Contacts of the strand formed by residues 245 - 255 (chain B) in PDB entry 2V9W
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 ILE 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B ARG* 3.9 18.8 - - + -
244B SER* 1.3 76.5 - - - +
246B GLY* 1.3 62.9 + - - +
272B SER* 4.3 3.3 + - - +
275B LYS* 3.7 31.6 - - + +
276B LEU* 3.3 26.6 - - + +
279B ARG* 3.1 43.1 - - - +
336B ARG* 4.0 2.0 - - - -
337B PHE* 3.0 35.0 + - - +
340B PHE* 3.4 11.4 - - + -
8F G 3.4 16.6 - - - +
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Residues in contact with GLY 246 (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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245B ILE* 1.3 75.6 - - - +
247B ARG* 1.3 65.4 + - - +
272B SER* 3.2 11.2 + - - -
275B LYS* 3.4 21.8 + - - -
335B VAL 3.1 15.0 - - - -
336B ARG* 3.4 18.1 - - - +
7F A 4.1 1.7 - - - +
8F G 2.8 11.3 + - - -
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 5.5 3.8 + - - -
246B GLY* 1.3 76.1 - - - +
248B ILE* 1.3 78.1 + - - +
249B VAL* 3.6 15.7 - - + +
267B ARG* 4.3 9.1 - - - +
268B ALA* 2.8 37.9 - - - +
271B GLU* 2.7 63.3 + - + +
272B SER* 3.5 12.1 + - - +
275B LYS* 4.6 5.4 - - - +
335B VAL 2.9 19.4 + - - -
336B ARG* 4.5 2.4 - - - +
6F DFT 3.2 23.2 + - - -
7F A 2.7 47.1 + - - -
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Residues in contact with ILE 248 (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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247B ARG* 1.3 94.7 + - - +
249B VAL* 1.3 71.2 + - - +
287B VAL* 5.0 11.2 - - + +
289B VAL* 3.6 22.4 - - + -
295B ILE* 6.3 0.2 - - + -
332B ARG* 3.6 36.1 - - + +
333B ILE 3.8 12.3 - - - +
334B GLY* 3.6 15.5 - - - +
6F DFT 3.5 33.7 - - + +
7F A 2.8 12.1 + - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 3.6 23.8 - - + +
248B ILE* 1.3 83.2 - - - +
250B THR* 1.3 67.2 + - - +
251B MET* 4.8 0.2 - - - +
264B TYR* 4.3 22.7 - - + +
267B ARG* 3.2 30.7 - - - +
268B ALA* 4.8 8.7 - - + +
271B GLU* 4.6 0.2 - - - +
332B ARG* 3.2 6.3 - - - +
333B ILE* 3.1 46.2 + - + +
6F DFT 3.5 9.4 - - - +
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Residues in contact with THR 250 (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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34B SER* 4.0 34.1 - - - +
36B ARG* 4.3 11.9 - - - +
249B VAL* 1.3 79.0 - - - +
251B MET* 1.3 73.9 + - - +
252B LYS* 4.1 3.3 + - - +
264B TYR* 4.1 10.2 - - - -
331B ARG* 3.7 15.9 - - + +
332B ARG* 3.0 21.7 - - + -
5F G 3.6 8.2 - - - +
6F DFT 2.8 25.2 + - - -
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Residues in contact with MET 251 (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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34B SER 5.8 1.1 - - - -
36B ARG* 3.0 22.4 + - - -
249B VAL 4.8 0.4 - - - +
250B THR* 1.3 78.0 - - - +
252B LYS* 1.3 66.9 + - - +
253B ARG 2.8 27.4 + - - +
254B ASN 3.8 0.2 - - - -
255B SER* 3.4 18.6 - - - +
260B GLU* 5.4 0.9 - - + +
261B ILE* 4.5 18.8 - - + -
264B TYR* 3.1 43.7 - - + -
330B ILE* 2.5 44.0 - - + +
331B ARG 3.0 16.0 + - - +
332B ARG* 4.6 4.0 - - - -
333B ILE* 4.8 5.8 - - - +
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Residues in contact with LYS 252 (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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35B GLY* 3.5 27.4 + - - +
36B ARG* 3.3 34.1 + - - +
250B THR 5.1 2.7 - - - +
251B MET* 1.3 71.2 - - - +
253B ARG* 1.3 83.9 + - + +
264B TYR* 2.9 27.1 + - + +
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Residues in contact with ARG 253 (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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36B ARG* 4.2 3.6 - - - +
251B MET* 2.9 29.6 - - - +
252B LYS* 1.3 96.5 - - + +
254B ASN* 1.3 69.7 + - - +
255B SER* 4.7 1.3 - - - -
260B GLU* 4.2 22.2 + - - +
264B TYR* 4.5 3.3 + - - -
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Residues in contact with ASN 254 (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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36B ARG* 3.2 17.3 + - - +
253B ARG* 1.3 80.3 - - - +
255B SER* 1.3 66.8 + - - +
291B GLU* 4.0 23.2 + - - +
329B LYS* 3.3 34.1 - - + +
330B ILE 3.1 10.1 - - - +
331B ARG* 3.0 46.2 - - - +
3F C 4.4 5.3 + - - -
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Residues in contact with SER 255 (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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251B MET* 3.4 9.1 - - - +
253B ARG 4.7 0.7 - - - -
254B ASN* 1.3 77.7 - - - +
256B ARG* 1.3 79.8 + - - +
257B ASN* 3.0 13.1 + - - +
260B GLU* 2.8 35.5 + - - +
261B ILE* 4.1 7.4 - - - -
329B LYS* 3.6 9.1 - - - +
330B ILE* 2.7 40.7 + - - +
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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