Contacts of the helix formed by residues 880 - 885 (chain S) in PDB entry 1NVU
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 880 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R ALA 5.1 2.9 - - - -
69R ASP* 3.7 13.7 - - - -
836S GLU* 3.2 36.4 - - - +
876S SER 3.1 8.4 + - - -
877S ALA 2.8 18.0 + - - -
879S ASN* 1.3 80.0 - - - +
881S SER* 1.3 60.7 + - - +
882S PRO* 3.4 10.3 - - - +
883S VAL 3.6 5.7 + - - -
884S TYR* 2.8 29.3 + - - +
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Residues in contact with SER 881 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP* 2.7 17.1 + - - +
73R ARG* 3.9 7.4 - - - +
102R ARG* 3.7 24.0 - - - +
103R VAL* 3.1 40.2 - - - +
879S ASN 3.8 0.2 + - - -
880S SER* 1.3 72.2 - - - +
882S PRO* 1.3 66.1 - - - +
883S VAL 3.4 0.2 + - - -
884S TYR* 4.5 0.3 - - - +
885S ARG* 3.4 26.2 + - - +
1010S PHE* 3.9 9.6 - - - -
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Residues in contact with PRO 882 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP* 4.1 2.5 - - - +
836S GLU* 4.0 9.6 - - + +
840S VAL* 4.1 10.9 - - + +
880S SER* 3.3 16.2 - - - +
881S SER* 1.3 95.8 - - - +
883S VAL* 1.3 60.6 + - + +
885S ARG* 3.8 1.0 - - - +
886S LEU* 3.6 10.4 - - - +
1006S THR 4.9 2.7 - - - +
1009S LEU* 3.9 37.9 - - + +
1010S PHE* 4.0 15.5 - - + +
1013S SER* 2.7 31.0 + - - -
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Residues in contact with VAL 883 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836S GLU* 4.1 20.2 - - + +
839S ILE* 4.0 42.0 - - + -
840S VAL* 4.5 1.8 - - + -
877S ALA 3.4 22.0 - - - +
878S MET* 3.9 10.1 - - - +
880S SER* 3.2 6.9 + - - +
882S PRO* 1.3 81.7 - - + +
884S TYR* 1.3 67.2 + - - +
885S ARG 3.1 2.7 - - - -
886S LEU* 3.0 20.9 + - + +
890S PHE* 3.5 30.6 - - + -
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Residues in contact with TYR 884 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R ARG* 3.5 48.1 - - - +
878S MET 3.5 13.1 + - - +
879S ASN* 3.6 25.6 - - - -
880S SER 2.8 21.6 + - - +
881S SER 4.5 1.3 - - - +
883S VAL* 1.3 73.3 - - - +
885S ARG* 1.3 63.9 + - + +
886S LEU 3.4 0.9 + - - -
887S ASP* 4.4 6.8 - - - +
890S PHE* 4.8 8.3 - - - -
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Residues in contact with ARG 885 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881S SER 3.4 19.2 + - - +
882S PRO 3.8 1.6 - - - +
884S TYR* 1.3 82.7 - - + +
886S LEU* 1.3 62.2 + - - +
887S ASP* 2.8 22.4 + - - +
1010S PHE* 3.8 20.1 - - - -
1013S SER* 2.9 40.6 + - - +
1014S LEU* 3.8 12.5 - - - +
1017S GLU* 2.6 34.7 + - - +
1018S PRO 3.7 1.8 + - - -
1019S ARG* 3.6 31.9 - - - +
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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