Contacts of the strand formed by residues 661 - 668 (chain B) in PDB entry 4Z2M
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 LYS 661 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B ASN 3.1 8.3 + - - +
660B PRO* 1.3 74.9 - - - +
662B LEU* 1.3 68.4 + - - +
663B LYS* 3.4 31.6 - - - +
679B SER* 3.1 28.3 + - - +
680B LEU 3.2 11.2 - - - +
681B GLU* 3.6 35.1 + - + +
690B THR* 4.3 13.7 + - - +
783B PHE* 3.6 10.3 - - - +
786B LYS* 5.6 1.9 + - - +
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Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B LYS* 1.3 79.7 - - - +
663B LYS* 1.3 62.7 + - - +
665B LEU* 3.3 24.4 - - + +
679B SER* 2.7 22.2 + - - -
680B LEU* 2.9 25.0 + - + +
720B LEU* 4.0 17.3 - - + -
779B ALA* 3.7 33.7 - - + +
780B PHE* 3.5 46.4 - - + -
783B PHE* 4.2 16.8 - - + -
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Residues in contact with LYS 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B LYS* 3.4 39.3 - - + +
662B LEU* 1.3 82.0 - - - +
664B ASP* 1.3 85.9 + - - +
665B LEU* 3.4 11.4 - - - +
678B GLY 4.0 2.0 - - - -
679B SER* 3.3 17.0 - - - +
742B THR* 4.3 1.6 + - - -
776B LEU* 6.2 0.2 - - - +
780B PHE* 5.5 1.4 - - - -
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Residues in contact with ASP 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B LYS* 1.3 85.0 - - - +
665B LEU* 1.3 51.3 + - - +
666B TYR* 5.1 2.7 - - - -
677B GLN* 3.5 27.5 + - - +
678B GLY 3.5 5.8 + - - -
741B TYR 3.7 0.7 - - - +
742B THR* 2.2 44.9 + - + +
776B LEU* 5.8 4.2 - - + +
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Residues in contact with LEU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 3.3 47.6 - - + +
663B LYS 3.4 7.9 - - - +
664B ASP* 1.3 74.0 - - - +
666B TYR* 1.3 63.4 + - - +
677B GLN* 3.6 2.9 - - - +
678B GLY* 2.8 35.8 + - - +
680B LEU* 3.7 22.4 - - + +
689B PHE* 3.7 10.5 - - + -
720B LEU* 5.4 0.2 - - + -
740B PHE* 3.9 29.4 - - + +
741B TYR 3.3 7.6 - - - +
742B THR* 4.0 6.1 - - - +
780B PHE* 3.5 31.4 - - + -
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Residues in contact with TYR 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B ASP 5.1 2.0 - - - -
665B LEU* 1.3 75.7 - - - +
667B ILE* 1.3 59.9 + - - +
670B ASN* 6.1 1.1 - - - +
675B ARG* 3.1 63.5 + - + -
676B MET 4.0 3.1 - - - -
677B GLN* 2.7 46.4 + - + -
739B GLN 3.6 0.9 - - - +
740B PHE* 3.3 9.1 - - - -
741B TYR* 3.0 67.2 + + + +
742B THR* 5.1 2.7 - - + -
743B GLU* 4.7 7.2 - - + -
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Residues in contact with ILE 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665B LEU 4.1 0.2 + - - -
666B TYR* 1.3 74.3 - - - +
668B ARG* 1.3 61.8 + - - +
669B PRO 2.7 30.1 - - - +
670B ASN* 3.5 15.5 + - - +
671B ILE* 4.7 10.1 - - + -
676B MET* 3.5 23.5 + - + +
689B PHE* 3.5 31.2 - - + -
697B VAL* 3.8 30.5 - - + -
730B PHE* 4.4 11.9 - - + -
738B VAL* 4.3 11.2 - - + -
739B GLN 3.6 6.3 - - - +
740B PHE* 4.1 15.5 - - + -
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B TYR 3.9 0.6 + - - -
667B ILE* 1.3 74.1 - - - +
669B PRO* 1.3 67.8 - - + +
670B ASN* 5.7 4.0 - - - +
717B ILE* 4.1 13.5 - - - +
738B VAL* 3.6 6.2 - - - +
739B GLN* 3.1 59.4 + - + +
741B TYR* 3.3 31.1 + - + +
827B ALA 4.4 0.2 + - - -
828B THR 3.4 24.7 + - - -
829B GLU* 4.2 1.2 - - - +
830B TRP* 3.4 57.3 - - + +
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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