Contacts of the strand formed by residues 802 - 808 (chain A) in PDB entry 2G30
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 ASN 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760A ASN* 4.1 6.4 - - - +
797A MET* 3.5 39.7 - - + +
798A GLU 4.1 9.9 + - - +
799A PRO* 3.0 31.6 + - + +
800A LEU 3.3 1.1 - - - +
801A ASN* 1.3 79.9 + - - +
803A LEU* 1.3 64.0 + - - +
804A GLN* 4.2 16.4 - - - +
817A SER* 3.6 21.5 + - - -
818A CYS 3.4 10.8 + - - +
819A LEU* 3.9 10.5 - - + +
820A ILE* 5.0 0.9 - - - +
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Residues in contact with LEU 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A PHE* 4.3 5.6 - - + -
738A MET* 3.9 20.4 - - + -
757A PHE* 3.7 42.0 - - + -
758A ASN 4.2 1.3 - - - +
760A ASN* 3.4 36.8 - - + +
764A VAL* 4.9 1.3 - - + -
802A ASN* 1.3 75.3 + - - +
804A GLN* 1.3 63.5 + - - +
805A VAL* 3.9 12.1 + - + +
816A PHE 4.0 0.2 - - - +
817A SER* 3.2 5.5 - - - -
818A CYS* 2.8 42.5 + - - +
820A ILE* 4.0 23.3 - - + -
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Residues in contact with GLN 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A PHE* 3.5 5.4 - - - +
758A ASN* 2.9 61.5 + - + +
759A LYS 5.7 0.8 + - - -
797A MET* 4.0 23.9 - - + +
802A ASN* 4.2 12.5 + - - +
803A LEU* 1.3 77.1 - - - +
805A VAL* 1.3 61.2 + - - +
816A PHE 3.7 5.2 - - - +
817A SER* 4.5 7.5 - - - -
8S PHE* 3.9 13.4 - - + -
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Residues in contact with VAL 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738A MET* 4.4 4.9 - - + -
755A ILE* 3.6 36.3 - - + -
756A GLN 3.5 5.6 - - - +
757A PHE* 4.0 9.4 - - + -
803A LEU* 3.9 31.2 - - + +
804A GLN* 1.3 80.8 - - - +
806A ALA* 1.3 65.2 + - - +
814A PHE 3.9 0.3 - - - +
815A TYR* 3.3 6.1 - - - +
816A PHE* 2.9 67.5 + - + +
818A CYS* 4.5 2.0 - - - -
8S PHE* 3.9 3.8 - - - -
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Residues in contact with ALA 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ALA 4.0 0.3 - - - +
755A ILE* 3.3 4.5 - - - +
756A GLN* 2.9 34.6 + - + +
805A VAL* 1.3 74.8 - - - +
807A VAL* 1.3 62.8 + - - +
808A LYS 4.4 0.2 + - - -
813A VAL* 4.1 10.5 - - + -
814A PHE 3.4 4.7 - - - -
815A TYR* 3.8 19.7 - - + -
7S ALA* 3.6 31.0 - - + -
8S PHE* 4.0 3.1 - - + -
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A LEU* 5.4 0.2 - - + -
723A LEU* 4.4 13.5 - - + -
725A ILE* 4.1 23.1 - - + -
740A MET* 6.0 0.2 - - - -
742A PHE* 4.4 14.8 - - + -
753A PHE* 4.5 2.5 - - + -
754A ALA 3.4 9.9 - - - +
755A ILE* 3.6 31.2 - - + -
770A LEU* 4.9 1.3 - - + -
805A VAL* 4.1 0.6 - - + -
806A ALA* 1.3 73.5 - - - +
808A LYS* 1.3 72.0 + - - +
813A VAL* 4.1 1.1 - - - -
814A PHE* 2.9 40.9 + - + +
816A PHE* 3.7 22.2 - - + -
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Residues in contact with LYS 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A ASP* 3.1 32.4 + - - +
753A PHE* 3.2 10.2 - - - -
754A ALA* 2.9 50.4 + - + +
806A ALA 4.2 0.2 - - - -
807A VAL* 1.3 77.9 - - - +
809A ASN* 1.3 72.5 + - - +
810A ASN* 5.7 0.2 - - - +
812A ASP 3.3 12.3 - - - +
813A VAL* 3.9 17.7 - - + -
814A PHE* 4.8 0.7 - - - -
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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