Contacts of the helix formed by residues 660 - 668 (chain B) in PDB entry 1Q99
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 660 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A PHE* 4.8 8.5 - - + -
625B LEU 3.6 14.8 - - - +
658B PHE* 3.9 10.1 - - + +
659B TRP* 1.3 93.6 - - - +
661B LEU* 1.3 65.9 + - - +
662B GLU* 3.2 7.9 - - + +
663B ASP* 3.1 26.7 + - - +
664B VAL* 3.1 17.0 + - - +
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Residues in contact with LEU 661 (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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595B PHE* 3.8 33.4 - - + -
603B LEU* 4.2 11.2 - - + -
625B LEU* 3.7 24.1 + - + +
626B LEU* 5.8 3.6 - - + -
660B PRO* 1.3 72.5 - - - +
662B GLU* 1.3 64.5 + - - +
664B VAL* 3.2 5.9 + - + +
665B LEU* 3.0 39.5 + - + +
680B SER* 4.0 22.7 - - - +
683B LEU* 3.9 31.0 - - + -
684B SER* 4.3 7.4 - - - +
687B LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 662 (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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660B PRO* 3.2 5.2 - - + +
661B LEU* 1.3 79.1 - - - +
663B ASP* 1.3 65.8 + - - +
665B LEU* 3.4 6.1 + - - +
666B THR* 2.9 33.8 + - - +
673B LYS* 3.9 14.9 - - - +
676B ALA* 3.8 22.2 - - + +
677B LYS* 2.9 52.6 + - - +
680B SER* 4.2 14.1 + - - +
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Residues in contact with ASP 663 (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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656A LEU 4.3 0.7 - - - +
658A PHE* 3.7 26.7 - - - -
659B TRP* 3.4 14.6 - - + -
660B PRO* 3.1 24.1 + - + +
662B GLU* 1.3 84.3 - - - +
664B VAL* 1.3 57.1 + - - +
666B THR* 4.4 4.3 - - - -
667B GLU* 2.6 62.2 + - - +
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Residues in contact with VAL 664 (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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595B PHE* 4.4 13.0 - - + -
603B LEU* 6.2 0.2 - - + -
625B LEU* 4.2 12.3 - - + -
659B TRP* 3.7 40.4 - - + +
660B PRO 3.1 17.1 + - - +
661B LEU* 3.2 8.7 + - + +
663B ASP* 1.3 76.3 - - - +
665B LEU* 1.3 59.3 + - - +
668B LYS* 2.8 44.2 + - + +
669B TYR* 3.1 27.1 + - + -
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Residues in contact with LEU 665 (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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595B PHE* 4.1 23.3 - - + -
598B ILE* 5.3 2.5 - - + -
599B THR* 4.6 4.0 - - + -
661B LEU* 3.0 34.8 + - + +
662B GLU 3.7 3.6 - - - +
664B VAL* 1.3 80.5 - - - +
666B THR* 1.3 57.5 + - - +
669B TYR* 3.2 13.2 - - + +
670B LYS 3.1 9.9 + - - -
671B PHE* 2.9 50.0 + - + -
676B ALA* 3.8 26.7 - - + +
679B ILE* 3.8 32.5 - - + -
680B SER 4.3 1.3 - - - +
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Residues in contact with THR 666 (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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662B GLU* 2.9 20.6 + - - +
663B ASP* 3.9 3.1 - - - -
665B LEU* 1.3 76.3 - - - +
667B GLU* 1.3 76.6 + - + +
670B LYS* 3.1 26.7 + - - +
671B PHE 3.2 20.0 + - - +
672B SER 4.0 1.9 + - - -
673B LYS* 4.1 11.0 + - + +
676B ALA* 3.6 11.1 - - - +
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Residues in contact with GLU 667 (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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654A SER* 2.8 45.0 + - - +
655A LYS* 2.8 8.4 - - - -
656A LEU* 2.5 41.5 + - - +
659B TRP* 3.2 14.3 + - + -
663B ASP* 2.6 49.4 + - - +
666B THR* 1.3 85.9 - - + +
668B LYS* 1.3 58.2 + - - +
670B LYS* 3.1 17.0 + - - +
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Residues in contact with LYS 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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655A LYS* 5.5 6.8 - - - +
601B ASP* 4.8 6.8 + - - +
659B TRP* 3.8 31.4 - - + -
664B VAL* 2.8 24.5 + - + +
667B GLU* 1.3 77.7 - - - +
669B TYR* 1.3 94.4 + - + +
670B LYS* 3.5 8.2 + - - +
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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