Contacts of the strand formed by residues 756 - 762 (chain B) in PDB entry 1EGI
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 756 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645B TYR 3.3 11.6 - - - +
646B ALA* 3.4 24.1 - - - +
647B LYS 4.6 0.3 + - - -
648B GLY 4.3 6.2 + - - +
652B LYS* 3.8 28.5 + - - +
693B LYS* 3.5 31.2 + - - +
694B LEU 3.2 23.3 + - - +
695B PHE* 3.6 11.2 - - + -
696B TRP* 3.0 18.3 + - - -
755B ASN* 1.3 83.3 - - - +
757B TRP* 1.3 70.1 + - - +
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Residues in contact with TRP 757 (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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645B TYR* 2.9 57.3 + + + +
647B LYS* 5.2 14.1 - - + -
651B GLU* 3.5 15.7 - - + -
652B LYS* 4.4 1.6 - - - -
653B LYS* 3.5 36.3 - - + -
658B SER* 3.6 27.8 - - - +
661B PHE* 3.1 53.5 - + + +
662B CYS* 3.8 19.7 - - - -
669B LEU* 4.3 0.9 - - + -
695B PHE* 3.8 2.1 - - - -
696B TRP* 3.5 18.6 - - + +
755B ASN 3.8 8.1 - - - -
756B ASN* 1.3 87.0 - - - +
758B ILE* 1.3 69.2 + - - +
759B CYS* 3.7 2.9 - - - -
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Residues in contact with ILE 758 (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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642B PHE* 4.4 7.9 - - + -
643B LYS 3.4 19.5 - - - +
644B LEU* 3.6 26.0 - - + -
669B LEU* 3.5 12.0 - - - +
670B ALA* 3.0 33.6 + - + +
681B ILE* 3.8 22.4 - - + -
695B PHE* 3.7 26.9 - - + -
696B TRP 3.3 7.7 + - - +
697B LEU* 4.4 8.3 - - + -
738B LEU* 3.9 11.7 - - + -
757B TRP* 1.3 84.1 - - - +
759B CYS* 1.3 74.9 + - - +
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Residues in contact with CYS 759 (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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632B TRP* 4.1 14.6 - - + -
642B PHE* 3.5 4.3 - - - -
643B LYS 3.1 28.7 + - - -
645B TYR* 3.6 27.3 - - + -
661B PHE* 3.9 4.3 - - - -
662B CYS* 2.0 51.4 - - + +
665B LEU* 4.0 4.5 - - + -
668B ASP 3.3 5.6 - - - +
670B ALA* 4.1 2.2 - - - -
757B TRP* 3.7 8.3 - - - -
758B ILE* 1.3 78.7 - - - +
760B GLN* 1.3 64.3 + - - +
761B ILE* 5.6 0.4 - - + -
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Residues in contact with GLN 760 (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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632B TRP* 4.2 0.9 - - - -
640B LEU* 3.5 29.2 - - + +
641B CYS 3.0 8.3 - - - +
642B PHE* 3.5 19.7 - - + -
667B GLY* 3.3 0.3 - - - -
668B ASP* 2.8 48.6 + - + +
669B LEU 4.0 6.5 + - - +
670B ALA* 3.9 2.2 - - - -
671B SER* 2.8 45.3 + - - +
759B CYS* 1.3 75.2 - - - +
761B ILE* 1.3 70.6 + - - +
762B GLN* 4.2 7.5 - - - +
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Residues in contact with ILE 761 (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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629B PRO* 4.5 6.1 - - + -
632B TRP* 3.5 38.4 - - + -
640B LEU* 3.7 3.6 - - - -
641B CYS* 3.0 32.5 + - + +
665B LEU* 4.0 17.0 - - + +
666B GLY 4.3 6.7 - - - +
667B GLY* 3.4 24.7 - - - +
759B CYS* 5.6 0.4 - - + -
760B GLN* 1.3 84.3 - - - +
762B GLN* 1.3 82.1 - - - +
765B GLN* 3.8 22.7 - - + +
766B THR 5.0 0.7 - - - -
767B PRO* 4.2 14.8 - - + -
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Residues in contact with GLN 762 (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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629B PRO* 4.8 0.7 - - - +
639B SER* 3.3 27.2 + - - +
640B LEU* 3.0 27.6 - - - +
641B CYS* 4.6 0.7 - - - -
666B GLY 5.6 0.6 + - - -
760B GLN* 4.2 8.9 - - - +
761B ILE* 1.3 80.8 - - - +
763B LYS* 1.3 71.2 + - - +
765B GLN* 3.0 32.2 + - + +
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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