Contacts of the strand formed by residues 90 - 99 (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 PHE 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 44.0 - - + -
2A ASP 4.1 6.1 - - - -
5A LYS* 3.5 44.0 - - + -
6A LEU* 3.9 35.4 - - + +
9A ALA* 3.4 9.2 - - - +
86A HIS* 3.0 3.6 - - - -
87A ILE 2.9 33.1 + - - +
88A ASP 3.7 2.2 - - - -
89A GLY* 1.3 74.3 - - - +
91A ILE* 1.3 59.7 + - - +
156A GLU 6.2 0.2 - - - -
157A ARG* 3.5 47.1 - - + +
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Residues in contact with ILE 91 (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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6A LEU* 3.3 23.1 - - - +
9A ALA* 4.2 2.2 - - - +
49A ALA* 4.1 13.0 - - + -
85A VAL 3.2 4.7 - - - +
86A HIS* 3.8 14.1 - - + -
89A GLY 3.5 16.4 + - - +
90A PHE* 1.3 75.0 - - - +
92A ALA* 1.3 75.3 + - - +
93A ASP* 4.2 2.5 - - + +
155A ILE* 3.7 22.1 - - + +
156A GLU 3.9 15.9 + - - +
159A LYS 4.0 4.7 - - - +
160A LEU* 4.0 29.2 - - + +
233A LEU* 3.8 26.7 - - + -
282A THR* 4.1 11.5 - - - +
293A THR* 5.2 0.3 + - - -
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Residues in contact with ALA 92 (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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6A LEU 4.7 0.2 - - - +
9A ALA* 3.3 37.2 - - + +
10A GLY* 3.3 13.9 - - - +
13A ALA* 3.9 9.0 - - + +
83A VAL 3.9 0.4 - - - +
84A GLY* 3.1 6.9 - - - -
85A VAL 2.9 28.9 + - - +
91A ILE* 1.3 75.8 - - - +
93A ASP* 1.3 59.6 + - - +
94A THR 4.2 0.7 - - - -
282A THR* 3.9 7.0 - - - -
293A THR* 4.6 2.0 - - - +
294A THR* 3.9 4.9 - - + -
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Residues in contact with ASP 93 (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 17.5 - - + -
82A ASP* 2.9 7.3 - - - +
83A VAL 3.6 3.1 - - - -
84A GLY* 4.4 0.4 - - - -
91A ILE* 4.4 4.0 - - + -
92A ALA* 1.3 73.2 - - - +
94A THR* 1.3 61.9 + - - +
153A HIS* 2.8 13.9 + - - -
155A ILE* 4.0 14.1 - - + -
160A LEU* 3.9 2.9 - - + +
185A ALA* 4.3 0.8 - - + +
280A GLU* 2.7 12.3 - - - +
281A HIS 3.6 3.6 - - - -
282A THR* 2.6 37.4 + - - +
294A THR* 4.3 0.4 - - - +
296A CO 2.0 27.6 + - - -
297A CO 2.0 28.1 + - - -
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Residues in contact with THR 94 (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* 3.8 21.5 - - + +
17A ARG* 2.9 36.3 + - - +
82A ASP* 3.1 4.0 - - - +
83A VAL* 2.8 54.5 + - + +
93A ASP* 1.3 75.8 + - - +
95A ALA* 1.3 63.9 + - - +
280A GLU* 2.8 25.2 + - - -
281A HIS* 3.7 3.5 + - - -
294A THR* 3.7 13.9 - - + -
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Residues in contact with ALA 95 (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* 4.4 6.2 - - - +
81A ILE 3.1 14.4 - - - +
82A ASP* 3.7 5.6 - - - -
94A THR* 1.3 81.9 + - - +
96A VAL* 1.3 63.6 + - - +
278A GLN* 3.6 33.0 - - + +
279A PHE* 3.5 5.7 - - - -
280A GLU* 3.0 39.9 + - + +
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Residues in contact with VAL 96 (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* 4.0 21.1 - - + +
21A ILE* 3.8 39.0 - - + -
79A LEU 3.6 0.5 - - - +
80A LYS* 3.4 2.9 - - - +
81A ILE* 2.9 43.4 + - + -
95A ALA* 1.3 76.0 - - - +
97A THR* 1.3 69.6 - - - +
98A VAL* 4.4 2.5 - - + -
278A GLN 3.5 9.3 - - - +
279A PHE* 3.4 21.1 - - + -
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Residues in contact with THR 97 (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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78A TYR* 4.3 16.2 - - + -
79A LEU 3.2 9.4 - - - +
80A LYS* 3.5 13.8 - - + +
96A VAL* 1.3 85.7 - - - +
98A VAL* 1.3 68.9 + - - +
108A MET* 3.4 32.7 - - + +
277A ALA* 4.3 7.2 - - - -
278A GLN 2.6 39.0 + - - -
279A PHE* 3.7 17.6 - - - -
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Residues in contact with VAL 98 (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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21A ILE* 4.0 41.5 - - + +
24A ALA* 4.6 17.0 - - + +
77A ASP 3.1 1.9 - - - +
78A TYR* 3.5 1.2 - - - -
79A LEU* 2.8 35.1 + - + +
81A ILE* 4.1 16.2 - - + -
96A VAL* 4.4 4.0 - - + -
97A THR* 1.3 81.3 - - - +
99A ARG* 1.3 73.2 + - - +
100A VAL* 3.3 8.2 + - - +
101A GLY 5.3 0.9 - - - +
102A MET 5.1 2.9 - - - +
108A MET* 4.1 3.4 - - - -
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Residues in contact with ARG 99 (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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76A GLY* 3.4 22.7 - - - +
77A ASP 3.2 4.0 - - - +
78A TYR* 3.5 38.7 + - + +
98A VAL* 1.3 75.4 - - - +
100A VAL* 1.3 53.6 + - - +
101A GLY 3.3 0.5 + - - -
102A MET* 2.7 72.8 + - + +
103A GLU* 2.8 42.7 + - - +
104A GLU 4.5 0.8 + - - -
105A ASP* 4.1 19.1 + - - +
108A MET* 3.9 18.5 - - + +
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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