Contacts of the helix formed by residues 263 - 275 (chain B) in PDB entry 3OVS
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 GLU 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B GLU 4.3 0.7 + - - +
262B ILE* 1.3 82.1 - - - +
264B PRO* 1.4 75.5 - - + +
265B GLU* 3.1 11.4 - - + +
266B ARG* 3.0 48.3 + - - +
267B LEU 3.2 8.5 + - - -
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Residues in contact with PRO 264 (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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262B ILE 3.8 4.0 - - - +
263B GLU* 1.4 85.4 - - + +
265B GLU* 1.3 56.9 + - - +
267B LEU* 3.2 7.8 + - + +
268B ARG* 2.9 31.6 + - - +
421B PHE* 3.5 43.2 - - + +
422B LYS* 5.3 7.9 - - + -
426B THR* 5.7 3.1 - - + -
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Residues in contact with GLU 265 (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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263B GLU* 3.1 11.8 + - + +
264B PRO* 1.3 79.5 - - - +
266B ARG* 1.3 61.3 + - - +
268B ARG* 2.5 46.9 + - - +
269B LYS* 3.2 23.0 + - + +
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Residues in contact with ARG 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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262B ILE* 3.5 39.9 - - + +
263B GLU* 3.0 29.6 + - - +
265B GLU* 1.3 76.0 - - - +
267B LEU* 1.3 60.7 + - - +
269B LYS* 3.3 8.7 + - + +
270B ILE* 2.9 48.7 + - + +
435B VAL* 4.1 17.6 - - - +
436B LYS 4.2 5.5 + - - -
437B ASP* 3.7 33.4 + - - +
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Residues in contact with LEU 267 (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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262B ILE* 3.7 19.0 - - + +
263B GLU 3.2 7.0 + - - +
264B PRO* 3.2 10.4 + - + +
266B ARG* 1.3 76.0 - - - +
268B ARG* 1.3 55.6 + - - +
270B ILE* 3.0 9.6 + - + +
271B VAL* 2.8 38.2 + - - +
421B PHE* 3.8 27.4 - - + -
426B THR* 3.8 33.4 - - + -
429B LEU* 3.8 18.8 - - + -
430B CYS* 3.8 18.8 - - - -
433B MET* 4.1 20.9 - - + -
435B VAL* 4.9 3.4 - - + -
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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
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264B PRO 2.9 16.1 + - - +
265B GLU* 2.5 45.7 + - - +
267B LEU* 1.3 74.6 - - - +
269B LYS* 1.3 62.3 + - - +
271B VAL* 3.3 1.4 + - - +
272B GLU* 2.5 74.8 + - + +
418B GLU* 3.3 31.1 + - - -
421B PHE* 3.8 29.7 - - + -
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Residues in contact with LYS 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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265B GLU* 3.2 16.5 + - + +
266B ARG* 3.3 13.0 - - + +
267B LEU 3.1 0.8 - - - -
268B ARG* 1.3 80.6 - - - +
270B ILE* 1.3 64.5 + - + +
272B GLU* 3.4 27.4 + - + +
273B GLU* 3.0 59.0 + - - +
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Residues in contact with ILE 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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365A PHE* 3.8 31.1 - - + -
262B ILE* 6.4 0.2 - - + -
266B ARG* 2.9 45.0 + - + +
267B LEU* 3.0 10.3 + - + +
269B LYS* 1.3 74.0 - - + +
271B VAL* 1.3 60.3 + - - +
273B GLU* 3.6 12.6 - - - +
274B ARG* 2.8 32.7 + - - +
433B MET* 3.8 23.3 - - + -
435B VAL* 4.1 26.2 - - + -
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Residues in contact with VAL 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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267B LEU* 2.8 23.0 + - + +
268B ARG* 3.8 6.7 - - + +
270B ILE* 1.3 72.3 - - - +
272B GLU* 1.3 58.3 + - - +
274B ARG* 3.2 8.6 + - - +
275B GLY* 2.9 23.7 + - - -
276B THR* 3.8 14.6 + - - +
278B VAL* 3.8 30.7 - - + +
421B PHE* 4.3 23.3 - - + -
429B LEU* 5.9 0.4 - - + -
433B MET* 3.8 29.2 - - + -
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Residues in contact with GLU 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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268B ARG* 2.5 62.4 + - + +
269B LYS* 3.5 32.9 - - + +
271B VAL* 1.3 75.0 - - - +
273B GLU* 1.3 67.9 + - + +
275B GLY* 3.3 13.9 + - - +
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Residues in contact with GLU 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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340A ARG* 3.9 22.0 - - - +
365A PHE* 6.2 2.5 - - + -
379A MET* 4.0 12.8 - - + +
269B LYS* 3.0 52.9 + - + +
270B ILE* 3.6 13.3 - - - +
272B GLU* 1.3 81.4 - - + +
274B ARG* 1.3 61.5 + - + +
275B GLY* 3.5 0.7 + - - -
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Residues in contact with ARG 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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340A ARG* 3.0 23.0 + - - -
341A VAL* 3.4 37.3 + - + +
365A PHE* 3.4 35.0 - - + -
377A PHE* 3.3 33.5 - - - +
379A MET* 5.1 0.9 - - + -
270B ILE* 2.8 19.5 + - - +
271B VAL* 3.2 6.3 + - - +
273B GLU* 1.3 78.8 - - - +
275B GLY* 1.3 57.5 + - - +
276B THR* 3.2 11.5 + - - +
332B GLU* 2.6 48.3 + - - -
433B MET* 2.6 51.5 + - - +
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Residues in contact with GLY 275 (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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337A GLU* 6.2 0.3 - - - +
338A ILE 4.8 0.5 - - - -
339A SER* 3.4 19.7 + - - -
340A ARG* 4.3 6.1 - - - -
271B VAL 2.9 8.3 + - - -
272B GLU* 3.3 10.9 + - - -
273B GLU 3.2 3.5 - - - -
274B ARG* 1.3 77.4 - - - +
276B THR* 1.3 61.7 + - - +
336B LYS* 3.6 19.0 - - - +
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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