Contacts of the helix formed by residues 662 - 672 (chain A) in PDB entry 2V9Y
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 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A ASN* 2.8 38.0 + - + +
525A LEU* 3.5 15.0 - - + +
614A ILE* 3.7 20.4 - - + -
615A ALA 2.6 35.1 + - - -
616A SER* 3.4 0.3 - - - -
620A HIS* 3.4 20.5 - + - -
660A ARG* 3.9 15.2 - - + +
661A ILE* 1.3 75.3 - - - +
663A SER* 1.3 58.9 + - - +
664A HIS 3.4 2.7 - - - -
665A SER* 3.9 5.2 - - - -
666A LEU* 2.9 43.0 + - + +
678A PHE* 4.5 3.1 - + + -
680A HIS* 4.6 1.1 - + - -
736A GLY* 3.4 28.4 - - - -
737A ALA* 4.0 11.7 - - + -
758A GLU* 3.8 22.2 - - - -
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Residues in contact with SER 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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521A VAL* 3.0 43.1 + - - +
522A ASN* 3.8 0.6 + - - -
525A LEU* 3.9 13.8 - - - +
531A PRO* 3.3 29.7 - - - +
562A ALA 4.4 6.7 - - - -
661A ILE* 3.5 6.2 - - - +
662A TYR* 1.3 78.6 - - - +
664A HIS* 1.3 61.4 - - - +
667A LEU* 3.3 26.9 - - - -
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Residues in contact with HIS 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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561A LYS 4.1 15.5 - - - +
562A ALA* 4.0 18.5 + - - +
563A GLY* 5.3 4.8 - - - -
661A ILE* 4.7 5.2 + - + +
663A SER* 1.3 79.1 + - - +
665A SER* 1.3 66.6 + - - +
667A LEU* 4.7 0.9 - - - +
668A PRO* 3.7 15.6 - - - +
756A HIS* 5.1 1.2 - - - -
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Residues in contact with SER 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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661A ILE 4.1 2.2 + - - -
662A TYR* 3.5 11.5 + - - -
664A HIS* 1.3 85.0 - - - +
666A LEU* 1.3 61.4 + - - +
668A PRO* 3.6 4.0 - - - +
669A VAL* 4.3 1.6 - - - +
756A HIS* 3.2 54.1 - - - +
758A GLU* 2.6 35.4 + - - +
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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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525A LEU* 4.2 7.6 - - + -
614A ILE* 3.9 23.1 - - + -
662A TYR* 2.9 39.0 + - + +
665A SER* 1.3 79.0 + - - +
667A LEU* 1.3 65.5 + - - +
668A PRO* 3.4 2.7 - - - -
669A VAL* 3.0 15.3 + - + +
670A LEU* 3.0 25.3 + - + +
678A PHE* 3.8 26.0 - - + -
739A LEU* 5.3 4.0 - - + -
753A ILE* 4.4 23.8 - - + -
756A HIS* 5.4 0.2 - - + -
758A GLU* 3.8 27.1 - - + -
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Residues in contact with LEU 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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525A LEU* 4.0 21.9 - - + +
528A GLY 4.2 3.1 - - - +
529A ALA 4.1 10.3 - - - +
530A GLU* 3.7 35.0 - - + +
531A PRO* 5.4 0.9 - - + -
663A SER 3.3 22.5 - - - -
664A HIS 4.7 0.9 - - - +
666A LEU* 1.3 76.9 - - - +
668A PRO* 1.4 62.7 - - + +
669A VAL 3.1 0.2 + - - -
670A LEU* 3.2 7.6 + - + +
671A ARG* 2.8 72.3 + - + +
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Residues in contact with PRO 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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664A HIS 3.7 12.3 - - - +
665A SER 3.6 14.8 - - - +
667A LEU* 1.4 90.3 - - + +
669A VAL* 1.3 59.7 + - - +
671A ARG* 3.2 9.8 + - + +
672A SER* 3.1 19.8 + - - -
756A HIS* 3.3 35.4 - - + +
633B LYS* 5.7 5.2 - - + +
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Residues in contact with VAL 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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665A SER 4.3 7.9 - - - +
666A LEU* 3.0 16.3 + - + +
668A PRO* 1.3 73.5 - - - +
670A LEU* 1.3 60.8 + - + +
672A SER* 2.6 32.1 + - - -
675A VAL* 3.6 4.0 - - + +
739A LEU* 4.3 13.9 - - + -
749A ILE* 3.9 25.4 - - + +
752A GLY* 3.9 31.0 - - - +
753A ILE* 4.0 24.0 - - + +
756A HIS* 4.1 10.8 - - + +
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Residues in contact with LEU 670 (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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525A LEU* 3.2 48.2 - - + +
528A GLY* 4.4 5.8 - - - -
599A LEU* 3.8 25.5 - - + +
666A LEU* 3.0 20.3 + - + +
667A LEU* 3.6 11.7 - - + +
669A VAL* 1.3 76.1 - - + +
671A ARG* 1.3 65.6 + - - +
672A SER 3.4 0.9 + - - -
673A GLY* 3.5 11.4 + - - -
675A VAL* 3.9 32.2 - - + +
678A PHE* 3.8 25.8 - - + -
739A LEU* 4.0 7.0 - - + -
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Residues in contact with ARG 671 (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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484A PHE* 5.4 1.8 - - - -
528A GLY* 2.7 31.5 + - - -
530A GLU* 3.7 23.8 + - - +
592A ALA 3.8 2.8 + - - -
593A MET* 3.4 15.4 - - - +
597A GLN* 3.5 54.3 + - - +
667A LEU* 2.8 45.6 + - + +
668A PRO* 3.7 9.0 - - + +
669A VAL 3.2 0.4 - - - -
670A LEU* 1.3 71.6 - - - +
672A SER* 1.3 61.6 + - - +
673A GLY* 3.1 4.0 + - - -
721B HIS* 2.9 31.8 + - + +
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Residues in contact with SER 672 (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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668A PRO 3.1 9.8 + - - -
669A VAL* 2.6 23.1 + - - -
671A ARG* 1.3 77.6 - - - +
673A GLY* 1.3 61.4 + - - +
674A HIS* 3.1 39.4 + - - +
749A ILE* 4.0 8.4 - - - +
721B HIS* 4.1 13.6 + - - -
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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