Contacts of the helix formed by residues 336 - 341 (chain B) in PDB entry 3NMV
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 SER 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP* 2.8 35.8 + - - -
163B VAL* 3.9 9.4 - - - +
165B ASP* 4.0 10.3 - - - -
252B SER* 3.6 4.7 - - - -
335B ALA* 1.3 74.4 - - - +
337B ASP* 1.3 59.4 + - - +
338B GLY 2.9 12.5 + - - -
339B LEU* 3.0 13.9 + - - +
340B TRP* 3.4 9.1 + - - -
403B ASN 3.9 1.9 + - - -
405B SER 3.1 18.1 + - - -
424B MG 4.0 1.1 - - - -
425B MG 3.5 12.1 - - - -
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Residues in contact with ASP 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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165B ASP* 3.5 2.8 - - - +
251B ASP* 3.4 33.7 + - + +
270B LYS* 5.4 0.5 + - - -
336B SER* 1.3 70.5 - - - +
338B GLY* 1.3 58.0 + - - +
339B LEU 3.1 0.7 - - - -
340B TRP* 3.7 13.6 - - + +
341B ASP* 2.8 58.4 + - - +
402B ASP* 3.0 5.4 - - - +
424B MG 2.4 30.5 - - - -
425B MG 2.8 18.3 - - - -
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Residues in contact with GLY 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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336B SER* 2.9 4.1 + - - -
337B ASP* 1.3 83.8 + - - +
339B LEU* 1.3 56.4 + - - +
341B ASP* 5.3 0.4 - - - +
342B VAL* 4.2 1.9 - - - +
395B ALA* 4.0 2.8 - - - +
400B SER* 2.8 35.1 + - - -
402B ASP* 3.8 8.0 + - - -
403B ASN 3.3 23.6 - - - -
404B ILE* 3.9 11.2 - - - +
424B MG 3.8 2.0 - - - -
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Residues in contact with LEU 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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333B ILE* 5.5 0.7 - - + -
335B ALA* 4.1 10.5 - - + -
336B SER 3.0 10.0 + - - +
338B GLY* 1.3 76.7 - - - +
340B TRP* 1.4 85.3 + - + +
341B ASP 3.3 0.2 - - - -
342B VAL* 3.2 18.0 + - - +
343B MET* 3.2 27.7 + - - -
348B VAL* 3.3 33.0 - - + -
391B LEU* 3.7 35.0 - - + +
395B ALA* 4.0 8.1 - - + -
404B ILE* 4.2 4.5 - - + +
406B VAL* 3.9 20.6 - - + -
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Residues in contact with TRP 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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251B ASP 4.8 2.0 - - - +
252B SER 4.7 1.3 - - - -
253B ARG* 3.3 70.7 + - + +
255B VAL* 3.4 26.9 - - + -
333B ILE* 4.1 12.6 - - + -
335B ALA* 2.8 40.1 + - + -
336B SER 3.4 22.4 - - - -
337B ASP* 3.3 8.3 + - + -
339B LEU* 1.4 79.2 - - + +
341B ASP* 1.3 66.2 + - - +
343B MET 3.1 20.3 + - - +
345B ASN* 3.4 17.0 - - - -
348B VAL* 3.6 38.1 - - + -
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Residues in contact with ASP 341 (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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270B LYS* 6.0 0.3 + - - -
337B ASP* 2.8 44.4 + - - +
338B GLY* 5.0 1.2 - - - -
340B TRP* 1.3 78.8 - - - +
342B VAL* 1.3 65.0 + - + +
400B SER* 5.9 0.9 - - - +
402B ASP* 4.8 4.3 - - - +
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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