Contacts of the strand formed by residues 810 - 815 (chain A) in PDB entry 6N8P
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 GLN 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A VAL* 3.2 6.6 - - - +
782A LEU* 2.8 47.3 + - + +
783A ASP 3.6 12.0 + - - -
784A GLY 4.3 5.5 + - - -
786A SER* 2.8 33.2 + - - -
808A SER* 3.1 23.8 + - - -
809A HIS* 1.3 76.6 - - - +
811A LEU* 1.3 60.7 + - - +
812A LEU 4.1 0.2 + - - -
821A VAL* 4.3 14.1 - - + -
822A PHE 3.2 14.6 - - - +
823A THR* 5.0 4.9 - - + +
824A LEU* 4.2 5.1 - - - +
830A LYS* 5.3 10.0 - - - +
879A PRO* 4.0 6.6 - - - +
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Residues in contact with LEU 811 (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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734A TRP* 3.5 35.7 - - + -
742A ILE* 5.4 0.4 - - + -
768A ILE* 4.2 6.1 - - + -
779A ILE* 3.9 20.9 - - + -
780A LEU 3.7 1.1 - - - +
781A VAL* 3.7 20.2 - - + -
810A GLN* 1.3 72.1 - - - +
812A LEU* 1.3 62.3 + - - +
813A VAL* 4.0 14.1 - - + -
821A VAL* 3.2 5.7 - - - -
822A PHE* 2.6 64.5 + - + +
824A LEU* 4.1 14.6 - - + +
827A VAL* 3.9 16.8 - - + -
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Residues in contact with LEU 812 (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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778A GLY 3.8 0.5 - - - +
779A ILE* 3.5 5.0 - - - +
780A LEU* 2.5 72.1 + - + +
782A LEU* 5.0 11.2 - - + -
810A GLN 4.1 0.6 + - - -
811A LEU* 1.3 72.2 - - - +
813A VAL* 1.3 67.2 + - - +
814A VAL* 4.1 18.4 - - + -
819A PHE* 4.8 1.6 - - + -
820A LYS 3.7 5.2 - - - +
821A VAL* 3.8 25.4 - - + +
864A LEU* 3.6 26.5 - - + -
878A LEU* 4.7 11.2 - - + -
881A LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 813 (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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742A ILE* 3.6 37.7 - - + -
770A LEU* 3.7 21.1 - - + -
776A VAL* 4.3 13.7 - - + -
778A GLY 3.6 2.5 - - - -
779A ILE* 5.1 4.5 - - + -
811A LEU* 4.0 18.4 - - + -
812A LEU* 1.3 77.2 - - - +
814A VAL* 1.3 66.8 + - - +
815A SER* 4.1 1.0 + - - +
818A GLN 4.1 0.3 - - - +
819A PHE* 3.7 3.1 - - - -
820A LYS* 2.8 41.5 + - + +
822A PHE* 3.8 21.5 - - + -
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Residues in contact with VAL 814 (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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776A VAL* 3.8 2.3 - - - +
777A VAL* 2.9 39.6 + - + +
778A GLY 2.7 22.0 + - - +
780A LEU* 6.3 0.2 - - + -
812A LEU* 4.1 12.6 - - + -
813A VAL* 1.3 76.1 - - - +
815A SER* 1.3 65.6 + - - +
818A GLN 4.1 2.2 - - - -
819A PHE* 3.5 43.3 - - + -
843A VAL* 4.2 2.5 - - + -
846A VAL* 4.0 24.5 - - + -
864A LEU* 4.0 15.3 - - + -
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Residues in contact with SER 815 (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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770A LEU* 4.2 15.7 - - - -
772A HIS* 3.2 23.4 + - - -
774A ALA* 4.1 6.3 - - - -
775A PRO 3.2 14.8 - - - -
776A VAL* 4.3 0.4 - - - +
777A VAL* 3.6 4.8 - - - +
813A VAL* 4.0 1.0 - - - -
814A VAL* 1.3 77.6 - - - +
816A GLU* 1.3 62.6 + - - +
817A GLU 3.3 3.0 + - - -
818A GLN 2.8 37.6 + - - +
843A VAL* 3.6 19.4 - - - +
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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