Contacts of the strand formed by residues 78 - 87 (chain B) in PDB entry 1XGS
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 TYR 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER 3.4 0.5 - - - +
56B ILE* 4.5 0.7 - - - -
57B ASN* 2.9 45.6 + - - +
76B GLY 3.5 15.0 - - - -
77B ASP* 1.3 69.8 - - - +
79B LEU* 1.3 59.8 + - - +
80B LYS* 3.3 9.5 + - - -
97B THR* 4.3 10.3 - - + -
98B VAL 3.5 5.6 - - - -
99B ARG* 3.8 21.0 + - + -
105B ASP* 2.5 39.9 + - - -
107B LEU* 4.4 9.4 - - + +
108B MET* 4.1 25.6 - - + -
275B ILE* 3.5 39.7 - - + +
276B VAL 4.3 5.4 - - - +
277B ALA* 5.4 0.2 - - + -
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Residues in contact with LEU 79 (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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24B ALA* 3.6 30.7 - - + -
30B LEU* 4.5 0.9 - - + -
33B LEU* 4.3 6.1 - - + -
54B LEU* 3.9 36.1 - - + -
55B SER 3.6 2.2 - - - +
56B ILE* 4.2 8.5 - - + +
73B LEU* 4.0 29.4 - - + -
77B ASP* 3.4 1.7 + - + -
78B TYR* 1.3 72.3 - - - +
80B LYS* 1.3 65.1 + - - +
81B ILE* 3.8 21.1 + - + +
96B VAL 3.7 1.0 - - - +
97B THR* 3.3 1.4 - - - -
98B VAL* 2.8 43.7 + - + +
100B VAL* 4.1 11.0 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN 3.3 6.4 - - - +
54B LEU* 3.4 2.9 - - - -
55B SER* 2.9 45.3 + - - +
57B ASN 2.8 28.9 + - - +
59B ILE 3.0 21.3 + - - -
60B ALA 3.9 11.0 - - - +
78B TYR 3.3 11.9 + - - +
79B LEU* 1.3 74.3 - - - +
81B ILE* 1.3 60.6 + - - +
82B ASP* 3.8 1.0 + - + +
96B VAL 3.5 3.4 - - - -
97B THR* 3.4 22.9 - - + +
276B VAL* 2.8 31.7 + - - +
278B GLN* 3.7 31.4 - - + +
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Residues in contact with ILE 81 (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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17B ARG* 5.3 6.3 - - + +
20B ALA* 3.9 48.7 - - + +
21B ILE* 4.1 11.7 - - + +
24B ALA* 4.6 0.2 - - + -
33B LEU* 5.3 1.1 - - + -
52B VAL* 4.4 3.6 - - + -
53B ASN 3.5 3.6 - - - -
54B LEU* 4.0 15.5 - - + -
79B LEU* 3.8 31.0 - - + +
80B LYS* 1.3 73.5 - - - +
82B ASP* 1.3 59.9 + - - +
83B VAL* 4.0 18.4 + - + +
95B ALA* 3.2 22.7 - - - +
96B VAL* 2.9 18.6 + - + +
98B VAL* 4.3 12.1 - - + -
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Residues in contact with ASP 82 (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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50B PHE* 3.5 15.6 - - - -
52B VAL* 3.6 2.8 - - - -
53B ASN* 2.9 52.8 + - + -
61B ALA* 6.0 2.1 - - - +
80B LYS* 3.8 1.5 + - + +
81B ILE* 1.3 71.9 - - - +
83B VAL* 1.3 60.7 + - - +
93B ASP* 3.0 7.8 - - - +
94B THR 3.0 8.0 - - - +
95B ALA* 3.8 8.1 - - + -
187B GLU* 3.9 2.3 - - - +
278B GLN* 3.2 22.4 + - - +
280B GLU* 3.6 3.4 - - - -
297B CO 2.0 32.0 + - - -
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Residues in contact with VAL 83 (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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13B ALA* 4.0 10.2 - - + +
16B VAL* 4.3 10.5 - - + -
17B ARG* 3.9 22.2 - - + -
37B ILE* 3.9 19.3 - - + -
41B ILE* 5.3 3.1 - - + -
50B PHE* 3.5 6.4 - - - -
52B VAL* 3.6 27.6 - - + +
81B ILE* 4.0 14.1 - - + +
82B ASP* 1.3 71.9 - - - +
84B GLY* 1.3 59.3 + - - +
92B ALA 3.9 0.5 - - - +
93B ASP* 3.6 1.6 - - - -
94B THR* 2.9 57.5 + - + +
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Residues in contact with GLY 84 (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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41B ILE* 3.9 6.3 - - - +
48B PRO* 3.5 9.0 - - - +
49B ALA* 2.9 21.0 + - - -
50B PHE* 3.3 31.2 + - - +
52B VAL* 5.8 0.2 - - - +
83B VAL* 1.3 75.4 - - - +
85B VAL* 1.3 65.5 + - - +
92B ALA 3.1 10.1 - - - -
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Residues in contact with VAL 85 (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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9B ALA* 3.7 26.6 - - - +
12B ILE* 4.0 23.3 - - + -
13B ALA* 3.8 28.7 - - + +
16B VAL* 4.7 1.3 - - + -
41B ILE* 4.0 20.2 - - + -
46B GLY* 4.2 10.8 - - - -
47B LYS 3.4 11.0 - - - +
49B ALA* 3.7 2.7 - - - +
83B VAL 5.4 0.2 - - - -
84B GLY* 1.3 80.3 - - - +
86B HIS* 1.3 71.5 + - - +
87B ILE* 4.9 0.2 - - + -
90B PHE 3.8 0.3 - - - +
91B ILE* 3.3 3.6 - - - +
92B ALA 2.9 30.3 + - - +
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Residues in contact with HIS 86 (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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9B ALA* 4.3 0.2 - - - -
47B LYS* 3.0 58.3 + - + +
48B PRO 3.4 18.6 + - - -
49B ALA* 3.8 2.1 - - + -
85B VAL* 1.3 77.9 - - - +
87B ILE* 1.3 66.3 + - - +
88B ASP* 3.8 4.8 + - - -
89B GLY* 3.1 30.5 - - - -
90B PHE 3.0 12.8 - - - +
91B ILE* 3.7 17.7 - - + -
158B TYR* 3.9 13.4 + + - -
233B LEU* 3.5 23.1 - - + +
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Residues in contact with ILE 87 (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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5B LYS* 3.8 35.4 - - + +
8B LYS* 4.0 13.5 - - + -
9B ALA* 3.8 26.2 - - - +
12B ILE* 4.0 9.6 - - + -
45B GLY 3.4 26.0 - - - +
46B GLY* 3.6 16.4 - - - -
86B HIS* 1.3 73.9 - - - +
88B ASP* 1.3 76.4 + - - +
90B PHE* 2.8 29.4 + - - +
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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