Contacts of the helix formed by residues 675 - 687 (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 PRO 675 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B GLN* 3.8 9.6 - - - +
673B PRO* 3.7 13.0 - - + -
674B THR* 1.3 96.3 - - - +
676B ALA* 1.3 63.4 + - - +
677B SER* 3.4 23.8 - - - +
678B ARG* 3.3 32.1 - - + +
679B LEU* 3.6 8.0 + - - +
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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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675B PRO* 1.3 71.5 - - - +
677B SER* 1.3 61.3 + - - +
678B ARG 3.2 0.2 - - - -
679B LEU* 3.1 23.6 + - + +
680B ALA* 2.9 26.9 + - - +
714B THR* 4.6 23.1 - - + -
715B GLY* 5.2 3.6 - - - +
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Residues in contact with SER 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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650B GLN* 3.9 10.4 + - - -
675B PRO* 3.4 19.3 - - - +
676B ALA* 1.3 75.5 - - - +
678B ARG* 1.3 61.9 + - - +
680B ALA* 3.4 8.5 - - - +
681B LEU* 2.9 40.6 + - - +
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Residues in contact with ARG 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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650B GLN* 3.4 27.0 - - - +
653B LEU* 3.4 27.7 - - - +
666B ILE* 5.1 1.2 - - - +
669B LEU* 3.4 32.6 - - - +
673B PRO* 4.6 6.1 - - + -
675B PRO* 3.3 29.7 + - + +
676B ALA 3.2 0.2 - - - -
677B SER* 1.3 83.0 + - - +
679B LEU* 1.3 52.7 + - + +
681B LEU* 4.0 8.1 - - - +
682B THR* 2.3 79.8 + - - +
685B LEU* 5.9 1.6 - - - +
701B CYS* 4.4 16.4 - - - +
705B ILE* 3.8 28.7 - - + +
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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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674B THR* 5.5 1.3 - - + -
675B PRO 3.8 9.0 - - - +
676B ALA* 3.3 24.5 - - + +
678B ARG* 1.3 75.0 - - - +
680B ALA* 1.3 57.5 + - - +
682B THR* 3.2 6.5 + - - -
683B ASP* 3.0 41.2 + - - +
702B LEU* 3.8 22.2 - - + +
705B ILE* 3.8 29.6 - - + -
706B ALA* 5.0 3.6 - - + +
709B MET* 3.7 34.1 - - + -
715B GLY* 4.8 8.1 - - - +
716B PRO* 5.9 1.3 - - + -
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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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676B ALA 2.9 13.0 + - - +
677B SER* 3.4 13.0 - - - +
679B LEU* 1.3 75.6 - - - +
681B LEU* 1.3 59.2 + - + +
683B ASP* 3.2 8.6 + - - +
684B ILE* 2.9 42.1 + - + +
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Residues in contact with LEU 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 ASP* 5.9 1.3 - - - +
650B GLN* 3.7 48.0 - - + +
651B TYR* 5.6 2.7 - - + -
653B LEU* 4.8 6.3 - - + +
654B ARG* 4.9 24.4 - - + +
677B SER* 2.9 21.5 + - - +
678B ARG* 4.0 10.5 - - - +
680B ALA* 1.3 73.7 - - + +
682B THR* 1.3 60.4 + - - +
684B ILE* 3.7 23.9 - - + +
685B LEU* 2.9 29.3 + - - +
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Residues in contact with THR 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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678B ARG* 2.3 57.9 + - - +
679B LEU* 3.3 8.7 - - - -
681B LEU* 1.3 76.7 - - - +
683B ASP* 1.3 63.5 + - - +
685B LEU* 3.1 10.4 + - + +
686B GLU* 3.0 41.8 + - - +
698B ALA* 3.8 16.8 - - + +
701B CYS* 4.5 4.4 - - + +
702B LEU* 3.7 24.7 - - + +
705B ILE* 5.4 0.9 - - - +
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Residues in contact with ASP 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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679B LEU* 3.0 24.0 + - - +
680B ALA* 3.7 6.1 - - - +
682B THR* 1.3 72.1 - - - +
684B ILE* 1.3 61.8 + - + +
686B GLU* 3.0 26.7 + - - +
687B GLN* 3.2 21.4 + - - +
702B LEU* 3.3 28.2 - - - +
721B SER* 5.7 0.2 + - - -
722B LEU* 3.8 23.9 - - + +
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Residues in contact with ILE 684 (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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654B ARG* 5.3 15.5 - - + +
680B ALA* 2.9 28.1 + - + +
681B LEU* 3.7 28.5 - - + +
683B ASP* 1.3 76.3 - - + +
685B LEU* 1.3 62.2 + - - +
687B GLN* 3.2 22.0 + - - +
688B GLU* 4.5 12.7 - - - +
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Residues in contact with LEU 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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653B LEU* 3.3 52.5 - - + +
654B ARG 4.8 5.4 - - - +
655B TYR* 6.0 0.9 - - + -
662B GLN* 5.0 10.8 - - - +
666B ILE* 5.0 7.4 - - + -
678B ARG* 5.9 1.3 - - - +
681B LEU 2.9 14.7 + - - +
682B THR* 3.1 13.9 + - + +
684B ILE* 1.3 77.3 - - - +
686B GLU* 1.3 60.1 + - + +
688B GLU* 6.1 0.4 - - - -
690B CYS* 4.2 23.3 - - + -
694B VAL* 4.4 23.6 - - + -
695B ARG* 3.1 26.4 + - + -
698B ALA* 5.1 7.6 - - + -
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Residues in contact with GLU 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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682B THR* 3.2 15.5 - - - +
683B ASP* 3.0 27.1 + - - +
685B LEU* 1.3 79.1 - - - +
687B GLN* 1.3 57.7 + - + +
695B ARG* 2.6 43.6 + - + +
698B ALA* 3.4 35.5 - - + +
699B CYS* 3.8 8.6 + - - -
702B LEU* 3.5 18.8 - - - +
722B LEU* 3.3 19.5 - - + +
726B MET* 3.6 16.8 - - + +
749B LEU* 4.6 3.9 - - + +
753B MET* 6.1 1.6 - - - -
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Residues in contact with GLN 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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683B ASP* 3.4 16.3 - - - +
684B ILE* 3.2 11.1 + - - +
685B LEU 3.2 0.2 - - - -
686B GLU* 1.3 83.6 - - + +
688B GLU* 1.3 66.9 + - - +
695B ARG* 3.8 0.2 - - - +
722B LEU* 3.3 31.5 - - - +
725B ARG* 4.5 17.5 - - - +
726B MET* 3.4 38.8 - - + +
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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