Contacts of the strand formed by residues 87 - 95 (chain B) in PDB entry 3UX9
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B GLN* 3.9 9.0 - - + -
41B GLN 3.2 20.0 - - - +
42B LEU* 3.5 17.9 - - + +
43B PRO* 4.9 0.9 - - - -
85B ASP 2.9 10.0 + - - +
86B GLU* 1.3 76.8 - - - +
88B ASP* 1.3 61.5 + - - +
89B TYR* 3.4 13.9 - - + -
108B LYS* 3.7 14.5 - - - +
109B LEU 2.9 28.1 + - - -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR 3.9 0.3 - - - +
40B GLN* 3.6 0.5 - - - -
41B GLN* 2.9 49.4 + - + +
42B LEU 5.8 0.7 - - - -
43B PRO* 5.9 1.2 - - - +
87B ALA* 1.3 75.9 - - - +
89B TYR* 1.3 64.5 + - - +
90B TYR* 3.6 30.2 + - + +
107B THR 3.2 7.9 - - - +
108B LYS* 3.4 29.7 + - - +
173B GLN* 5.1 2.1 + - - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.0 13.0 + - - -
22B ILE* 3.9 21.8 - - + -
38B TRP* 4.8 3.1 - - + -
39B TYR 3.4 7.6 - - - +
40B GLN* 2.8 36.4 + - + -
50B LEU* 3.7 17.3 - - + -
65B PHE* 4.3 7.5 - + - -
76B LEU* 3.7 22.4 - - + -
78B ILE* 4.2 9.5 - - + +
85B ASP* 2.4 42.8 + - - +
87B ALA* 3.4 19.7 - - + -
88B ASP* 1.3 78.8 - - - +
90B TYR* 1.3 61.8 + - - +
106B GLY* 3.3 1.2 - - - -
107B THR* 2.9 33.3 + - - +
109B LEU* 3.5 17.9 - - + -
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.5 1.8 - - - -
38B TRP* 3.2 7.7 - - - -
39B TYR* 2.7 49.3 + - + +
40B GLN 5.8 0.2 - - - -
41B GLN* 3.9 16.5 + - + -
47B PRO* 5.9 0.2 - - + -
88B ASP* 3.6 33.3 - - + +
89B TYR* 1.3 77.1 - - - +
91B CYS* 1.3 66.2 + - - +
103B PHE* 4.1 11.4 - - + -
104B GLY 3.5 19.3 - - - -
105B GLY 4.1 0.9 + - - -
106B GLY* 3.5 20.9 - - - -
173B GLN* 3.3 22.4 + - - -
177B LYS 4.7 0.2 - - - -
178B GLY* 3.3 12.3 - - - -
179B LEU* 3.4 44.2 - - + -
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Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.6 12.8 - - + -
8B GLN* 3.3 20.5 + - - -
24B CYS* 2.0 46.7 - - + -
36B VAL* 4.7 4.0 - - + -
37B SER 3.3 6.7 - - - +
38B TRP* 3.7 19.4 - - + -
90B TYR* 1.3 76.3 - - - +
92B GLN* 1.3 63.5 + - - +
103B PHE* 3.3 6.4 - - - -
104B GLY* 3.1 26.5 + - - -
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 5.0 0.9 - - - -
36B VAL* 3.6 4.1 - - - +
37B SER* 2.8 48.2 + - - +
39B TYR* 3.5 22.9 + - + -
91B CYS* 1.3 78.7 - - - +
93B VAL* 1.3 76.0 + - - +
101B TRP* 3.0 38.5 - - - +
102B VAL 3.3 13.2 - - - +
103B PHE* 3.6 28.9 - - + -
238B ASP 3.2 13.6 + - - -
240B MET* 3.6 13.1 - - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.6 24.0 - - + -
30B ASN* 3.6 30.3 - - + +
31B ILE* 4.1 8.5 - - + +
34B ASN* 3.5 26.5 - - + +
35B TYR 3.6 15.0 - - - +
36B VAL* 4.3 8.7 - - + -
92B GLN* 1.3 87.3 - - - +
94B ARG* 1.3 78.0 + - - +
102B VAL* 2.9 29.4 + - + +
238B ASP 5.3 0.9 - - - -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.8 26.3 + - - -
31A MET* 3.6 16.5 + - + -
32A ASP 3.6 9.9 - - - +
33A ARG* 2.9 36.7 + - - +
30B ASN* 3.2 23.0 - - - +
34B ASN* 3.1 29.6 + - - +
35B TYR 5.0 0.8 + - - -
93B VAL* 1.3 81.4 - - - +
95B ASP* 1.3 61.2 + - - +
96B ASN* 3.9 11.0 + - - +
100B GLU 3.5 7.9 - - - +
101B TRP* 3.4 37.7 - - + +
236B PHE 4.5 2.0 - - - -
237B GLY 4.0 3.4 - - - +
238B ASP* 2.4 40.9 + - - +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 4.8 2.0 - - - +
27B SER* 5.2 0.2 - - - -
29B SER* 2.9 17.8 + - - -
30B ASN* 2.8 29.0 + - + +
93B VAL 4.0 0.4 + - - -
94B ARG* 1.3 72.3 - - - +
96B ASN* 1.3 63.3 + - - +
97B ASN* 3.0 11.0 + - - +
98B GLU* 2.8 41.0 + - + +
99B ASN* 3.2 20.1 + - - -
100B GLU* 2.8 21.2 + - + +
102B VAL* 4.1 15.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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