58A SER* 2.9 39.5 + - - -
91A HIS* 1.3 80.6 - - - +
93A GLY* 1.3 59.8 + - - +
101A PHE 3.4 6.5 - - - -
102A ASN* 3.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 3.5 18.6 + - - +
57A GLY* 3.6 6.1 - - - -
92A SER* 1.3 75.6 - - - +
94A VAL* 1.3 65.7 + - - +
99A TRP 3.9 0.2 - - - +
100A ARG* 3.6 2.6 - - - +
101A PHE* 2.9 35.3 + - - +
102A ASN* 4.2 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA 4.5 4.4 + - - +
56A PRO 5.0 0.2 - - - -
57A GLY* 5.1 0.2 - - - -
93A GLY* 1.3 76.8 - - - +
95A MET* 1.3 59.0 + - - +
96A ASP 3.7 2.3 + - - -
97A GLN* 3.8 33.1 + - - +
99A TRP 3.1 13.5 - - - +
100A ARG* 3.6 24.5 - - + +
22B SER 5.7 4.0 - - - +
23B ASP* 3.6 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 3.5 28.7 + - + +
56A PRO* 3.9 29.1 + - + -
93A GLY 4.0 1.8 + - - -
94A VAL* 1.3 69.3 - - - +
96A ASP* 1.3 87.4 + - - +
97A GLN 3.1 1.8 - - - -
99A TRP* 2.9 54.6 + - + +
101A PHE* 3.6 25.8 - - + -
----------------------------------------------------------
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