Contacts of the strand formed by residues 858 - 866 (chain A) in PDB entry 3I7K
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 LEU 858 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764A SER* 4.8 3.0 + - - +
791A LEU* 4.7 5.8 - - + +
793A ILE* 4.3 17.0 - - + -
803A HIS* 3.6 36.1 + - + +
805A HIS* 4.1 14.6 - - + +
829A PHE* 5.1 2.5 - - + -
851A PHE* 3.6 43.3 - - + -
852A GLN 3.2 15.3 - - - +
853A TYR* 3.6 25.9 - - + +
857A LYS* 1.3 94.8 + - - +
859A GLN* 1.3 60.0 + - - +
860A THR* 4.2 1.6 + - - +
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Residues in contact with GLN 859 (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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851A PHE* 3.1 6.8 - - - -
852A GLN* 2.5 65.6 + - + +
854A SER* 5.3 1.7 + - - -
857A LYS* 5.0 3.6 - - + +
858A LEU* 1.3 72.7 - - - +
860A THR* 1.3 66.8 + - - +
861A VAL* 3.2 15.8 + - - +
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Residues in contact with THR 860 (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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805A HIS* 4.3 11.6 + - - -
847A ARG* 6.2 0.2 - - - +
849A VAL* 4.3 18.6 - - + -
850A VAL 3.9 8.7 - - - +
851A PHE* 3.7 17.6 - - - -
858A LEU* 4.2 2.9 + - - +
859A GLN* 1.3 75.3 + - - +
861A VAL* 1.3 63.7 + - - +
862A ALA 4.3 9.4 - - - +
863A GLU* 5.6 4.0 - - + -
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Residues in contact with VAL 861 (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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828A TYR* 3.8 18.6 - - + -
850A VAL* 2.8 20.4 + - + +
852A GLN* 3.7 24.2 - - + +
859A GLN* 3.7 25.1 - - - +
860A THR* 1.3 76.4 - - - +
862A ALA* 1.3 58.2 + - - +
893A TRP* 3.7 29.6 - - + -
897A LYS* 4.4 19.6 - - + +
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Residues in contact with ALA 862 (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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848A ILE 4.4 1.1 - - - -
849A VAL* 3.4 8.7 - - - +
850A VAL* 2.8 34.5 + - + +
860A THR* 3.8 3.9 - - - +
861A VAL* 1.3 78.6 - - - +
863A GLU* 1.3 62.7 + - - +
893A TRP* 3.6 32.5 - - + -
897A LYS 4.1 6.5 - - - +
898A ASP* 5.1 2.0 - - - +
899A VAL* 5.0 8.3 - - + +
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Residues in contact with GLU 863 (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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768A SER* 2.5 43.2 + - - -
769A LYS 5.2 0.7 + - - -
770A LEU* 2.8 32.2 + - + +
847A ARG* 3.5 22.0 + - - +
848A ILE 3.5 4.9 - - - -
849A VAL* 4.6 3.8 - - + +
860A THR* 5.6 3.8 - - + -
862A ALA* 1.3 77.5 - - - +
864A LYS* 1.3 62.3 + - - +
898A ASP* 5.6 1.7 - - - +
899A VAL* 4.8 2.1 - - - +
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Residues in contact with LYS 864 (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* 4.3 1.3 - - - -
847A ARG* 3.2 8.9 - - - +
848A ILE* 3.0 41.8 + - + +
863A GLU* 1.3 72.4 - - - +
865A GLU* 1.3 78.1 + - - +
866A VAL* 4.3 3.4 - - + +
891A TYR* 4.1 23.6 - - + -
899A VAL* 2.6 60.2 + - + -
900A ARG* 4.1 11.3 - - - +
901A THR* 5.2 3.9 - - - +
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Residues in contact with GLU 865 (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* 3.8 41.8 - - + +
771A PHE* 3.8 24.8 - - + -
845A GLN* 4.9 6.4 + - - +
846A GLY 4.1 4.7 - - - +
864A LYS* 1.3 89.7 - - + +
866A VAL* 1.3 72.6 + - - +
867A LYS* 5.7 7.8 - - + +
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Residues in contact with VAL 866 (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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771A PHE* 5.4 0.2 - - - -
845A GLN* 3.8 3.6 - - - +
846A GLY 2.9 32.8 + - - +
847A ARG* 4.6 1.3 - - - -
848A ILE* 4.4 12.6 - - + -
864A LYS* 4.3 4.0 - - + +
865A GLU* 1.3 86.2 - - - +
867A LYS* 1.3 66.0 + - - +
868A GLY 3.1 20.9 + - - +
870A VAL* 3.8 16.4 - - + -
884A ILE* 3.6 25.8 - - + -
891A TYR* 3.3 31.0 - - + +
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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