Contacts of the helix formed by residues 262 - 269 (chain B) in PDB entry 1NVB
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 GLY 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASP* 2.9 6.0 + - - -
260B GLU 3.4 0.8 - - - -
261B GLY* 1.3 81.9 - - - +
263B LEU* 1.3 66.3 - - - +
264B ARG 3.3 0.9 - - - -
265B ASN* 3.0 27.7 + - - +
377B THR 3.3 11.5 - - - +
378B ARG* 3.6 22.4 - - - -
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Residues in contact with LEU 263 (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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252B TYR* 4.1 28.3 - - + +
253B VAL* 3.6 17.6 - - + +
256B ALA* 3.8 26.0 - - + -
257B ASP* 3.4 15.3 + - + +
262B GLY* 1.3 72.3 - - - +
264B ARG* 1.3 58.0 + - - +
265B ASN 2.9 6.5 + - - -
266B LEU* 3.1 49.8 + - + +
377B THR* 3.3 27.9 + - + -
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Residues in contact with ARG 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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149B ILE 4.5 0.2 + - - -
150B GLY* 3.1 33.9 + - - -
152B LYS* 3.0 37.7 - - - +
167B ILE* 4.9 1.2 - - - +
169B GLN* 4.8 0.6 - - - +
250B LYS* 4.3 0.6 - - - +
253B VAL* 3.7 11.4 - - + +
254B VAL* 3.1 28.4 - - - +
257B ASP* 2.9 32.3 + - + +
258B GLU 3.1 27.2 + - - -
260B GLU* 3.6 20.3 - - + +
263B LEU* 1.3 71.2 - - - +
265B ASN* 1.3 64.3 + - - +
266B LEU 3.2 0.7 - - - -
267B LEU* 3.3 15.9 + - + +
268B ASN 4.2 0.9 + - - -
501B CRB 2.7 42.3 + - - +
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Residues in contact with ASN 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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260B GLU* 2.9 39.6 + - - +
261B GLY 5.4 0.9 - - - +
262B GLY* 3.0 17.9 + - - +
263B LEU 2.9 1.2 + - - -
264B ARG* 1.3 77.3 - - - +
266B LEU* 1.3 54.6 + - - +
268B ASN* 2.7 34.7 + - - +
357B LYS* 4.0 13.0 - - + +
364B LYS* 4.3 10.9 + - - -
366B VAL* 3.2 8.0 - - - +
378B ARG* 3.9 4.9 + - - +
379B ALA* 3.1 45.2 + - + +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.4 28.3 - - + +
249B HIS* 6.4 0.2 - - - +
253B VAL* 5.1 7.2 - - + -
263B LEU* 3.3 41.5 - - + +
265B ASN* 1.3 77.4 - - - +
267B LEU* 1.3 56.8 + - - +
268B ASN 2.9 5.1 + - - -
269B TRP* 3.2 17.5 + - - +
366B VAL* 3.7 24.2 - - + -
374B PRO* 3.7 24.2 - - + -
376B GLU 3.5 18.6 - - - +
377B THR* 4.1 9.2 - - + -
378B ARG 4.0 13.7 - - - +
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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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146B ASP* 5.3 0.2 - - - +
197B LYS* 2.7 38.4 + - - +
198B THR* 5.1 5.8 - - + +
201B ILE* 4.2 17.0 - - + -
249B HIS* 5.0 2.9 - - + -
250B LYS* 3.9 46.9 - - + -
253B VAL* 3.7 33.2 - - + -
254B VAL* 4.1 8.7 - - + -
264B ARG* 3.3 13.6 + - + +
265B ASN 3.0 1.0 + - - -
266B LEU* 1.3 74.6 - - - +
268B ASN* 1.3 54.4 + - - +
269B TRP 3.4 2.0 - - - -
271B HIS* 4.3 0.2 - - - -
501B CRB 3.2 36.8 + - + +
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Residues in contact with ASN 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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260B GLU* 4.6 6.5 - - - +
265B ASN 2.7 16.8 + - - +
267B LEU* 1.3 78.6 - - - +
269B TRP* 1.3 63.2 + - - +
270B GLY 3.4 0.7 + - - -
271B HIS* 3.2 37.0 + - - +
272B SER* 4.0 8.0 + - - -
275B HIS* 4.8 0.9 + - - -
298B GLU* 4.3 0.3 - - - +
355B ASP* 4.4 1.9 - - - +
357B LYS* 2.8 37.5 + - + +
366B VAL* 3.9 6.6 - - - +
501B CRB 3.1 45.7 + - - +
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Residues in contact with TRP 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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196B ILE* 6.0 0.9 - - + -
197B LYS* 3.5 28.1 - - + +
200B ALA* 3.5 26.7 - - + -
201B ILE* 3.8 12.8 - - + -
266B LEU 3.2 14.7 + - - +
267B LEU 3.4 2.2 - - - -
268B ASN* 1.3 76.1 - - - +
270B GLY* 1.3 57.9 + - - +
271B HIS* 3.1 14.6 + - - -
295B MET* 3.4 61.3 - - + +
298B GLU* 3.3 28.0 + - - +
299B ALA* 4.5 11.1 - - + +
308B LEU* 5.7 0.2 - - + -
316B ILE* 3.9 22.7 - - + -
366B VAL* 3.4 26.9 + - + -
368B LEU* 3.3 40.9 - - + +
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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