Contacts of the helix formed by residues 676 - 683 (chain B) in PDB entry 4PQP
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 SER 676 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627B LEU* 3.3 24.3 - - - +
631B HIS* 3.4 24.0 + - - -
672B GLU 4.3 0.6 + - - -
673B LEU* 2.8 22.7 + - - +
674B SER 3.7 0.4 - - - -
675B ASN* 1.3 76.3 - - - +
677B GLN* 1.3 65.7 + - - +
678B LEU* 3.4 11.1 + - - +
679B LEU* 3.7 10.1 - - - +
680B ALA* 3.1 20.4 + - - +
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Residues in contact with GLN 677 (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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675B ASN 3.3 9.1 + - - +
676B SER* 1.3 71.7 + - - +
678B LEU* 1.3 55.4 + - - +
680B ALA* 3.1 11.3 + - - +
681B ASP* 2.6 67.2 + - - +
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Residues in contact with LEU 678 (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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623B LEU* 3.9 10.5 - - + +
626B LYS* 3.5 50.5 - - + +
627B LEU* 3.8 17.3 - - + -
630B PHE* 3.8 23.8 - - + -
631B HIS* 5.3 0.9 - - + +
676B SER* 3.4 10.3 + - - +
677B GLN* 1.3 77.9 - - - +
679B LEU* 1.3 61.6 + - - +
681B ASP* 3.8 8.6 + - + +
682B PHE* 3.1 23.4 + - - +
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Residues in contact with LEU 679 (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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563B ALA* 5.8 1.6 - - + -
623B LEU* 4.2 19.1 - - + -
627B LEU* 4.5 5.1 - - + +
664B LEU* 4.9 5.2 - - + -
667B LEU* 4.1 31.6 - - + -
668B LEU* 3.5 29.6 - - + +
673B LEU* 4.4 26.5 - - + +
676B SER* 3.2 18.2 + - - +
677B GLN 3.1 0.4 - - - -
678B LEU* 1.3 79.2 - - - +
680B ALA* 1.3 65.6 + - - +
682B PHE* 3.2 6.8 + - + +
683B LEU* 3.1 39.1 + - + +
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Residues in contact with ALA 680 (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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565B TRP* 4.5 19.5 - - + -
676B SER 3.1 10.7 + - - +
677B GLN* 3.4 18.6 - - - +
679B LEU* 1.3 80.2 - - - +
681B ASP* 1.3 55.8 + - - +
683B LEU* 3.1 11.3 + - - +
684B SER* 2.4 27.4 + - - -
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Residues in contact with ASP 681 (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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615B ARG* 3.3 10.4 + - - -
677B GLN* 2.6 47.8 + - - +
678B LEU* 3.8 9.3 + - + +
680B ALA* 1.3 71.5 - - - +
682B PHE* 1.3 65.0 + - - +
683B LEU 3.0 1.2 + - - -
684B SER* 3.1 21.5 + - - -
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Residues in contact with PHE 682 (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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591B ILE* 3.7 20.9 - - + -
613B VAL* 3.7 6.9 - - - +
615B ARG* 2.8 59.1 + - + +
619B GLU* 3.6 26.5 - - + -
620B PHE* 3.9 23.8 - + - -
623B LEU* 3.7 37.9 - - + -
664B LEU* 4.1 12.8 - - + -
678B LEU 3.1 11.6 + - - +
679B LEU* 3.2 11.9 + - + +
681B ASP* 1.3 78.7 - - - +
683B LEU* 1.3 70.4 + - + +
684B SER 3.6 0.2 + - - -
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Residues in contact with LEU 683 (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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565B TRP* 4.0 20.4 - - + -
567B ILE* 4.1 17.3 - - + -
591B ILE* 4.1 19.5 - - + -
593B VAL* 3.6 23.8 - - + +
611B TRP* 2.9 25.3 + - - -
613B VAL* 4.1 5.2 - - - -
664B LEU* 4.4 9.4 - - + -
668B LEU* 4.1 27.6 - - + -
679B LEU* 3.1 26.5 + - + +
680B ALA* 3.1 5.2 + - - +
681B ASP 3.0 1.8 + - - -
682B PHE* 1.3 95.7 - - + +
684B SER* 1.3 59.2 + - - +
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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