Contacts of the helix formed by residues 663 - 667 (chain A) in PDB entry 3KXX
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 PRO 663 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A ASP* 3.8 21.3 - - - +
627A ARG* 3.1 25.8 - - - +
661A ARG 4.3 3.4 - - - +
662A LEU* 1.4 83.3 - - + +
664A VAL* 1.3 64.7 + - - +
665A LYS 3.2 0.2 - - - -
666A TRP* 3.2 41.1 + - + +
667A MET* 3.4 12.5 + - - +
519D ASP* 4.2 15.3 - - + +
520D ALA 3.6 11.4 - - - +
521D THR* 3.9 2.0 - - - +
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A PRO* 1.3 70.9 - - - +
665A LYS* 1.3 67.5 + - + +
666A TRP 3.0 5.1 + - - -
667A MET* 3.3 39.3 + - + +
672A LEU* 4.6 8.0 - - + +
706A VAL* 3.2 50.7 - - + -
709A LEU* 4.3 11.9 - - + +
710A PHE* 4.3 17.0 - - + -
713A LEU* 5.4 0.9 - - - +
518D SER 5.1 0.4 - - - +
520D ALA 3.4 7.6 + - - +
521D THR 4.3 0.2 - - - -
522D GLU* 3.8 24.9 - - + +
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Residues in contact with LYS 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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663A PRO* 3.2 1.2 - - - +
664A VAL* 1.3 81.9 - - + +
666A TRP* 1.3 75.0 + - + +
667A MET 3.7 1.1 - - - -
684A TRP* 5.3 0.8 + - - -
688A VAL* 3.5 22.3 - - - +
699A SER* 5.2 1.4 - - - -
700A PRO* 3.0 39.4 + - + +
701A TYR* 3.3 29.2 + - + -
702A PRO* 5.4 0.4 - - - +
703A GLY 5.4 1.2 - - - +
704A VAL* 3.5 22.0 + - - +
706A VAL* 4.8 8.3 - - - +
709A LEU* 4.0 20.2 - - + -
518D SER* 3.2 47.1 - - - +
519D ASP* 6.3 0.2 - - - +
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Residues in contact with TRP 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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570A ARG* 3.7 9.2 - - - -
623A ASP* 5.1 5.8 - - - +
624A LEU 3.4 25.1 - - - +
625A ALA* 3.4 7.1 - - + +
627A ARG* 3.5 24.2 - - - -
663A PRO* 3.2 34.7 + - + +
664A VAL 3.0 0.8 - - - -
665A LYS* 1.3 95.7 - - + +
667A MET* 1.3 62.9 + - - +
684A TRP* 3.9 4.4 - - - -
685A SER* 2.7 37.0 + - - +
688A VAL* 3.6 24.7 - - + +
689A LEU 4.9 0.7 - - - -
692A GLU* 3.3 38.6 + - - -
700A PRO* 3.3 29.4 - - + -
518D SER* 4.7 2.2 - - - -
519D ASP* 4.5 17.9 - - + -
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Residues in contact with MET 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ARG 5.5 0.9 - - - +
656A LYS* 4.8 2.2 - - - -
662A LEU* 2.9 36.3 - - + +
663A PRO 3.4 6.5 + - - +
664A VAL* 3.3 32.8 + - + +
665A LYS 5.1 0.5 - - - -
666A TRP* 1.3 78.8 - - - +
668A ALA* 1.3 62.6 + - - +
669A PRO* 4.4 0.2 - - - +
672A LEU* 3.9 29.5 - - + +
677A TYR* 3.4 28.3 - - - +
684A TRP* 3.2 16.7 + - - -
685A SER* 5.0 0.2 - - - -
713A LEU* 5.4 3.5 - - - +
522D GLU* 3.1 40.8 - - + +
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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