Contacts of the helix formed by residues 662 - 669 (chain A) in PDB entry 4K33
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 ALA 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A TRP 4.0 0.4 + - - -
661A MET* 1.3 74.9 - - - +
663A PRO* 1.3 78.7 - - + +
664A GLU* 3.5 29.2 - - - +
665A ALA* 2.9 7.7 + - + +
666A LEU* 2.9 15.6 + - - +
675A SER* 4.2 13.1 + - - -
678A TRP* 3.5 33.0 - - + +
738A ARG* 3.6 2.7 - - - +
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Residues in contact with PRO 663 (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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661A MET 3.6 0.8 - - - +
662A ALA* 1.3 82.0 - - + +
664A GLU* 1.3 60.9 + - - +
666A LEU* 2.6 28.8 + - + -
667A PHE* 2.8 36.8 - - + -
678A TRP* 3.4 39.0 - - + -
704A PHE* 4.9 3.8 - - + -
707A LEU* 4.7 17.9 - - + +
708A LYS* 6.4 0.4 - - - -
712A ARG* 5.1 5.4 - - - +
733A ALA* 5.6 6.5 - - + +
738A ARG* 4.2 1.8 - - - +
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Residues in contact with GLU 664 (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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662A ALA* 3.5 10.8 - - - +
663A PRO* 1.3 74.4 - - - +
665A ALA* 1.3 55.4 + - - +
667A PHE* 4.5 3.8 - - - -
668A ASP* 3.0 44.7 + - + +
669A ARG 3.3 1.7 + - - -
670A VAL* 3.5 22.4 + - + +
672A THR* 4.8 3.5 + - + +
675A SER* 3.6 10.9 + - - -
733A ALA 4.3 2.8 - - - +
735A PRO* 3.7 22.2 - - + +
738A ARG* 2.6 48.2 + - - -
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Residues in contact with ALA 665 (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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656A LEU* 6.0 0.2 - - - +
661A MET* 3.9 15.1 - - + +
662A ALA* 2.9 21.1 + - + +
663A PRO 2.8 1.6 + - - -
664A GLU* 1.3 79.3 - - - +
666A LEU* 1.3 64.6 + - - +
669A ARG* 3.1 22.7 - - - +
670A VAL 3.4 19.1 - - - +
671A TYR* 3.7 28.3 + - + -
675A SER* 4.6 4.7 - - - -
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Residues in contact with LEU 666 (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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656A LEU* 6.3 0.2 - - + -
658A VAL* 3.8 35.4 - - + +
661A MET* 3.5 50.5 - - + +
662A ALA 2.9 10.7 + - - +
663A PRO* 2.6 9.7 + - + +
665A ALA* 1.3 73.0 - - - +
667A PHE* 1.4 89.6 + - + -
669A ARG* 4.6 4.1 - - - +
703A LEU* 5.3 0.7 - - + -
704A PHE* 4.6 7.2 - - + -
707A LEU* 4.1 20.9 - - + -
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Residues in contact with PHE 667 (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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663A PRO* 2.8 39.2 + - + -
664A GLU* 4.3 2.5 - - - -
666A LEU* 1.4 100.2 - - + +
668A ASP* 1.3 76.2 + - - +
669A ARG* 3.2 9.4 + - - +
704A PHE* 2.8 69.8 - + + -
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Residues in contact with ASP 668 (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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649A LYS* 3.3 21.7 - - - -
664A GLU* 3.0 25.9 + - + +
667A PHE* 1.3 89.4 - - - +
669A ARG* 1.3 71.9 + - - +
670A VAL* 3.0 17.2 + - + +
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Residues in contact with ARG 669 (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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648A TYR 3.6 0.9 - - - +
649A LYS* 3.4 9.0 - - + +
650A GLU* 3.0 58.9 + - + +
651A THR* 5.3 5.1 + - - +
652A THR 5.0 6.9 + - - -
653A ASN* 5.5 7.6 + - - -
656A LEU* 5.8 8.3 - - - -
665A ALA 3.1 20.5 + - - +
666A LEU 5.0 4.0 - - - +
667A PHE* 4.4 10.0 + - - +
668A ASP* 1.3 83.4 - - - +
670A VAL* 1.3 58.1 + - - +
671A TYR* 3.7 10.5 - - - +
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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