Contacts of the helix formed by residues 692 - 708 (chain B) in PDB entry 6MZL
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 TYR 692 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B GLU* 3.6 24.5 - - + +
691B PHE* 1.3 85.3 - + + +
693B ARG* 1.3 67.1 + - + +
694B VAL 3.2 0.2 - - - -
695B ARG* 2.8 28.2 + - - +
696B MET* 3.3 9.2 + - - +
744B PHE* 4.6 10.7 - - + +
745B GLN* 3.5 50.6 + - + +
748B PHE* 3.6 39.0 - + + -
749B LEU* 5.4 0.9 - - - +
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Residues in contact with ARG 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO* 5.3 10.7 - - - +
390B GLU* 3.3 26.9 + - - -
393B HIS* 3.6 35.7 + - + -
397B GLU* 5.4 1.6 + - - -
663B GLN* 3.0 18.7 + - - +
691B PHE* 3.2 15.8 - - + -
692B TYR* 1.3 76.2 - - + +
694B VAL* 1.3 64.3 + - - +
696B MET* 3.1 34.3 + - + +
697B SER* 3.0 17.7 + - - -
748B PHE* 4.0 25.8 - - + -
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Residues in contact with VAL 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B VAL* 4.1 16.2 - - + -
662B GLN* 3.6 31.2 - - + +
663B GLN* 3.4 17.4 - - + +
666B ILE* 3.5 11.1 - - + +
685B LEU* 4.4 21.8 - - + -
690B CYS* 5.4 1.6 - - + -
691B PHE* 3.2 33.9 - - + +
693B ARG* 1.3 75.2 - - - +
695B ARG* 1.3 65.1 + - + +
697B SER* 3.1 5.9 + - - -
698B ALA* 2.9 26.0 + - - +
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Residues in contact with ARG 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LEU* 3.1 21.1 + - + +
686B GLU* 2.6 45.3 + - + +
687B GLN* 3.8 0.4 - - - +
688B GLU* 2.6 42.1 + - - +
689B GLN* 4.8 0.2 - - - -
690B CYS* 3.1 34.1 - - - +
691B PHE 3.3 18.4 + - - +
692B TYR* 2.8 15.3 + - - +
694B VAL* 1.3 77.9 - - + +
696B MET* 1.3 56.5 + - - +
698B ALA* 3.3 7.8 - - - +
699B CYS* 2.9 34.8 + - - -
726B MET* 5.0 3.0 - - - +
745B GLN* 5.2 3.0 + - - +
749B LEU* 4.0 25.3 - - + +
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Residues in contact with MET 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B TYR 3.3 9.1 + - - +
693B ARG* 3.1 46.2 + - + +
695B ARG* 1.3 76.8 - - + +
697B SER* 1.3 63.0 + - - +
699B CYS* 3.1 15.5 + - - +
700B PHE* 3.2 23.5 + - + -
748B PHE* 4.5 23.8 - - + +
749B LEU* 5.5 2.7 - - + -
751B LYS* 6.5 1.1 - - + -
752B THR* 3.2 41.7 - - + +
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Residues in contact with SER 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B GLN* 3.2 24.2 + - - -
666B ILE* 3.3 23.3 - - - +
667B LEU* 6.0 1.6 - - - -
670B GLU* 3.7 2.9 - - - +
693B ARG 3.0 6.6 + - - -
694B VAL 3.1 12.3 + - - -
696B MET* 1.3 76.5 - - - +
698B ALA* 1.3 56.7 + - - +
700B PHE* 3.2 14.0 + - - +
701B CYS* 2.9 30.6 + - - -
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Residues in contact with ALA 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ILE* 4.5 7.4 - - + -
682B THR* 3.8 9.6 - - + +
685B LEU* 5.1 9.0 - - + -
686B GLU* 3.4 26.4 - - + +
694B VAL* 2.9 18.6 + - + +
695B ARG* 3.3 11.7 - - + +
696B MET 3.1 0.2 - - - -
697B SER* 1.3 74.2 + - - +
699B CYS* 1.3 64.9 + - - +
701B CYS* 3.1 13.4 + - - +
702B LEU* 3.0 21.1 + - - +
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Residues in contact with CYS 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B GLU* 4.2 10.8 - - - -
695B ARG 2.9 24.8 + - - -
696B MET* 3.1 12.1 + - - +
698B ALA* 1.3 77.4 - - - +
700B PHE* 1.3 58.1 + - + +
702B LEU* 3.2 6.1 + - - +
703B ALA 2.9 21.7 + - - -
719B MET* 4.1 10.3 - - + -
749B LEU* 4.6 4.5 - - - -
752B THR* 4.4 8.1 - - + -
753B MET* 3.5 37.2 - - - -
756B ALA* 3.3 26.1 - - + +
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Residues in contact with PHE 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B GLU* 3.1 16.6 - - - +
696B MET* 3.2 19.5 + - + -
697B SER* 3.7 11.0 - - - +
698B ALA 3.2 0.6 - - - -
