Contacts of the strand formed by residues 762 - 766 (chain B) in PDB entry 3LZB
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 762 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B LYS 3.6 1.4 - - - +
722B GLU* 3.6 1.6 - - - +
723B LEU* 2.9 73.6 + - + +
725B GLU* 5.4 12.9 - - + +
735B ILE* 4.6 10.3 - - + -
756B ILE* 4.0 14.4 - - + -
757B CYS 3.7 2.2 - - - -
758B LEU* 3.7 26.2 - - + -
761B THR* 1.3 74.1 - - - +
763B GLN* 1.3 62.1 + - - +
764B LEU* 4.4 5.8 - - + -
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Residues in contact with GLN 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B GLU* 4.5 7.1 + - - -
688B PHE* 3.6 25.0 - - + -
690B LYS* 2.5 33.5 + - - +
720B ILE* 3.9 15.3 - - + +
721B LYS 3.4 1.8 - - - -
722B GLU* 3.5 30.0 + - + -
755B GLY 4.5 0.2 - - - -
756B ILE* 3.2 10.2 - - - +
757B CYS* 2.9 48.8 + - + +
759B THR* 3.9 13.5 + - - -
761B THR* 3.6 11.9 + - - -
762B VAL* 1.3 73.3 - - - +
764B LEU* 1.3 63.6 + - - +
765B ILE* 4.1 4.0 + - + +
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Residues in contact with LEU 764 (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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1B ITI 3.7 43.1 - - + +
719B ALA 3.6 0.7 - - - +
720B ILE* 3.3 4.2 - - - -
721B LYS* 2.7 46.6 + - + +
723B LEU* 4.2 19.7 - - + -
739B ALA* 5.8 0.2 - - + -
742B MET* 5.6 3.8 - - - -
753B LEU* 3.5 25.1 - - + -
755B GLY 3.7 2.0 - - - -
756B ILE* 3.7 28.7 - - + -
762B VAL* 4.4 6.1 - - + -
763B GLN* 1.3 74.9 - - - +
765B ILE* 1.3 61.0 + - - +
834B LEU* 4.2 14.6 - - + -
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Residues in contact with ILE 765 (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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681B ARG* 4.6 13.2 - - - +
683B LEU* 3.6 26.9 - - + -
688B PHE* 4.6 13.0 - - + -
707B TRP* 6.3 0.2 - - + -
718B VAL* 3.7 28.5 - - + -
719B ALA 3.2 8.5 - - - +
720B ILE* 3.1 44.4 - - + -
753B LEU* 3.5 3.4 - - - +
754B LEU* 2.8 27.6 + - + +
755B GLY* 2.9 21.3 + - - +
756B ILE* 4.5 1.3 - - - +
763B GLN* 4.6 4.0 - - + +
764B LEU* 1.3 76.8 - - - +
766B THR* 1.3 67.5 + - - +
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Residues in contact with THR 766 (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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1B ITI 3.0 64.2 - - + -
718B VAL* 3.8 7.2 - - - +
719B ALA* 2.9 28.1 + - + +
751B CYS* 3.7 12.6 - - - -
752B ARG 3.2 16.2 + - - -
754B LEU* 4.0 12.5 - - - +
765B ILE* 1.3 77.5 - - - +
767B GLN* 1.3 73.5 + - - +
768B LEU 3.3 0.2 + - - -
769B MET* 5.2 0.7 - - - +
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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