Contacts of the strand formed by residues 684 - 691 (chain B) in PDB entry 3K5N
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 TYR 684 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640B ASP 3.9 18.2 - - - +
641B TRP* 4.8 2.2 - - - -
642B THR* 2.9 23.6 - - - -
683B VAL* 1.3 74.5 - - - +
685B ARG* 1.3 60.8 + - - +
729B LYS* 3.4 2.4 - - - -
730B TYR* 2.8 73.9 + + + +
731B VAL* 4.3 3.4 - - - -
732B TRP* 4.5 3.8 - + + -
751B HIS* 2.8 42.1 - + - -
752B TYR* 3.7 24.9 - + - -
755B ARG* 3.8 4.3 - - - +
756B GLN* 3.6 25.3 - - + +
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Residues in contact with ARG 685 (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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639B THR* 3.9 28.8 + - + +
640B ASP* 4.1 8.4 + - - +
641B TRP 5.0 5.5 + - - -
643B PRO* 4.8 14.6 - - - +
646B GLN* 5.9 2.8 - - - +
683B VAL* 3.9 27.3 + - - +
684B TYR* 1.3 74.4 - - - +
686B LYS* 1.3 67.2 + - - +
727B THR* 3.7 25.1 - - + -
728B ILE 3.2 4.9 - - - -
729B LYS* 3.7 28.8 - - + +
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Residues in contact with LYS 686 (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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639B THR* 6.1 1.1 - - - -
640B ASP* 3.8 26.8 + - + +
684B TYR 4.3 0.2 - - - -
685B ARG* 1.3 77.2 - - - +
687B ARG* 1.3 90.9 + - - +
702B HIS* 3.0 42.8 - - + +
727B THR* 4.3 3.1 - - - -
728B ILE* 2.9 41.3 + - - +
730B TYR* 3.8 19.7 + - + +
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Residues in contact with ARG 687 (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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638B ARG* 5.0 11.1 - - - +
639B THR* 4.6 17.7 - - - +
640B ASP* 4.3 11.1 - - - +
686B LYS* 1.3 108.2 - - - +
688B LEU* 1.3 64.4 + - - +
689B ARG* 3.8 46.8 + - + +
702B HIS* 3.3 15.8 + - - -
726B GLY 2.9 12.8 - - - +
727B THR* 4.1 8.3 - - + +
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Residues in contact with LEU 688 (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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687B ARG* 1.3 74.6 - - - +
689B ARG* 1.3 54.3 + - - +
690B ARG 3.5 4.5 - - - +
692B LEU* 4.8 6.1 - - + -
695B TYR* 4.4 10.3 - - + +
702B HIS* 4.3 9.2 - - + +
703B VAL* 3.8 38.1 - - + +
706B ALA* 3.9 8.1 - - + -
722B TYR* 3.9 21.8 - - + +
725B ARG* 2.4 42.8 - - - +
726B GLY 2.5 21.6 + - - +
728B ILE* 2.1 46.9 - - + -
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Residues in contact with ARG 689 (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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687B ARG* 3.8 43.3 + - + +
688B LEU* 1.3 69.4 - - - +
690B ARG* 1.3 63.7 + - + +
695B TYR* 4.0 8.3 + - - +
725B ARG* 1.8 40.5 - - - +
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Residues in contact with ARG 690 (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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688B LEU* 4.7 3.5 - - - +
689B ARG* 1.3 89.8 - - + +
691B PRO* 1.3 71.4 - - - +
692B LEU* 3.0 4.2 + - - +
694B GLU* 2.9 58.5 + - + +
695B TYR* 3.4 31.6 + - + -
725B ARG* 4.1 9.8 + - - -
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Residues in contact with PRO 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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690B ARG* 1.3 78.7 - - - +
692B LEU* 1.3 68.4 + - - +
693B SER* 3.0 9.7 + - - +
694B GLU* 3.0 41.0 + - + +
695B TYR* 3.7 0.5 - - - -
723B GLN 3.5 8.7 - - - +
724B ASN* 4.0 24.0 - - - +
725B ARG* 2.4 36.3 - - - +
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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