Contacts of the helix formed by residues 660 - 668 (chain A) in PDB entry 1Q8Z
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A LEU 4.1 10.8 - - - +
658A PHE* 4.1 6.5 - - + +
659A TRP* 1.3 87.9 - - + +
661A LEU* 1.3 60.1 + - - +
662A GLU* 4.3 7.2 - - + +
663A ASP* 3.0 32.8 + - - +
664A VAL* 2.9 28.1 + - - +
656B LEU 5.9 0.4 - - - +
658B PHE* 5.2 11.0 - - + -
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Residues in contact with LEU 661 (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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595A PHE* 3.7 35.2 - - + -
603A LEU* 4.1 12.1 - - + -
625A LEU* 3.5 23.3 + - + +
626A LEU* 6.3 2.0 - - + -
660A PRO* 1.3 68.0 - - - +
662A GLU* 1.3 66.8 + - - +
664A VAL* 3.0 7.6 + - + +
665A LEU* 2.8 37.9 + - + +
680A SER* 4.0 23.8 - - - +
683A LEU* 4.0 31.0 - - + -
684A SER* 4.3 8.1 - - - +
687A LEU* 4.6 12.6 - - + -
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Residues in contact with GLU 662 (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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660A PRO* 3.2 6.3 - - + +
661A LEU* 1.3 78.1 - - - +
663A ASP* 1.3 69.0 + - - +
665A LEU* 3.2 6.5 + - - +
666A THR* 3.0 29.5 + - + +
673A LYS* 4.6 9.2 - - - +
676A ALA* 4.2 17.3 - - + -
677A LYS* 3.1 52.5 + - + +
680A SER* 4.1 17.4 + - - +
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Residues in contact with ASP 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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659A TRP* 3.5 20.7 - - + +
660A PRO* 3.0 38.6 + - - +
662A GLU* 1.3 82.0 - - - +
664A VAL* 1.3 61.0 + - - +
666A THR* 3.9 6.6 + - - -
667A GLU* 2.8 52.9 + - - +
656B LEU 5.1 1.7 - - - +
658B PHE* 4.7 14.4 - - - -
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Residues in contact with VAL 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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595A PHE* 4.4 13.9 - - + -
603A LEU* 5.8 1.3 - - + -
625A LEU* 4.1 8.3 - - + -
659A TRP* 3.9 46.0 - - + +
660A PRO 2.9 25.9 + - - +
661A LEU* 3.0 14.3 + - + +
663A ASP* 1.3 75.6 - - - +
665A LEU* 1.3 57.8 + - - +
668A LYS* 3.0 35.1 + - + +
669A TYR* 3.3 24.8 + - + -
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Residues in contact with LEU 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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595A PHE* 4.2 23.1 - - + -
598A ILE* 5.4 1.8 - - + -
599A THR* 4.6 3.8 - - + -
661A LEU* 2.8 35.1 + - + +
662A GLU 3.6 4.9 - - - +
663A ASP 3.1 0.4 - - - -
664A VAL* 1.3 76.3 - - - +
666A THR* 1.3 61.1 + - - +
669A TYR* 3.5 14.2 - - + +
670A LYS 3.3 6.4 + - - -
671A PHE* 3.0 48.1 + - + +
676A ALA* 3.8 26.9 - - + +
679A ILE* 3.6 33.4 - - + -
680A SER* 4.4 1.8 - - - +
683A LEU* 5.4 0.4 - - + -
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Residues in contact with THR 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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662A GLU* 3.0 16.6 + - + +
663A ASP* 3.5 8.8 + - - -
665A LEU* 1.3 75.0 - - - +
667A GLU* 1.3 78.2 + - - +
670A LYS* 3.2 22.0 + - - +
671A PHE 3.4 18.4 - - - +
673A LYS* 3.9 20.2 - - + +
676A ALA* 3.3 27.4 - - + -
649B LEU* 4.1 20.6 - - - +
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Residues in contact with GLU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TRP* 2.8 26.5 + - + -
663A ASP* 2.8 38.6 + - - +
666A THR* 1.3 82.2 + - - +
668A LYS* 1.3 60.3 + - - +
670A LYS* 2.8 31.4 + - - +
649B LEU* 4.4 15.7 - - + -
654B SER* 3.0 32.1 - - - +
655B LYS* 4.1 2.2 - - - +
656B LEU* 3.1 31.8 + - + +
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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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601A ASP* 4.6 8.5 + - - +
659A TRP* 4.3 25.1 - - + -
664A VAL* 3.0 23.4 + - + +
667A GLU* 1.3 78.1 - - - +
669A TYR* 1.3 99.0 + - + +
670A LYS* 3.8 10.7 + - - +
654B SER* 4.8 5.4 - - - -
655B LYS* 5.1 6.3 - - + +
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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