Contacts of the helix formed by residues 666 - 671 (chain B) 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 LEU 666 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B LEU* 4.3 6.7 - - + -
614B ILE* 4.0 24.2 - - + -
662B TYR* 2.9 45.4 + - + +
665B SER* 1.3 80.3 - - - +
667B LEU* 1.3 67.0 + - - +
668B PRO* 3.3 2.9 - - - -
669B VAL* 3.0 23.6 + - + +
670B LEU* 3.1 18.7 + - + +
678B PHE* 3.9 21.5 - - + -
739B LEU* 5.5 3.8 - - + -
753B ILE* 4.1 26.5 - - + -
758B GLU* 4.1 19.1 - - + -
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Residues in contact with LEU 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 4.2 20.3 - - + +
528B GLY 4.8 0.7 - - - +
529B ALA 4.3 0.9 - - - +
530B GLU* 3.7 44.4 - - + +
531B PRO* 5.4 0.9 - - + -
662B TYR 4.1 0.6 + - - -
663B SER 3.3 23.0 + - - +
664B HIS 4.5 1.6 - - - +
666B LEU* 1.3 76.2 - - - +
668B PRO* 1.4 62.7 - - + +
670B LEU* 3.2 7.9 + - + +
671B ARG* 2.9 73.5 + - + +
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Residues in contact with PRO 668 (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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664B HIS 3.6 14.4 - - - +
665B SER 3.7 3.4 - - - +
666B LEU 3.4 3.8 - - - -
667B LEU* 1.4 93.2 - - + +
669B VAL* 1.3 60.2 + - - +
671B ARG* 3.3 16.3 + - + +
672B SER* 3.3 11.6 + - - -
756B HIS* 3.4 44.2 - - + +
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Residues in contact with VAL 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B SER 4.6 4.5 - - - +
666B LEU* 3.0 22.2 + - + +
668B PRO* 1.3 72.7 - - - +
670B LEU* 1.3 63.7 + - + +
672B SER* 2.6 30.4 + - - -
675B VAL* 3.6 5.9 - - + +
739B LEU* 4.1 20.4 - - + -
749B ILE* 3.7 32.8 - - + +
752B GLY* 3.9 33.2 - - - +
753B ILE* 3.9 13.5 - - + +
756B HIS* 4.7 3.4 - - - +
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU* 3.4 41.5 - - + +
528B GLY* 4.4 7.9 - - - -
599B LEU* 3.6 22.5 - - + +
666B LEU* 3.1 18.4 + - + +
667B LEU* 3.6 9.4 - - + +
669B VAL* 1.3 78.6 - - + +
671B ARG* 1.3 73.2 + - - +
672B SER 3.2 1.3 + - - -
673B GLY* 3.4 13.3 + - - -
674B HIS 4.8 0.2 + - - -
675B VAL* 3.7 35.5 - - + +
678B PHE* 4.0 21.8 - - + -
739B LEU* 4.1 5.6 - - + -
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Residues in contact with ARG 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B PHE* 5.7 1.8 - - - -
528B GLY* 2.8 33.3 + - - -
530B GLU* 3.7 21.8 + - - +
592B ALA 3.9 1.8 + - - -
593B MET* 3.5 14.8 - - - +
597B GLN* 3.4 42.4 + - - +
667B LEU* 2.9 45.1 + - + +
668B PRO* 3.3 9.6 + - + +
669B VAL 3.2 0.6 - - - -
670B LEU* 1.3 86.5 + - - +
672B SER* 1.3 63.2 + - - +
673B GLY* 3.1 3.2 + - - -
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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