Contacts of the helix formed by residues 672 - 687 (chain B) 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 SER 672 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670B LYS 3.7 2.6 + - - -
671B PHE* 1.3 74.0 - - - +
673B LYS* 1.3 67.8 + - - +
674B ASP* 3.9 5.5 + - - +
675B GLU* 3.1 32.3 + - - +
676B ALA* 2.8 20.1 + - - +
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Residues in contact with LYS 673 (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* 5.0 7.3 - - + +
666B THR* 4.1 17.1 + - + +
671B PHE 3.6 1.6 + - - -
672B SER* 1.3 72.1 - - - +
674B ASP* 1.3 61.3 + - - +
676B ALA* 3.3 2.3 + - - +
677B LYS* 2.9 57.0 + - - +
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Residues in contact with ASP 674 (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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672B SER* 3.2 5.8 + - - +
673B LYS* 1.3 81.1 - - - +
675B GLU* 1.3 58.8 + - - +
677B LYS* 3.1 11.4 + - - +
678B GLU* 2.9 30.4 + - - +
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Residues in contact with GLU 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 3.8 16.5 - - - +
671B PHE* 3.6 30.9 - - + -
672B SER* 3.0 27.9 + - - +
674B ASP* 1.3 78.2 - - - +
676B ALA* 1.3 62.9 + - - +
678B GLU* 3.5 8.5 + - - +
679B ILE* 3.0 38.1 + - + +
705B TRP* 5.4 5.2 - - + +
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Residues in contact with ALA 676 (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* 3.9 11.8 - - + +
665B LEU* 3.8 28.8 - - + +
666B THR* 3.3 26.7 - - - +
671B PHE* 4.1 10.0 - - + +
672B SER 2.8 12.6 + - - +
673B LYS 3.5 3.8 - - - +
675B GLU* 1.3 77.8 - - - +
677B LYS* 1.3 55.9 + - - +
679B ILE* 3.5 0.4 + - - -
680B SER* 3.0 30.3 + - - -
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Residues in contact with LYS 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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662B GLU* 2.7 43.7 + - - +
673B LYS* 2.9 39.5 + - - +
674B ASP* 3.5 12.8 - - - +
676B ALA* 1.3 78.3 - - - +
678B GLU* 1.3 57.7 + - - +
680B SER* 3.2 6.4 + - - -
681B ASP* 2.9 42.4 + - - +
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Residues in contact with GLU 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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674B ASP 2.9 16.1 + - - +
675B GLU* 4.0 8.6 - - + +
677B LYS* 1.3 78.3 - - - +
679B ILE* 1.3 61.9 + - - +
681B ASP* 3.4 6.4 + - - +
682B PHE* 3.3 20.8 + - - +
703B HIS* 3.8 11.9 - - + -
704B PRO* 3.4 13.2 - - + +
705B TRP* 3.2 48.3 + - + +
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Residues in contact with ILE 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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267B LEU* 5.1 0.9 - - + -
598B ILE* 4.4 14.6 - - + -
665B LEU* 3.6 23.6 - - + -
671B PHE* 3.8 40.2 - - + -
675B GLU* 3.0 25.6 + - + +
678B GLU* 1.3 76.2 - - - +
680B SER* 1.3 57.0 + - - +
682B PHE* 3.1 10.1 + - + +
683B LEU* 3.0 45.5 + - + +
705B TRP* 3.7 35.0 - - + +
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Residues in contact with SER 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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661B LEU* 3.8 20.9 - - - +
662B GLU* 4.0 25.4 + - - +
665B LEU* 4.8 0.4 - - - -
676B ALA 3.0 19.5 + - - -
677B LYS* 3.2 7.4 + - - -
679B ILE* 1.3 73.9 - - - +
681B ASP* 1.3 58.1 + - - +
682B PHE 3.0 5.4 - - - -
684B SER* 2.7 53.0 + - - -