699B CYS* 1.3 74.6 - - - +
701B CYS* 1.3 65.0 + - - +
703B ALA* 3.3 5.9 + - + +
704B LYS* 3.1 23.4 + - - +
752B THR* 4.4 17.0 - - + -
755B VAL* 4.1 17.0 - - + -
756B ALA* 3.6 31.2 - - + -
759B LEU* 4.3 12.1 - - + -
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Residues in contact with CYS 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ILE* 3.5 48.9 - - - -
670B GLU* 3.1 15.4 + - + -
678B ARG* 4.4 12.3 - - - +
682B THR* 4.5 8.5 - - + -
697B SER 2.9 24.3 + - - -
698B ALA* 3.1 11.2 + - - +
700B PHE* 1.3 76.6 - - - +
702B LEU* 1.3 58.3 + - - +
704B LYS* 3.3 2.3 + - - +
705B ILE* 3.0 41.9 + - + +
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Residues in contact with LEU 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 3.8 29.4 - - + -
682B THR* 3.7 22.7 - - + +
683B ASP* 3.3 23.6 - - - +
686B GLU* 3.5 19.7 - - - +
698B ALA 3.0 13.3 + - - +
699B CYS 3.2 7.4 + - - +
701B CYS* 1.3 77.8 - - - +
703B ALA* 1.3 57.0 + - - +
705B ILE* 4.8 2.0 - - + -
706B ALA* 2.9 37.0 + - + +
718B ALA* 5.7 6.1 - - + -
719B MET* 3.8 36.1 - - + -
722B LEU* 4.2 0.9 - - + -
760B LEU* 4.1 2.5 - - + -
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Residues in contact with ALA 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B CYS 2.9 12.1 + - - +
700B PHE* 3.3 13.7 - - + +
701B CYS 3.2 0.2 - - - -
702B LEU* 1.3 77.2 - - - +
704B LYS* 1.3 61.8 + - + +
706B ALA 3.9 0.3 - - - -
707B ASN* 2.6 36.9 + - - +
756B ALA* 4.0 5.1 - - + +
759B LEU* 3.7 37.2 - - + -
760B LEU* 3.7 13.3 - - - +
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Residues in contact with LYS 704 (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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667B LEU 5.6 0.2 + - - -
670B GLU* 3.3 61.2 + - + +
671B LYS* 5.5 2.2 - - - +
700B PHE 3.1 11.4 + - - +
701B CYS 3.9 5.4 - - - +
703B ALA* 1.3 79.9 - - + +
705B ILE* 1.3 60.1 + - + +
707B ASN* 3.1 10.9 + - - +
708B SER* 3.0 24.9 + - - -
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Residues in contact with ILE 705 (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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669B LEU 3.4 26.5 - - - +
670B GLU* 5.1 2.5 - - - +
673B PRO* 3.6 13.7 - - + +
674B THR* 3.5 29.4 - - + +
675B PRO 5.0 0.2 - - - +
678B ARG* 3.8 28.3 - - + +
679B LEU* 3.8 22.7 - - + -
682B THR* 5.4 1.8 - - - +
701B CYS* 3.0 26.4 + - + +
702B LEU* 4.4 1.3 - - + +
704B LYS* 1.3 81.4 - - + +
706B ALA* 1.3 57.5 + - - +
708B SER* 2.3 29.9 + - - -
709B MET* 3.2 9.5 + - - +
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Residues in contact with ALA 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 5.0 3.9 - - + +
702B LEU* 2.9 20.3 + - + +
705B ILE* 1.3 73.4 - - - +
707B ASN* 1.3 61.4 + - - +
709B MET* 3.1 30.7 + - - +
718B ALA* 4.9 12.6 - - + -
760B LEU* 3.7 20.6 - - + -
761B ARG 4.0 2.3 + - - +
762B ASP* 3.0 21.5 - - - +
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Residues in contact with ASN 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B ALA* 2.6 35.1 + - - +
704B LYS* 3.1 9.5 + - - +
706B ALA* 1.3 76.3 - - - +
708B SER* 1.3 56.4 + - - +
709B MET 3.2 0.4 - - - -
710B VAL* 3.4 22.0 - - - +
759B LEU* 3.0 21.3 + - - +
760B LEU* 4.6 0.2 - - - -
761B ARG* 2.7 47.2 + - - +
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Residues in contact with SER 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B PHE 5.8 1.8 - - - -
673B PRO 4.2 1.0 + - - -
674B THR* 2.3 35.4 + - - +
704B LYS 3.0 10.2 + - - -
705B ILE* 2.3 26.3 + - - -
707B ASN* 1.3 73.7 - - - +
709B MET* 1.3 54.7 + - - +
710B VAL* 3.3 8.5 + - - -
711B SER 5.2 0.2 + - - -
712B THR* 4.5 8.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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