Contacts of the strand formed by residues 690 - 696 (chain B) in PDB entry 4A9C
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 ASP 690 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B THR* 4.5 10.3 - - + +
432B ASN* 4.2 5.3 - - - +
472B GLN* 4.1 6.4 - - - +
606B GLY 3.4 6.7 - - - +
607B ASP* 3.8 20.6 - - - +
657B PHE* 4.7 5.4 - - - -
660B THR* 2.7 29.5 + - - +
688B TRP* 3.4 1.4 - - - -
689B CYS* 1.3 74.3 - - - +
691B ARG* 1.3 67.7 + - - +
707B TYR* 4.3 1.2 + - - -
718B HIS* 2.9 36.4 + - - +
719B SER 4.1 3.8 - - - +
721B VAL* 3.7 32.0 - - + +
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Residues in contact with ARG 691 (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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430B THR* 3.9 1.6 - - - +
605B PHE* 3.2 24.3 - - - +
606B GLY 3.3 12.4 + - - +
608B LEU* 4.0 13.6 - - + +
610B TYR* 4.9 1.2 - - - +
635B ASP* 2.8 42.8 + - - -
637B LEU* 3.5 24.4 - - + +
638B ASN* 3.3 11.3 + - - -
652B GLU* 2.7 39.3 + - - +
655B ILE* 3.6 16.9 - - - +
657B PHE* 5.6 0.9 - - - -
688B TRP* 3.0 36.9 + - - +
689B CYS 4.2 1.3 - - - +
690B ASP* 1.3 81.5 - - - +
692B ILE* 1.3 63.9 + - - +
693B LEU* 3.9 15.0 - - + -
707B TYR* 3.4 7.2 - - - -
721B VAL* 5.1 0.2 - - - -
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Residues in contact with ILE 692 (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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428B ILE* 3.4 47.8 - - + +
430B THR* 3.8 14.8 - - + -
603B PHE* 4.9 4.3 - - + -
604B TRP 3.7 2.7 - - - -
605B PHE* 3.9 4.3 - - + -
652B GLU* 3.4 23.6 - - - +
691B ARG* 1.3 78.1 - - - +
693B LEU* 1.3 68.1 + - - +
694B TRP* 4.7 4.1 - - - -
707B TYR* 3.2 17.6 + - + -
721B VAL* 3.9 13.0 - - + +
722B PHE 3.6 23.3 - - - +
723B GLY* 3.6 3.4 - - - +
725B PHE* 3.8 27.8 - - + -
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Residues in contact with LEU 693 (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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603B PHE* 3.5 5.5 - - - +
604B TRP 2.7 41.3 + - - +
608B LEU* 3.8 29.4 - - + -
637B LEU* 3.9 8.3 - - + -
641B ARG* 3.8 42.6 - - - +
647B PHE* 4.1 20.0 - - + -
650B PHE* 4.0 18.2 - - + -
651B SER 3.4 5.4 - - - +
652B GLU* 4.0 10.1 - - + +
691B ARG* 3.9 12.8 - - + -
692B ILE* 1.3 80.1 - - - +
694B TRP* 1.3 60.6 - - - +
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Residues in contact with TRP 694 (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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602B LEU 3.2 7.6 - - - +
603B PHE* 3.6 24.5 - + + -
650B PHE* 3.7 4.5 - - - -
651B SER* 2.7 72.4 + - - -
652B GLU* 3.8 4.5 - - - -
653B GLU* 3.4 37.5 - - + -
692B ILE 4.7 3.1 - - - -
693B LEU* 1.3 78.5 - - - +
695B LYS* 1.3 59.6 + - - +
696B SER* 3.9 11.4 - - - +
702B ILE* 3.7 40.9 + - + +
704B CYS* 4.0 22.2 - - + -
725B PHE* 3.4 27.4 - + - -
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Residues in contact with LYS 695 (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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596B SER* 3.1 44.7 + - - +
597B LEU* 3.7 17.5 - - - +
599B PHE 4.9 1.9 - - - +
600B THR 4.3 0.7 - - - +
601B HIS* 3.8 0.3 - - - -
602B LEU* 2.8 41.5 + - + +
648B LEU* 3.8 22.5 + - - +
649B ARG* 3.6 32.7 - - - +
650B PHE* 3.8 29.4 - - + -
694B TRP* 1.3 73.7 - - - +
696B SER* 1.3 66.0 + - - +
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Residues in contact with SER 696 (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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599B PHE 5.4 0.7 - - - -
600B THR 3.3 4.7 - - - -
601B HIS* 2.8 31.3 + - - -
694B TRP* 3.9 6.0 - - - +
695B LYS* 1.3 81.9 + - - +
697B TYR* 1.4 67.5 + - - +
698B PRO* 3.9 1.9 - - - +
700B THR* 3.5 11.0 - - - -
702B ILE* 3.5 26.7 - - - +
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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