Contacts of the strand formed by residues 695 - 702 (chain A) in PDB entry 6BM0
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 VAL 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A MET* 3.8 20.0 - - - +
660A SER 5.4 0.5 - - - +
661A ALA 5.4 1.7 - - - +
663A GLY* 3.9 33.7 + - - +
665A VAL* 4.4 6.5 - - + -
691A HIS* 4.4 18.1 + - + +
693A SER 4.7 2.5 - - - +
694A LYS* 1.3 74.2 - - - +
696A ILE* 1.3 65.7 + - - +
697A THR 3.8 14.1 - - - +
698A LEU* 4.1 4.9 - - + -
787A LEU* 3.8 44.6 - - + -
788A VAL 3.6 5.4 - - - +
789A ARG* 4.1 6.3 - - + +
927A ARG* 5.8 0.2 + - - -
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Residues in contact with ILE 696 (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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659A MET* 3.3 6.5 - - - +
694A LYS* 3.8 13.0 - - + +
695A VAL* 1.3 76.9 - - - +
697A THR* 1.3 60.9 + - + +
788A VAL* 2.7 18.4 + - + +
789A ARG 4.1 2.0 - - - +
790A GLU* 3.7 38.4 - - + +
845A LEU* 5.6 9.9 - - + -
846A VAL* 3.3 31.2 - - + +
847A LYS 5.2 0.4 - - - +
927A ARG* 2.8 41.5 + - - +
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Residues in contact with THR 697 (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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648A GLN* 3.5 15.6 + - - -
659A MET* 3.8 7.2 - - - -
695A VAL* 3.8 2.5 - - - +
696A ILE* 1.3 78.7 - - + +
698A LEU* 1.3 81.6 + - - +
788A VAL* 3.3 33.2 + - + -
846A VAL* 3.8 17.0 - - + -
847A LYS 3.8 18.1 + - - +
848A GLU* 4.0 1.0 - - - +
849A VAL* 3.8 37.6 + - + +
927A ARG* 4.7 1.1 - - - -
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Residues in contact with LEU 698 (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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648A GLN* 3.0 20.2 + - - +
649A CYS* 6.2 0.9 - - - -
650A ALA* 5.4 7.4 - - + +
657A VAL* 3.7 30.7 - - + +
659A MET* 3.7 33.2 - - + +
665A VAL* 4.2 7.6 - - + -
695A VAL* 4.1 3.1 - - + -
697A THR* 1.3 87.6 + - - +
699A CYS* 1.3 60.9 - - - +
700A LEU* 6.4 0.2 - - + -
785A CYS* 4.5 9.4 - - - -
786A LEU* 3.3 18.6 - - - +
787A LEU* 3.8 28.5 - - + -
788A VAL* 6.3 0.2 - - - -
849A VAL* 3.2 18.6 - - - +
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Residues in contact with CYS 699 (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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650A ALA* 4.7 7.2 - - - -
698A LEU* 1.3 78.6 - - - +
700A LEU* 1.3 92.5 + - - +
701A TYR* 5.0 0.2 - - - -
785A CYS* 4.1 1.4 - - - -
786A LEU* 3.0 43.3 + - + +
849A VAL 3.5 11.9 - - - +
850A LEU* 3.7 13.9 - - - -
851A LEU* 2.9 42.4 - - - +
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Residues in contact with LEU 700 (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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650A ALA* 3.5 40.4 - - + +
652A ALA* 4.2 28.4 - - + +
653A ASP* 5.0 1.8 - - - -
655A TYR 4.0 14.8 - - - +
657A VAL* 3.8 22.0 - - + -
698A LEU* 6.4 0.2 - - + -
699A CYS* 1.3 92.5 - - - +
701A TYR* 1.3 65.3 + - - +
784A TRP 3.5 2.7 - - - +
785A CYS* 3.7 31.6 - - + -
786A LEU 5.0 0.2 - - - +
799A LEU* 3.8 19.5 - - + -
850A LEU* 5.3 1.0 - - - +
851A LEU 3.8 4.0 - - - +
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Residues in contact with TYR 701 (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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653A ASP* 4.5 7.3 + - - -
700A LEU* 1.3 79.3 - - - +
702A ARG* 1.3 75.2 + - - +
703A ASP* 3.2 25.2 + - - -
706A GLY* 5.6 1.9 - - - -
708A PHE* 3.5 28.5 - + - -
783A HIS* 3.6 2.5 - - - +
784A TRP* 2.7 43.4 + + + +
799A LEU* 5.9 0.2 - - - +
851A LEU* 3.8 38.8 - - + -
852A VAL* 3.8 4.0 - - - -
853A ALA* 3.3 40.5 - - + +
858A GLN 4.5 3.5 + - - -
859A SER 4.6 1.4 + - - -
861A PRO* 3.3 26.9 - - + +
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Residues in contact with ARG 702 (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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653A ASP* 2.6 44.9 + - - +
654A PRO* 5.6 1.4 - - - +
701A TYR* 1.3 96.7 + - - +
703A ASP* 1.3 64.8 + - - +
704A LEU* 3.4 43.5 + - + +
781A PRO* 3.7 19.3 - - - +
782A THR 3.3 17.5 - - - +
783A HIS* 3.5 25.1 - - + -
853A ALA* 5.2 1.4 - - - +
858A GLN* 6.1 0.3 - - - +
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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