Contacts of the helix formed by residues 666 - 670 (chain A) in PDB entry 2PY3
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 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A ARG 5.1 1.3 - - - +
626A ASP* 3.4 19.5 - - + +
630A ARG* 3.2 24.9 - - - +
647A LEU* 4.8 1.1 - - + -
664A ARG 3.9 7.0 - - - +
665A LEU* 1.3 83.3 - - + +
667A VAL* 1.3 66.2 + - - +
668A LYS 3.3 1.1 - - - -
669A TRP* 3.2 38.4 + - + +
670A MET* 3.4 9.5 + - - +
522B ASP* 3.6 18.8 - - + +
523B ALA 3.7 8.1 - - - +
524B THR* 3.9 5.1 - - + -
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Residues in contact with VAL 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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665A LEU 3.0 7.7 + - - +
666A PRO* 1.3 70.7 - - - +
668A LYS* 1.3 62.5 + - - +
669A TRP 3.2 1.4 + - - -
670A MET* 3.2 27.0 + - - +
675A LEU* 5.0 4.3 - - + -
709A VAL* 3.6 34.1 - - + +
712A LEU* 4.0 12.5 - - + +
713A PHE* 3.4 34.1 - - + -
522B ASP 5.1 0.2 - - - -
523B ALA 3.0 18.8 + - - +
524B THR* 3.9 0.7 - - - -
525B GLU* 3.8 27.6 - - + +
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Residues in contact with LYS 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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666A PRO 3.3 1.4 + - - -
667A VAL* 1.3 76.0 - - - +
669A TRP* 1.3 75.7 + - + +
670A MET 5.3 0.4 - - - -
687A TRP* 5.2 0.9 + - - -
691A VAL* 3.7 12.8 - - - +
703A PRO* 3.1 22.6 + - + +
704A TYR* 3.1 49.4 + - + -
705A PRO* 5.0 0.8 - - - +
706A GLY 5.1 1.0 - - - +
707A ILE 2.9 29.7 + - - +
708A PRO 4.8 0.4 - - - -
709A VAL* 4.4 17.5 - - + +
712A LEU* 3.8 20.0 - - + -
521B ASP* 2.8 46.4 + - - +
522B ASP* 5.9 0.2 - - - +
523B ALA 4.9 0.4 + - - -
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Residues in contact with TRP 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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573A ARG* 6.2 1.1 - - - -
626A ASP* 6.1 2.2 - - - +
627A LEU 3.2 28.0 - - - +
628A ALA* 3.3 9.8 - - + +
630A ARG* 3.8 21.5 - - + +
666A PRO* 3.2 23.6 + - + +
667A VAL 3.2 0.8 - - - -
668A LYS* 1.3 94.5 - - + +
670A MET* 1.3 59.7 + - - +
687A TRP* 3.7 5.1 - - - -
688A SER* 2.7 37.1 + - - +
691A VAL* 3.3 30.2 - - + +
692A LEU 4.6 0.2 - - - -
695A GLU* 2.7 38.9 + - - -
703A PRO* 3.6 22.0 - - + -
521B ASP* 4.6 6.1 - - - -
522B ASP* 3.8 26.0 - - + -
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Residues in contact with MET 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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662A ASN* 3.0 45.8 - - + +
665A LEU* 3.5 33.7 - - + +
666A PRO 3.4 8.9 + - - +
667A VAL* 3.2 23.3 + - - +
668A LYS 3.5 0.4 - - - -
669A TRP* 1.3 78.4 - - - +
671A ALA* 1.3 74.7 + - - +
672A PRO* 3.5 2.4 - - - +
674A ALA* 3.7 12.6 - - + -
675A LEU* 3.7 24.9 - - + -
680A TYR* 5.8 1.8 - - + -
687A TRP* 3.4 12.5 + - - -
688A SER* 4.8 0.7 - - - -
713A PHE* 4.1 17.5 - - + -
716A LEU* 4.7 3.1 - - - +
525B GLU* 6.0 0.4 - - - -
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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