Contacts of the helix formed by residues 758 - 762 (chain B) in PDB entry 2NVX
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 PHE 758 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757B PRO* 1.3 78.8 - - + +
759B PRO* 1.3 72.7 - - - +
760B ASP* 3.2 8.3 - - - -
761B HIS* 3.4 37.6 + + + -
1024B ALA* 3.1 29.2 - - + +
1027B ILE* 4.3 23.6 - - + -
1028B GLU* 4.4 17.0 - - - -
1031B LEU* 3.5 34.3 - - + -
1043B ASP 3.7 3.6 - - - -
1044B ALA* 3.2 33.7 + - + -
1045B SER 5.1 4.0 - - - -
1046B PRO 5.4 0.7 - - - -
1048B THR* 5.6 0.9 - - - -
1050B ILE* 3.9 25.4 - - + -
1055B ILE* 6.3 0.2 - - + -
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Residues in contact with PRO 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A PHE* 3.9 12.7 - - + -
749B LEU* 4.1 15.9 - - + -
753B ALA 5.0 0.2 - - - +
756B ILE* 3.5 32.5 - - + +
757B PRO 3.6 0.4 - - - -
758B PHE* 1.3 90.0 - - - +
760B ASP* 1.3 65.9 + - - +
761B HIS 3.2 0.2 - - - -
762B ASN* 3.3 13.6 + - + +
767B ASN* 2.9 36.6 + - - +
1046B PRO* 3.4 37.0 - - + -
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Residues in contact with ASP 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A GLY* 4.0 0.2 - - - -
808A LEU* 3.2 51.0 + - + +
813A PHE* 4.6 12.8 - - + -
728B ARG* 3.4 20.4 + - - -
758B PHE* 3.4 12.3 - - - -
759B PRO* 1.3 79.4 - - + +
761B HIS* 1.3 80.4 + - - -
762B ASN 3.2 3.8 + - - +
1046B PRO* 3.0 32.2 - - + +
1047B PHE* 5.1 9.0 - - + -
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Residues in contact with HIS 761 (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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804A TYR* 3.1 39.5 + - - +
805A LEU 3.3 13.8 + - - -
806A ARG 3.3 28.0 - - - -
807A GLY* 3.4 4.8 - - - -
728B ARG* 4.0 7.4 + - - -
758B PHE* 3.4 36.1 + + + +
759B PRO 3.2 1.2 - - - -
760B ASP* 1.3 107.3 + - - +
762B ASN* 1.3 58.8 + - - +
1023B VAL* 3.5 7.8 - - - +
1024B ALA* 3.5 13.2 + - - -
1027B ILE* 3.5 23.9 - - + +
1046B PRO 5.3 0.2 + - - -
1050B ILE 4.6 9.4 + - - -
1051B THR* 6.3 1.3 - - + -
1052B VAL* 5.7 2.0 - - + -
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Residues in contact with ASN 762 (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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804A TYR* 3.6 10.5 - - - -
808A LEU* 4.9 0.2 - - - +
813A PHE* 4.9 1.7 - - - -
816A HIS* 4.1 6.2 - - - -
758B PHE 4.1 1.6 - - - +
759B PRO 3.5 19.1 - - - +
760B ASP 3.2 4.3 + - - +
761B HIS* 1.3 78.3 - - - +
763B GLN* 1.3 63.9 + - - +
764B SER* 3.6 2.9 + - - -
766B ARG* 3.5 25.8 - - - +
767B ASN* 3.3 22.5 + - - +
984B HIS* 3.6 20.0 + - - +
1021B MET 4.5 0.9 - - - -
1022B THR* 3.3 25.9 + - - -
1024B ALA* 3.2 27.1 + - + +
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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