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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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677B LYS* 2.9 30.2 + - - +
678B GLU* 3.9 7.8 - - - +
679B ILE 3.4 0.2 - - - -
680B SER* 1.3 78.4 - - - +
682B PHE* 1.3 57.3 + - - +
684B SER* 4.8 1.5 - - - -
685B PRO* 3.0 25.3 - - - +
703B HIS* 3.6 4.3 - - + +
723B TYR* 3.4 31.8 + - + +
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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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274B SER* 4.6 1.1 - - - -
278B LEU* 3.9 7.6 - - + -
594B ILE* 3.7 20.6 - - + -
678B GLU 3.3 12.5 + - - +
679B ILE* 3.1 10.7 + - + +
680B SER 3.0 0.8 - - - -
681B ASP* 1.3 78.8 - - - +
683B LEU* 1.3 79.1 + - + +
685B PRO* 3.5 4.2 - - - +
686B MET* 3.4 29.2 - - + +
700B LEU* 3.4 37.6 - - + +
703B HIS* 3.5 31.2 - + + +
705B TRP* 3.6 32.8 - + + -
706B LEU* 3.7 36.1 - - + -
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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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591B ALA* 4.4 11.7 - - + +
594B ILE* 4.0 18.6 - - + -
595B PHE* 4.5 29.8 - - + -
598B ILE* 4.6 5.6 - - + -
661B LEU* 3.9 20.4 - - + -
679B ILE* 3.0 32.5 + - + +
682B PHE* 1.3 98.5 - - + +
684B SER* 1.3 64.9 + - - +
685B PRO 3.3 2.9 - - - -
686B MET* 2.8 26.1 + - + +
687B LEU* 2.9 20.5 + - + +
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Residues in contact with SER 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU* 5.5 8.2 - - - +
661B LEU* 4.2 7.9 - - - +
680B SER* 2.7 43.1 + - - -
681B ASP* 4.8 1.8 - - - -
683B LEU* 1.3 71.7 - - - +
685B PRO* 1.3 66.4 - - - +
687B LEU* 2.9 21.3 + - - +
688B GLN* 3.1 11.3 + - - +
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Residues in contact with PRO 685 (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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681B ASP* 3.0 27.4 - - - +
682B PHE 3.5 6.3 - - - +
683B LEU 3.4 4.0 - - - -
684B SER* 1.3 93.8 - - - +
686B MET* 1.3 59.8 + - - +
688B GLN* 3.2 23.9 - - + +
693B LYS 4.7 0.6 - - - +
694B ARG* 3.7 0.3 - - - +
695B ALA* 3.5 34.6 + - + -
700B LEU* 4.6 4.3 - - + -
723B TYR* 4.0 20.2 - - + +
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Residues in contact with MET 686 (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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278B LEU* 4.3 8.5 - - + -
587B ILE* 3.4 31.0 - - + +
588B TRP* 3.8 9.0 - - - -
590B THR* 4.2 9.6 - - - -
591B ALA* 3.6 34.3 - - + -
594B ILE* 4.3 5.4 - - + -
682B PHE* 3.4 50.7 - - + +
683B LEU* 2.8 12.7 + - + +
685B PRO* 1.3 78.5 - - - +
687B LEU* 1.3 59.4 + - - +
688B GLN 3.1 0.4 + - - -
694B ARG* 3.2 27.0 + - - -
695B ALA 4.8 0.7 - - - -
700B LEU* 3.6 25.1 - - + -
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Residues in contact with LEU 687 (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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588B TRP* 3.3 37.7 - - + +
591B ALA* 3.4 29.2 - - + -
592B CYS* 4.7 0.9 - - - -
603B LEU* 3.7 30.7 - - + -
604B PHE* 4.5 0.9 - - + -
625B LEU* 4.5 13.5 - - + -
626B LEU* 3.3 34.1 - - + +
661B LEU* 4.5 19.1 - - + -
683B LEU* 2.9 15.2 + - + +
684B SER* 2.9 10.6 + - - +
686B MET* 1.3 76.2 - - - +
688B GLN* 1.3 64.1 + - - +
689B LEU* 3.1 3.6 + - - +
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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