Contacts of the helix formed by residues 333 - 340 (chain B) in PDB entry 3NVN
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 MET 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B PHE* 3.9 11.7 - - + -
240B TRP* 3.6 30.1 - - + -
245B TYR* 3.7 36.1 - - + -
264B MET* 3.6 30.3 - - + -
299B LEU* 3.7 19.5 - - + -
304B ASP 3.2 22.9 + - - +
306B TRP* 3.8 25.6 - - - +
331B PHE 3.4 1.2 + - - -
332B ARG* 1.3 71.5 - - - +
334B SER* 1.3 57.6 + - - +
336B ILE* 3.2 7.6 + - + +
337B GLN* 2.9 29.1 + - - +
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Residues in contact with SER 334 (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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4B NAG 3.7 27.3 - - - +
240B TRP* 3.7 9.2 - - - -
304B ASP 4.7 1.0 + - - -
332B ARG* 4.1 16.5 - - - +
333B MET* 1.3 78.7 - - - +
335B GLU* 1.3 62.7 + - - +
337B GLN* 3.7 2.9 + - - +
338B ALA* 3.2 26.5 + - - +
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Residues in contact with GLU 335 (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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332B ARG* 3.0 40.9 + - + +
334B SER* 1.3 81.2 + - - +
336B ILE* 1.3 62.3 + - - +
338B ALA* 4.3 1.8 - - - -
339B ARG* 3.0 68.5 + - - +
363B VAL* 3.7 21.2 - - + +
364B GLN* 4.0 14.5 + - - +
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Residues in contact with ILE 336 (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 TYR* 4.1 11.4 - - + -
264B MET* 3.4 40.6 - - + +
279B ALA* 4.3 8.9 - - + +
281B LEU* 3.6 31.0 - - + -
306B TRP* 6.4 0.4 - - + -
331B PHE* 4.4 12.3 - - + -
332B ARG 3.2 12.7 + - - +
333B MET* 3.2 12.7 + - + +
335B GLU* 1.3 76.7 - - - +
337B GLN* 1.3 58.3 + - - +
339B ARG 3.3 0.9 + - - -
340B ALA* 3.0 32.3 + - + +
363B VAL* 3.7 28.3 - - + -
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Residues in contact with GLN 337 (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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4B NAG 3.3 40.6 + - - +
240B TRP* 3.1 23.6 - - + -
241B ASN* 3.5 10.0 + - - +
245B TYR* 3.5 16.6 + - - +
266B ARG* 3.6 40.8 + - - +
333B MET 2.9 14.6 + - - +
334B SER* 4.0 4.9 - - - +
336B ILE* 1.3 78.5 - - - +
338B ALA* 1.3 61.4 + - - +
339B ARG 3.6 0.2 + - - -
340B ALA* 3.7 16.7 + - - +
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Residues in contact with ALA 338 (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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334B SER 3.2 17.1 + - - +
335B GLU* 3.8 6.5 - - - +
337B GLN* 1.3 81.9 - - - +
339B ARG* 1.3 66.2 + - + +
340B ALA 3.8 1.0 + - - +
341B LYS* 2.8 21.1 + - - -
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Residues in contact with ARG 339 (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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278B GLN 4.0 3.8 - - - +
279B ALA* 4.1 3.3 - - - +
335B GLU* 3.0 55.6 + - - +
336B ILE 3.8 0.4 - - - +
338B ALA* 1.3 84.1 - - + +
340B ALA* 1.3 62.3 + - - +
341B LYS* 3.3 14.5 + - - +
361B GLU* 3.6 36.8 + - + +
362B ARG 3.5 23.7 + - - -
363B VAL* 3.8 23.9 - - + +
364B GLN 5.7 0.2 - - - +
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Residues in contact with ALA 340 (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 MET 5.3 1.3 - - - +
266B ARG* 4.8 13.1 + - + -
276B GLN 3.5 11.8 - - - +
277B GLY* 3.7 9.6 - - - +
278B GLN 3.7 26.2 - - - +
279B ALA* 4.0 4.0 - - + +
336B ILE* 3.0 20.9 + - + +
337B GLN* 4.0 12.6 - - - +
338B ALA 3.5 2.0 - - - +
339B ARG* 1.3 74.5 - - - +
341B LYS* 1.3 64.0 + - - +
342B ARG* 5.5 0.5 + - - -
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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