Contacts of the strand formed by residues 670 - 675 (chain C) in PDB entry 3EQL
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 GLN 670 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C LEU* 3.9 4.7 - - + +
573C ARG* 3.4 35.7 - - - +
575C GLN* 2.9 29.1 - - + +
669C GLY* 1.3 82.0 - - - +
671C ASN* 1.3 67.3 + - - +
672C VAL* 2.9 6.1 - - - +
699C PHE* 2.8 74.8 + - + -
700C TYR* 2.8 30.6 + - + +
994C ILE 3.1 15.6 + - - +
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Residues in contact with ASN 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C GLN* 3.6 17.2 + - - +
576C ALA 2.9 23.3 + - - +
578C VAL* 2.6 54.4 + - + +
670C GLN* 1.3 75.2 - - - +
672C VAL* 1.3 58.8 + - - +
697C ARG* 5.6 0.3 + - - -
699C PHE* 3.9 14.4 - - - -
900C ARG* 4.5 6.5 + - - -
991C GLN* 4.7 9.6 + - + +
992C MET 3.7 8.1 - - - +
993C PHE* 3.0 22.7 - - - +
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Residues in contact with VAL 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C GLN* 2.9 19.7 - - + +
671C ASN* 1.3 74.9 - - - +
673C LEU* 1.3 71.5 + - - +
674C VAL* 3.2 6.4 + - - +
694C LEU* 4.5 10.8 - - + -
697C ARG* 6.2 0.7 - - - +
699C PHE* 5.0 1.8 - - + -
700C TYR* 3.3 23.8 - - + +
868C ASP* 3.3 32.5 - - + +
869C VAL* 3.7 17.5 - - + -
990C GLY 4.1 0.7 - - - -
991C GLN* 4.4 2.9 - - - -
992C MET 3.0 29.1 + - - +
994C ILE* 4.6 8.3 - - + -
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Residues in contact with LEU 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672C VAL* 1.3 74.9 - - - +
674C VAL* 1.3 60.2 + - - +
861C LEU* 5.3 12.8 - - + -
865C THR* 4.9 4.5 - - + +
866C PRO 3.9 8.1 - - - +
867C VAL* 3.4 38.4 - - + +
868C ASP* 2.6 42.8 + - - +
869C VAL 3.5 0.3 + - - -
892C LEU* 6.3 1.6 - - + -
895C TYR* 3.5 53.2 - - + +
896C PHE* 5.7 1.8 - - + -
989C VAL* 5.0 7.2 - - + -
990C GLY* 3.3 20.4 - - - +
991C GLN* 4.6 3.3 - - - +
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Residues in contact with VAL 674 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C VAL 3.3 10.8 - - - +
673C LEU* 1.3 75.9 - - - +
675C ALA* 1.3 70.3 + - - +
676C ILE* 4.0 3.9 + - + +
867C VAL* 4.5 1.6 - - - -
869C VAL* 3.1 31.9 - - + +
871C LEU* 3.7 28.3 - - + -
888C THR* 4.6 4.8 - - - +
989C VAL* 3.0 7.0 - - - -
990C GLY 2.8 40.6 + - - +
992C MET* 3.4 29.4 - - + -
994C ILE* 5.1 0.4 - - + -
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Residues in contact with ALA 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674C VAL* 1.3 74.6 - - - +
676C ILE* 1.3 60.1 + - - +
677C MET* 3.6 13.2 + - + -
867C VAL* 3.5 32.5 - - + +
869C VAL 3.2 4.5 + - - +
870C ILE* 3.2 10.6 - - + +
871C LEU 3.1 21.3 + - - -
974C LEU* 3.8 14.6 - - + -
988C VAL 4.3 0.2 - - - +
989C VAL* 3.6 17.0 - - + -
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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