Contacts of the strand formed by residues 90 - 99 (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 PHE 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 46.0 - - + -
2B ASP* 4.3 12.3 - - + -
5B LYS* 3.6 36.1 - - + -
6B LEU* 3.7 34.5 - - + +
9B ALA* 3.5 7.5 - - - +
86B HIS* 3.0 3.1 - - - -
87B ILE 2.8 46.8 + - - +
88B ASP 3.8 2.7 - - - -
89B GLY* 1.3 75.8 - - - +
91B ILE* 1.3 59.3 + - - +
156B GLU 6.1 0.2 - - - -
157B ARG* 3.8 46.2 - - + +
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Residues in contact with ILE 91 (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 20.9 - - - +
9B ALA* 4.4 2.0 - - - -
49B ALA* 3.8 14.6 - - + -
85B VAL 3.3 4.7 - - - +
86B HIS* 3.7 13.7 - - + -
89B GLY 3.4 16.3 + - - +
90B PHE* 1.3 75.6 - - - +
92B ALA* 1.3 76.2 + - - +
93B ASP* 4.3 2.7 - - + +
155B ILE* 3.7 18.8 - - + +
156B GLU 4.0 14.3 + - - +
158B TYR* 4.3 0.7 - - - +
159B LYS 4.0 6.1 - - - +
160B LEU* 4.0 30.7 - - + +
233B LEU* 4.0 26.5 - - + -
282B THR* 4.0 12.2 - - - +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU 4.7 0.7 - - - +
9B ALA* 3.4 11.4 - - + +
10B GLY* 3.4 38.1 - - - +
13B ALA* 3.9 5.9 - - + +
83B VAL 3.9 0.7 - - - +
84B GLY* 3.1 5.4 - - - -
85B VAL 2.9 30.8 + - - +
91B ILE* 1.3 75.4 - - - +
93B ASP* 1.3 59.9 + - - +
94B THR 4.2 0.2 - - - -
282B THR* 3.9 6.5 - - - -
293B THR* 4.5 2.2 - - - +
294B THR* 3.9 10.1 - - + -
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Residues in contact with ASP 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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50B PHE* 3.3 16.3 - - + -
82B ASP* 3.0 6.6 - - - +
83B VAL 3.6 2.9 - - - -
84B GLY* 4.4 0.7 - - - -
91B ILE 4.2 0.4 - - - -
92B ALA* 1.3 73.7 - - - +
94B THR* 1.3 62.9 + - - +
153B HIS* 2.8 15.2 + - - -
155B ILE* 4.0 14.6 - - + -
160B LEU* 4.0 8.1 - - + +
185B ALA* 4.2 1.1 - - + +
280B GLU* 2.8 11.1 - - - +
281B HIS 3.6 3.8 - - - -
282B THR* 2.7 38.0 + - - +
294B THR* 4.4 0.6 - - - +
296B CO 2.0 27.8 + - - -
297B CO 2.0 28.3 + - - -
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Residues in contact with THR 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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13B ALA* 3.9 22.2 - - + +
17B ARG* 3.0 35.3 + - - +
82B ASP* 3.0 3.8 - - - +
83B VAL* 2.9 52.3 + - + +
93B ASP* 1.3 75.9 + - - +
95B ALA* 1.3 64.4 + - - +
280B GLU* 2.7 25.6 + - - -
281B HIS* 3.7 1.0 + - - -
294B THR* 3.7 14.4 - - + -
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Residues in contact with ALA 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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17B ARG* 5.0 5.0 + - - -
81B ILE 3.2 13.2 - - - +
82B ASP* 3.8 4.5 - - - -
94B THR* 1.3 81.5 + - - +
96B VAL* 1.3 62.5 + - - +
278B GLN* 3.6 33.7 - - - +
279B PHE* 3.5 5.7 - - - -
280B GLU* 3.0 40.5 + - + +
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Residues in contact with VAL 96 (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* 4.2 20.2 - - + -
18B GLU* 5.8 0.4 - - - +
21B ILE* 3.8 38.4 - - + -
79B LEU 3.7 0.2 - - - +
80B LYS* 3.5 2.6 - - - -
81B ILE* 2.9 38.8 + - + -
95B ALA* 1.3 75.2 - - - +
97B THR* 1.3 63.8 + - - +
98B VAL* 4.4 7.2 - - + -
104B GLU* 5.5 1.3 - - - +
112B LYS* 5.8 0.7 - - - +
278B GLN 3.6 5.7 - - - +
279B PHE* 3.2 30.1 - - + -
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Residues in contact with THR 97 (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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78B TYR* 4.3 14.4 - - + -
79B LEU 3.3 9.2 - - - +
80B LYS* 3.4 18.6 - - + +
96B VAL* 1.3 79.2 - - - +
98B VAL* 1.3 70.6 + - - +
104B GLU* 4.4 2.3 - - - +
108B MET* 3.2 33.9 - - + +
277B ALA* 4.3 5.4 - - - -
278B GLN 2.8 39.1 + - - -
279B PHE* 3.7 21.3 - - - -
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Residues in contact with VAL 98 (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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21B ILE* 4.0 41.1 - - + +
24B ALA* 4.7 16.4 - - + +
77B ASP 3.3 1.2 - - - +
78B TYR* 3.5 1.4 - - - -
79B LEU* 2.8 41.4 + - + +
81B ILE* 4.3 15.5 - - + -
96B VAL* 4.4 4.5 - - + -
97B THR* 1.3 78.4 - - - +
99B ARG* 1.3 71.6 + - - +
100B VAL* 3.5 8.1 + - - +
101B GLY 5.3 0.7 - - - +
102B MET 5.7 0.7 - - - +
108B MET* 4.1 3.1 - - - -
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Residues in contact with ARG 99 (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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76B GLY* 4.0 19.3 + - - +
77B ASP 3.2 5.4 - - - +
78B TYR* 3.8 30.9 + - + +
98B VAL* 1.3 74.1 - - - +
100B VAL* 1.3 60.2 + - - +
101B GLY 3.2 0.9 + - - -
102B MET* 2.9 66.7 + - + +
103B GLU* 2.9 37.6 + - - +
104B GLU 4.7 0.2 + - - -
105B ASP* 3.9 23.8 + - - +
108B MET* 3.9 20.5 - - + +
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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