Contacts of the strand formed by residues 838 - 842 (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 SER 838 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A SER* 4.6 4.3 - - - -
355A GLY 4.8 1.9 + - - -
482A PHE* 3.3 23.6 - - - +
833B TYR 3.6 7.8 + - - -
834B ASN* 3.4 34.8 + - - +
835B GLN 3.7 5.8 - - - -
836B GLU 3.5 0.4 - - - -
837B ASP* 1.3 78.8 - - - +
839B MET* 1.3 68.1 + - - +
988B GLY* 5.2 0.8 - - - -
989B THR 3.2 12.6 + - - -
990B ILE 4.5 0.7 - - - -
991B GLY* 4.0 11.2 - - - -
1012B ILE* 4.4 3.3 - - - +
1013B ASN* 4.3 8.3 + - - +
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Residues in contact with MET 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B TYR 4.4 0.7 - - - -
834B ASN* 3.9 3.6 - - - -
838B SER* 1.3 77.7 - - - +
840B ILE* 1.3 66.3 + - - +
841B MET* 4.5 2.2 - - + -
980B PHE* 3.5 40.2 - - + -
981B ALA* 6.5 0.2 - - - -
986B GLN 6.1 0.7 - - - +
988B GLY* 3.9 16.4 - - - +
989B THR 2.9 16.4 + - - +
990B ILE* 3.4 12.7 - - + -
991B GLY* 2.6 30.3 + - - -
992B ILE 3.8 0.9 + - - -
1010B LEU* 3.7 34.3 - - + -
1011B ILE 3.2 16.2 - - - +
1012B ILE* 3.6 24.7 - - + -
1092B TYR* 5.4 6.1 - - + -
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Residues in contact with ILE 840 (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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830B TYR* 3.8 24.9 - - + -
831B SER* 3.5 21.8 - - - +
833B TYR 4.2 5.2 - - - +
834B ASN* 3.9 19.1 - - + +
839B MET* 1.3 76.3 - - - +
841B MET* 1.3 62.5 + - - +
842B ASN 4.2 0.2 - - - -
992B ILE* 3.4 22.4 - - + +
994B TYR* 3.5 31.4 - - + -
999B MET* 3.5 13.7 - - + -
1010B LEU* 3.4 6.7 - - - +
1011B ILE* 2.8 51.4 + - + +
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Residues in contact with MET 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B MET* 4.0 5.7 + - + -
840B ILE* 1.3 73.3 - - - +
842B ASN* 1.3 70.1 + - - +
843B GLN 3.0 3.6 + - - -
846B ILE* 3.5 30.3 - - + -
850B LEU* 4.1 19.5 - - + -
851B PHE* 4.2 14.1 - - + -
974B PRO* 4.1 7.2 - - - -
980B PHE* 4.3 14.6 - - + -
990B ILE* 3.4 39.0 - - + -
992B ILE 3.0 10.7 + - - +
993B THR* 3.2 21.9 - - + +
994B TYR 3.4 2.6 + - - -
1009B ASP 3.5 9.9 - - - +
1010B LEU* 3.7 23.6 - - + -
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Residues in contact with ASN 842 (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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840B ILE 4.2 0.2 - - - -
841B MET* 1.3 66.5 - - - +
843B GLN* 1.3 60.9 + - - +
844B SER* 2.9 28.2 + - - -
845B SER* 2.6 50.2 + - - +
846B ILE* 3.1 13.7 + - - +
848B ARG* 4.7 0.2 - - - +
994B TYR 3.4 12.5 - - - +
996B ARG* 3.5 10.6 + - - +
999B MET* 3.9 11.6 - - - -
1007B VAL* 3.3 27.0 - - - +
1008B PRO 3.4 18.3 + - - +
1009B ASP* 3.1 11.1 + - - +
8J PHE 4.6 0.2 + - - -
9J SER 4.5 7.5 + - - -
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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