Contacts of the strand formed by residues 265 - 274 (chain B) in PDB entry 4A8W
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 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG 3.1 6.5 + - - -
89B HIS* 3.1 16.9 - - + +
90B MET 2.8 26.8 + - - -
211B ILE* 3.6 29.6 - - + -
220B PHE* 3.6 35.9 - - + -
222B SER* 3.7 31.2 - - - -
247B LYS* 3.4 20.9 - - + +
248B ASP* 4.8 5.4 - - - -
249B ALA* 4.1 7.2 - - - -
263B GLY* 3.7 22.7 - - - -
264B PHE* 1.3 78.6 - - - +
266B CYS* 1.3 65.7 + - - +
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Residues in contact with CYS 266 (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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89B HIS* 3.3 8.0 + - - -
90B MET* 4.9 2.5 - - - +
93B PHE* 3.4 19.1 - - - +
94B PRO 3.5 13.2 - - - +
95B MET* 3.8 4.9 - - - +
246B SER 5.2 0.4 - - - -
247B LYS* 2.7 34.1 + - - +
248B ASP 3.7 19.7 - - - -
249B ALA* 3.9 13.5 - - - -
251B ARG* 3.6 28.3 - - - -
252B LEU* 4.6 3.1 - - - -
265B PHE* 1.3 74.7 - - - +
267B GLU* 1.3 64.1 + - - +
268B ARG 3.9 0.3 + - - -
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Residues in contact with GLU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B HIS* 4.1 15.5 - - + -
90B MET 4.2 0.9 - - - +
91B ASN* 3.1 35.1 - - - +
92B GLY* 2.8 32.1 + - - -
93B PHE 2.8 15.7 + - - +
94B PRO* 3.5 5.3 - - + +
95B MET* 2.8 29.7 + - - +
205B ALA* 3.7 21.3 - - + +
206B GLN 4.3 3.1 - - - +
207B SER* 3.4 20.4 - - - +
247B LYS* 5.0 0.2 - - - -
266B CYS* 1.3 72.4 - - - +
268B ARG* 1.3 70.7 + - - +
269B ARG* 3.5 0.6 + - + -
528B PRO 4.8 1.6 - - - +
529B GLU 5.3 1.6 - - - +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B HIS* 5.1 2.6 + - - -
95B MET* 3.8 11.2 - - + -
205B ALA* 3.6 5.0 - - - -
206B GLN* 3.0 74.6 + - + +
209B ASP* 3.7 27.6 - - + +
225B ARG* 3.3 50.8 - - + +
247B LYS* 4.4 5.5 - - - +
266B CYS 3.9 1.2 + - - -
267B GLU* 1.3 75.6 - - - +
269B ARG* 1.3 68.7 + - - +
270B ARG* 3.1 34.7 - - - +
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Residues in contact with ARG 269 (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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32B PHE* 3.7 11.1 - - - -
33B LYS 4.3 11.7 + - - -
94B PRO* 3.4 42.8 - - + +
95B MET* 3.6 26.8 - - + +
98B ALA* 4.4 16.3 - - + +
99B THR* 5.4 3.8 + - - +
203B TYR* 3.2 36.7 + - + +
204B ARG 3.3 16.2 - - - +
205B ALA* 4.5 6.1 - - + +
267B GLU* 3.5 2.6 + - + +
268B ARG* 1.3 82.3 + - - +
270B ARG* 1.3 62.8 + - - +
271B THR 4.4 0.3 + - - -
369B ALA 3.6 21.6 + - - -
370B PRO 3.6 16.0 + - - -
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Residues in contact with ARG 270 (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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203B TYR* 3.4 6.3 - - - -
204B ARG* 2.8 48.9 + - + +
205B ALA 5.7 0.2 - - - -
206B GLN* 3.0 41.7 + - + +
268B ARG* 3.1 46.0 - - - +
269B ARG* 1.3 75.6 - - - +
271B THR* 1.3 66.1 + - - +
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Residues in contact with THR 271 (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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99B THR* 4.2 21.7 - - + +
101B PRO* 4.6 14.1 - - + +
201B VAL* 3.7 15.9 - - - +
203B TYR* 3.8 22.9 - - - -
269B ARG 4.4 0.6 + - - -
270B ARG* 1.3 78.2 - - - +
272B ALA* 1.3 63.2 + - - +
273B MET* 4.5 11.0 - - - +
393B SER* 4.6 3.8 + - - -
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Residues in contact with ALA 272 (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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201B VAL* 3.6 6.1 - - - +
202B VAL* 2.8 47.6 + - + +
204B ARG* 4.0 30.5 - - + +
270B ARG 4.6 0.9 - - - +
271B THR* 1.3 75.2 + - - +
273B MET* 1.3 63.5 + - - +
393B SER* 3.4 10.5 - - - +
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Residues in contact with MET 273 (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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101B PRO* 5.2 7.0 - - + -
199B TYR* 3.8 20.0 - - + -
200B TYR 3.5 3.8 - - - +
201B VAL* 4.1 17.7 - - - -
202B VAL* 4.8 2.7 - - - -
271B THR* 4.5 10.1 - - - +
272B ALA* 1.3 76.4 - - - +
274B GLY* 1.3 59.1 + - - +
275B GLY 4.0 0.2 - - - -
365B VAL* 3.6 32.1 - - + -
389B VAL* 3.9 14.6 - - + -
391B LEU 5.3 0.2 - - - +
392B SER* 3.4 31.2 - - - +
393B SER* 2.7 25.9 + - - +
394B GLY* 2.9 27.7 + - - +
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Residues in contact with GLY 274 (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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152B CYS* 3.7 21.7 - - - +
198B ALA 4.4 0.7 - - - +
199B TYR* 3.4 4.5 - - - -
200B TYR* 2.8 43.8 + - - +
202B VAL* 4.7 4.3 - - - +
273B MET* 1.3 71.8 - - - +
275B GLY* 1.3 64.2 + - - +
394B GLY* 4.7 0.4 - - - -
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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