Contacts of the helix formed by residues 813 - 818 (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 ASP 813 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808S VAL 4.7 0.9 - - - -
811S LYS* 3.2 3.7 - - + +
812S GLU* 1.3 91.7 - - - +
814S LYS* 1.3 64.3 + - - +
815S GLU* 3.2 3.8 - - - +
816S ILE* 3.0 28.6 + - + +
817S ASN* 2.9 38.2 + - - +
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Residues in contact with LYS 814 (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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63R GLU* 2.8 21.2 + - - +
808S VAL 3.6 13.7 + - - +
809S TRP* 3.4 30.1 - - - +
810S THR* 5.0 2.5 - - - -
811S LYS 3.1 17.2 + - - +
812S GLU* 3.3 5.1 - - - +
813S ASP* 1.3 77.6 - - - +
815S GLU* 1.3 69.4 + - + +
817S ASN 4.4 0.9 - - - +
818S SER* 2.7 33.9 + - - +
822S LEU* 3.5 14.7 - - + +
826S ARG* 4.9 0.7 - - - +
1048S PO4 2.6 40.1 + - - -
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Residues in contact with GLU 815 (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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812S GLU 5.6 2.9 - - - +
813S ASP* 3.2 1.0 - - - -
814S LYS* 1.3 86.0 - - + +
816S ILE* 1.3 63.9 + - + +
819S PRO* 3.7 21.8 - - - +
822S LEU* 3.8 9.4 - - - +
826S ARG* 2.6 45.4 + - - -
1048S PO4 3.7 11.1 + - - -
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Residues in contact with ILE 816 (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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706S ARG* 5.9 0.5 + - - -
813S ASP* 3.0 31.9 + - + +
815S GLU* 1.3 83.2 - - + +
817S ASN* 1.3 71.3 + - - +
819S PRO* 3.6 11.1 - - - +
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Residues in contact with ASN 817 (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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706S ARG* 4.7 16.8 + - - +
802S SER* 4.3 4.4 + - - +
803S GLU* 3.4 22.9 + - - +
808S VAL* 4.0 34.0 + - + +
811S LYS* 6.2 1.2 - - - +
813S ASP* 2.9 37.0 + - - +
814S LYS 4.6 0.2 - - - +
816S ILE* 1.3 85.7 - - - +
818S SER* 1.3 59.6 + - - +
819S PRO* 3.2 8.1 - - - +
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Residues in contact with SER 818 (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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803S GLU* 2.8 37.5 + - - -
808S VAL* 3.5 2.9 - - - +
809S TRP* 3.3 33.2 + - - -
814S LYS 2.7 21.2 + - - -
817S ASN* 1.3 77.2 - - - +
819S PRO* 1.4 58.4 - - - +
821S LEU* 3.3 5.9 + - - -
822S LEU* 3.0 30.6 + - - +
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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