Contacts of the strand formed by residues 78 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A SER 3.5 2.4 - - - +
56A ILE* 3.4 3.3 - - - -
57A ASN* 2.9 44.2 + - - +
76A GLY 3.5 15.5 - - - -
77A ASP* 1.3 69.2 - - - +
79A LEU* 1.3 61.4 + - - +
80A LYS* 3.5 3.3 + - - -
97A THR* 4.3 10.1 - - + -
98A VAL 3.5 5.8 - - - -
99A ARG* 3.5 24.6 + - + +
105A ASP* 2.6 41.1 + - - -
107A LEU* 4.4 9.1 - - + +
108A MET* 4.0 21.5 - - + -
275A ILE* 3.6 37.9 - - + -
276A VAL 4.4 4.0 - - - +
277A ALA* 5.4 0.4 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA* 3.6 30.7 - - + -
30A LEU* 4.4 1.6 - - + -
33A LEU* 4.1 8.5 - - + -
54A LEU* 4.1 22.4 - - + -
55A SER 3.8 1.1 - - - -
56A ILE* 4.0 15.7 - - + +
73A LEU* 3.7 29.8 - - + -
77A ASP 3.2 1.0 + - - -
78A TYR* 1.3 71.7 - - - +
80A LYS* 1.3 70.4 + - - +
81A ILE* 3.7 21.1 + - + +
96A VAL 3.6 1.4 - - - +
97A THR* 3.2 2.8 - - - -
98A VAL* 2.8 43.1 + - + +
100A VAL* 4.0 11.4 - - + -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 3.4 5.0 - - - +
54A LEU* 3.5 2.6 - - - -
55A SER* 2.8 48.9 + - - +
57A ASN 3.1 13.1 + - - +
59A ILE 2.9 29.4 + - - -
60A ALA* 3.5 21.3 - - - +
78A TYR 3.5 8.9 + - - -
79A LEU* 1.3 72.8 - - - +
81A ILE* 1.3 61.3 + - - +
82A ASP* 3.9 1.2 + - - +
96A VAL 3.4 4.5 - - - +
97A THR* 3.5 21.1 - - + +
276A VAL* 3.1 36.4 + - + +
278A GLN* 3.8 29.8 - - + +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 5.3 3.7 - - + +
20A ALA* 3.9 43.7 - - + +
21A ILE 4.3 0.7 - - - +
24A ALA* 4.5 0.2 - - + -
33A LEU* 5.5 0.9 - - + -
52A VAL* 4.7 2.5 - - + -
53A ASN 3.5 3.6 - - - +
54A LEU* 4.1 16.2 - - + -
79A LEU* 3.8 32.1 - - + +
80A LYS* 1.3 71.3 - - - +
82A ASP* 1.3 60.7 + - - +
83A VAL* 3.9 22.3 + - + +
95A ALA* 3.1 5.2 - - - -
96A VAL* 2.9 44.2 + - + +
98A VAL* 4.1 23.1 - - + -
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.3 15.2 - - - -
52A VAL* 3.8 0.5 - - - -
53A ASN* 3.0 45.6 + - + +
80A LYS 3.9 1.1 - - - +
81A ILE* 1.3 72.7 - - - +
83A VAL* 1.3 64.6 + - - +
93A ASP* 2.9 7.1 - - - +
94A THR 3.1 6.6 - - - +
95A ALA* 3.7 6.3 - - + -
187A GLU* 3.7 2.8 - - - +
278A GLN* 2.9 26.3 + - - +
280A GLU* 3.4 4.3 - - - -
297A CO 2.0 32.1 + - - -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.0 18.3 - - + +
16A VAL* 4.6 9.2 - - + -
17A ARG* 4.2 13.2 - - + -
20A ALA* 5.5 0.2 - - + -
37A ILE* 4.1 21.5 - - + -
41A ILE* 5.2 3.4 - - + -
50A PHE* 3.3 7.2 - - - -
52A VAL* 4.1 12.6 - - + +
81A ILE* 3.9 22.0 - - + -
82A ASP* 1.3 78.8 + - - +
84A GLY* 1.3 60.0 + - - +
85A VAL* 5.8 0.4 - - + -
92A ALA 3.9 0.5 - - - +
93A ASP* 3.6 0.2 - - - -
94A THR* 2.8 60.0 + - + +
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Residues in contact with GLY 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 4.0 5.9 - - - +
48A PRO* 3.5 8.1 - - - +
49A ALA* 3.0 20.1 + - - -
50A PHE* 3.2 30.9 + - - +
52A VAL* 6.0 0.6 - - - +
83A VAL* 1.3 76.5 - - - +
85A VAL* 1.3 66.9 + - - +
92A ALA 3.1 10.1 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA* 3.6 21.5 - - - +
12A ILE* 4.0 13.0 - - + -
13A ALA* 3.9 27.4 - - + +
16A VAL* 5.7 0.2 - - + -
41A ILE* 3.8 31.2 - - + -
46A GLY* 4.0 11.2 - - - -
47A LYS 3.4 11.2 - - - +
49A ALA* 3.7 4.2 - - - +
83A VAL* 5.5 0.7 - - + -
84A GLY* 1.3 80.2 - - - +
86A HIS* 1.3 73.3 + - - +
87A ILE* 4.6 1.1 - - + -
91A ILE* 3.2 3.6 - - - -
92A ALA 2.9 31.3 + - - -
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA* 4.4 0.2 - - - -
47A LYS* 2.9 76.8 + - + +
48A PRO 3.4 20.5 + - - -
49A ALA* 4.1 2.7 - - + -
85A VAL* 1.3 76.1 - - - +
87A ILE* 1.3 67.0 + - - +
88A ASP* 3.5 6.2 + - - -
89A GLY* 3.0 31.1 + - - -
90A PHE 3.0 10.8 - - - +
91A ILE* 3.8 18.6 - - + -
158A TYR* 4.0 11.1 + + - -
229A GLU 6.0 0.4 - - - -
230A TYR 5.9 0.9 - - - -
233A LEU* 3.5 21.1 - - + +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.9 29.8 - - + +
8A LYS* 3.8 23.8 - - + +
9A ALA* 3.8 26.5 - - - +
12A ILE* 4.3 5.4 - - + -
45A GLY 3.6 11.0 - - - +
46A GLY* 3.6 22.9 - - - -
85A VAL* 4.6 1.1 - - + -
86A HIS* 1.3 81.7 - - - +
88A ASP* 1.3 80.3 + - - +
90A PHE* 2.9 26.0 + - - +
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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