Contacts of the strand formed by residues 881 - 888 (chain A) in PDB entry 4G34
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 881 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A ARG* 3.8 3.7 - - - +
625A LEU* 2.9 51.2 + - + -
632A ARG* 3.7 28.1 - - - +
658A LEU* 4.3 15.9 - - + -
659A GLU 3.6 12.8 - - - +
868A LYS* 4.6 9.9 - - + -
880A LYS* 1.3 81.9 - - - +
882A TYR* 1.3 75.4 + - - +
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Residues in contact with TYR 882 (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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622A ARG* 3.7 49.0 + - + -
623A ILE 3.4 14.8 - - - +
624A ARG* 3.8 34.8 - - + -
625A LEU* 5.1 0.4 - - - -
657A TRP 3.9 0.2 - - - +
658A LEU* 3.3 7.5 - - - +
659A GLU* 2.8 42.0 + - + +
868A LYS 5.3 1.1 - - - -
869A ASN* 4.7 20.4 - - + -
880A LYS* 5.0 8.0 - - + +
881A VAL* 1.3 80.7 - - - +
883A LEU* 1.3 59.2 + - - +
884A TYR* 4.1 12.4 + - + -
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Residues in contact with LEU 883 (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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621A LYS 3.4 1.7 - - - +
622A ARG* 3.4 3.8 - - - -
623A ILE* 2.9 49.0 + - + +
625A LEU* 3.9 11.6 - - + +
635A VAL* 3.9 20.9 - - + -
636A MET* 3.9 8.3 - - + -
639A VAL* 3.6 31.2 - - + -
656A ALA* 4.5 4.7 - - + -
657A TRP 3.5 14.8 - - - +
658A LEU* 3.8 19.1 - - + -
881A VAL 4.4 0.2 + - - -
882A TYR* 1.3 72.5 - - - +
884A TYR* 1.3 73.0 + - - +
885A ILE* 4.2 17.8 + - + +
957A LEU* 4.6 1.1 - - + -
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Residues in contact with TYR 884 (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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588A TYR* 3.6 38.2 - + + +
607A PHE* 5.8 1.1 - + - -
620A ILE* 3.7 20.6 - - + -
621A LYS 3.3 2.7 - - - -
622A ARG* 3.5 43.0 + - + -
656A ALA* 3.1 6.6 - - - +
657A TRP* 2.8 80.4 + + + +
659A GLU* 3.6 31.1 + - + -
882A TYR* 4.2 10.6 - - + +
883A LEU* 1.3 77.6 - - - +
885A ILE* 1.3 63.3 + - - +
886A GLN 4.2 0.4 - - - -
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Residues in contact with ILE 885 (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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619A ALA 3.6 1.4 - - - +
620A ILE* 3.4 5.7 - - - +
621A LYS* 2.9 46.8 + - + +
623A ILE* 4.6 7.2 - - + -
639A VAL* 4.7 9.0 - - + -
642A LEU* 5.5 0.9 - - + -
653A TYR* 4.2 11.4 - - + -
655A ASN 3.5 7.2 - - - +
656A ALA* 4.4 6.1 - - + -
883A LEU* 4.3 18.6 - - + +
884A TYR* 1.3 79.2 - - - +
886A GLN* 1.3 60.9 + - - +
887A MET* 3.7 29.7 + - + +
957A LEU* 3.5 32.5 - - + -
1101A 924 4.3 19.3 - - + -
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Residues in contact with GLN 886 (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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587A ARG* 5.1 1.4 + - - -
592A PHE* 3.5 23.7 - - - -
611A ASN* 5.0 2.2 + - - +
614A ASP* 5.1 1.2 + - - -
618A TYR* 3.3 57.2 - - + -
619A ALA 3.7 3.4 - - - -
620A ILE* 3.9 12.8 - - + -
653A TYR* 4.2 0.2 - - - -
654A PHE* 2.9 37.7 + - + +
655A ASN* 2.7 34.5 + - - +
657A TRP* 4.1 10.6 - - + -
884A TYR 4.2 0.6 - - - -
885A ILE* 1.3 69.4 - - - +
887A MET* 1.3 63.7 + - - +
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Residues in contact with MET 887 (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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618A TYR* 3.6 7.8 - - - +
619A ALA* 2.8 32.4 + - + +
651A VAL* 3.2 40.6 - - + +
652A ARG 3.6 5.6 - - - +
653A TYR* 3.8 13.9 - - - -
654A PHE* 3.9 4.9 - - - -
885A ILE* 3.7 24.5 - - + +
886A GLN* 1.3 75.4 - - - +
888A GLN* 1.3 67.9 + - - +
889A LEU 3.4 0.3 + - - -
1101A 924 3.6 74.0 - - + +
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Residues in contact with GLN 888 (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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618A TYR* 4.7 2.0 - - - -
619A ALA* 4.0 0.2 - - - +
651A VAL* 3.4 10.2 - - + +
652A ARG* 3.0 55.1 + - + +
654A PHE* 3.6 17.3 - - + -
887A MET* 1.3 70.9 - - - +
889A LEU* 1.3 72.3 + - - +
890A CYS* 3.5 2.2 + - - -
945A THR* 3.8 26.8 - - - +
946A MET 6.2 0.4 - - - -
951A LYS* 4.8 4.9 + - - -
1101A 924 2.9 24.8 + - - -
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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