Contacts of the strand formed by residues 276 - 285 (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 VAL 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ASN 3.0 14.2 + - - +
58B GLU 4.2 5.6 - - - +
60B ALA* 4.2 13.0 - - + -
78B TYR* 4.3 3.5 - - - +
80B LYS* 2.8 33.1 + - - +
147B ILE* 3.7 21.1 - - + -
189B PHE* 3.7 30.3 - - + -
190B ALA 3.4 3.6 - - - +
191B THR* 3.8 5.6 - - - +
270B GLU* 3.8 18.2 - - + -
274B GLY 3.5 15.0 - - - +
275B ILE* 1.3 82.8 - - - +
277B ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 277 (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* 5.4 0.9 - - + -
80B LYS* 4.5 0.2 - - - -
97B THR* 3.6 10.5 - - + +
107B LEU* 3.7 37.7 - - + +
108B MET* 4.1 17.9 - - + -
111B ALA* 4.0 7.1 - - + +
188B PRO 3.9 0.2 - - - +
189B PHE* 3.3 4.5 - - - -
190B ALA 2.9 31.2 + - - +
276B VAL* 1.3 76.6 - - - +
278B GLN* 1.3 61.5 + - - +
279B PHE* 5.3 0.2 - - + -
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Residues in contact with GLN 278 (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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60B ALA 4.7 1.8 - - - +
61B ALA* 5.9 1.2 - - - +
80B LYS* 3.7 25.6 - - + +
82B ASP* 3.2 22.5 + - - +
95B ALA* 3.6 20.2 - - - +
96B VAL 3.6 4.7 + - - -
97B THR* 2.8 34.0 + - - -
111B ALA* 4.3 1.5 - - - +
187B GLU* 2.9 28.8 + - + +
188B PRO 3.3 10.5 - - - +
189B PHE* 3.3 35.2 - - + -
277B ALA* 1.3 74.8 - - - +
279B PHE* 1.3 78.8 + - - +
280B GLU* 3.9 1.4 + - - -
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Residues in contact with PHE 279 (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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95B ALA 3.5 5.8 - - - -
96B VAL* 3.2 36.1 - - + -
97B THR* 3.7 30.7 - - - -
104B GLU* 3.7 9.2 - - - -
108B MET* 3.3 26.7 - - + -
111B ALA* 3.7 8.7 - - + +
112B LYS* 3.4 57.0 - - + -
115B LEU* 3.8 17.5 - - + -
187B GLU* 3.4 4.2 - - - +
188B PRO* 3.2 28.4 + - - +
278B GLN* 1.3 84.8 - - - +
280B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 280 (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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82B ASP* 3.2 8.8 - - - +
93B ASP* 2.8 20.9 - - - +
94B THR* 2.7 28.8 + - - -
95B ALA* 3.0 23.8 + - + +
115B LEU* 3.7 4.9 - - - +
185B ALA* 3.3 6.9 - - - +
186B ILE 3.2 15.9 - - - +
187B GLU* 2.7 18.6 - - + +
278B GLN* 4.6 0.2 - - - +
279B PHE* 1.3 78.5 - - - +
281B HIS* 1.3 69.4 + - - +
296B CO 2.0 28.6 + - - -
297B CO 2.0 27.6 + - - -
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Residues in contact with HIS 281 (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* 3.3 27.1 + - - -
93B ASP 3.6 6.5 - - - -
115B LEU* 3.6 31.3 - - + +
116B ASN* 5.8 1.8 - - - -
119B ILE* 4.0 14.1 - - + -
185B ALA* 3.4 2.3 - - - -
186B ILE* 3.0 30.9 + - - +
280B GLU* 1.3 77.8 + - - +
282B THR* 1.3 60.8 + - - +
283B ILE* 5.0 2.2 - - + -
292B VAL* 3.5 21.9 - - + +
294B THR* 2.8 29.5 + - - -
295B GLU* 3.8 16.6 + - - +
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Residues in contact with THR 282 (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* 5.8 0.4 - - + -
91B ILE 4.0 13.5 - - - +
92B ALA* 4.4 0.2 - - - -
93B ASP* 2.7 43.5 + - - +
155B ILE* 4.0 7.1 - - + +
183B VAL* 3.7 27.8 - - + -
184B PHE 3.3 7.9 - - - +
185B ALA* 4.1 0.8 - - - +
281B HIS* 1.3 74.2 + - - +
283B ILE* 1.3 64.1 + - - +
292B VAL* 3.6 6.1 - - - +
293B THR* 3.1 42.6 + - + +
294B THR* 3.2 8.4 + - - -
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Residues in contact with ILE 283 (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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119B ILE* 4.4 7.9 - - + -
122B ALA* 4.4 7.6 - - + -
131B LEU* 5.5 1.3 - - + -
178B LEU* 5.5 2.9 - - + -
182B ASP 3.7 0.2 - - - +
183B VAL* 3.2 8.0 - - - +
184B PHE* 2.7 55.8 + - + +
186B ILE* 4.1 30.3 - - + -
281B HIS 5.0 2.0 - - - +
282B THR* 1.3 80.4 - - - +
284B ILE* 1.3 63.1 + - - +
285B VAL* 4.0 15.9 - - + -
290B VAL* 3.9 37.5 - - + -
291B ILE 3.1 11.4 - - - +
292B VAL* 4.2 14.8 - - + -
293B THR 4.7 0.2 - - - +
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Residues in contact with ILE 284 (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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3B THR* 4.4 21.1 - - + -
6B LEU* 4.1 30.3 - - + -
7B MET* 4.5 6.5 - - - -
181B GLY* 4.3 15.0 - - - +
182B ASP 3.3 8.1 - - - +
183B VAL* 4.4 6.3 - - + -
283B ILE* 1.3 74.8 - - - +
285B VAL* 1.3 67.8 + - - +
286B GLU* 3.5 18.0 + - - +
290B VAL* 3.3 4.3 - - - -
291B ILE* 2.9 48.7 + - + +
293B THR* 3.6 28.3 - - + -
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Residues in contact with VAL 285 (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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123B ARG* 3.6 8.3 - - - +
124B ALA* 3.3 35.2 - - + +
178B LEU* 4.1 20.2 - - + -
179B LYS 3.2 21.8 - - - +
180B GLU* 3.6 0.9 - - - +
181B GLY* 2.9 25.1 + - - -
182B ASP* 2.8 29.9 + - + +
184B PHE* 4.6 1.6 - - + -
283B ILE* 4.0 21.1 - - + -
284B ILE* 1.3 73.5 - - - +
286B GLU* 1.3 69.7 + - - +
290B VAL* 4.0 5.8 - - + -
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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