Contacts of the helix formed by residues 645 - 653 (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 ALA 645 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535B PHE* 5.4 3.2 - - - -
619B MET* 4.7 21.5 - - + -
644B GLN* 1.3 74.5 - - - +
646B ASP* 1.3 62.3 + - - +
647B PHE* 4.3 11.2 - - + +
648B MET* 2.9 46.4 + - + +
649B TRP* 3.0 11.5 - - - -
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Residues in contact with ASP 646 (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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644B GLN 3.6 9.0 - - - +
645B ALA* 1.3 72.4 - - - +
647B PHE* 1.3 65.7 + - + +
649B TRP* 3.3 13.4 + - - +
650B GLN* 2.9 43.3 + - - +
669B LEU* 4.8 1.3 - - + -
672B PHE* 3.2 40.1 - - + -
673B PRO* 5.4 1.9 - - + +
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Residues in contact with PHE 647 (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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617B SER* 4.3 11.0 - - - +
618B ALA* 3.6 25.8 - - + -
619B MET* 3.5 50.0 - - + -
645B ALA* 4.6 8.7 - - + -
646B ASP* 1.3 81.6 - - + +
648B MET* 1.3 56.2 + - + +
650B GLN* 3.8 14.4 - - - +
651B TYR* 2.8 33.6 + - - +
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Residues in contact with MET 648 (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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535B PHE* 5.4 11.0 - - + -
618B ALA* 5.7 4.0 - - + -
623B SER* 5.4 7.6 - - - -
625B LEU* 3.4 39.0 - - + +
626B LEU* 3.2 36.8 - - + +
627B TRP* 2.5 27.8 + - - +
628B ILE* 6.4 1.1 - - + -
644B GLN* 3.3 21.3 - - + +
645B ALA* 2.9 39.7 + - + +
647B PHE* 1.3 75.0 - - + +
649B TRP* 1.3 59.7 + - - +
651B TYR* 4.5 3.1 - - - -
652B GLN 2.9 12.5 + - - -
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Residues in contact with TRP 649 (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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642B PHE* 3.4 52.9 - + - -
643B GLU* 4.4 0.7 - - - -
644B GLN* 3.3 36.8 + - + +
645B ALA 3.0 22.7 - - - -
646B ASP* 3.4 19.5 + - + +
648B MET* 1.3 77.5 - - - +
650B GLN* 1.3 57.0 - - - +
652B GLN* 3.2 11.8 + - - +
653B LEU* 3.0 30.3 + - - +
664B GLU* 4.5 4.7 - - + -
665B SER* 3.2 31.8 - - - +
668B ALA* 3.6 32.1 - - + -
669B LEU* 3.6 23.6 - - + -
672B PHE* 5.0 4.6 - + - -
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Residues in contact with GLN 650 (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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646B ASP* 2.9 31.3 + - - +
647B PHE* 3.9 14.0 - - - +
649B TRP* 1.3 74.6 - - - +
651B TYR* 1.3 58.4 + - - +
653B LEU* 3.0 10.1 + - - +
654B ARG* 2.9 22.2 + - - +
669B LEU* 3.7 21.2 - - + +
673B PRO* 5.1 2.8 - - - +
675B PRO* 3.8 15.2 - - - +
677B SER* 3.9 9.7 + - - -
678B ARG* 3.4 38.4 - - - +
681B LEU* 3.7 33.6 - - + +
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Residues in contact with TYR 651 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B MET* 5.5 0.8 - - + +
613B ASP* 3.2 20.0 - - + +
614B MET* 3.7 0.7 + - - -
615B ASP* 3.2 46.4 + - + -
617B SER* 4.8 4.7 - - - -
626B LEU* 4.7 16.2 - - + -
627B TRP* 3.6 22.9 - + + -
647B PHE 2.8 19.3 + - - +
648B MET* 3.9 4.7 - - - +
650B GLN* 1.3 74.3 - - - +
652B GLN* 1.3 63.2 + - - +
653B LEU 3.1 0.4 - - - -
654B ARG* 2.3 59.5 + - + +
655B TYR 3.2 12.2 + - - +
681B LEU* 5.6 2.5 - - + -
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Residues in contact with GLN 652 (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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627B TRP* 3.2 49.2 - - - +
628B ILE 4.8 1.0 + - - -
629B ARG* 3.7 13.4 + - - +
644B GLN* 4.7 3.1 + - - +
648B MET 2.9 7.4 + - - +
649B TRP* 3.3 15.2 - - - +
651B TYR* 1.3 76.2 - - - +
653B LEU* 1.3 62.5 + - - +
655B TYR 3.0 24.6 - - - -
656B GLU* 3.3 28.8 + - + +
661B ALA* 3.4 28.0 - - + +
662B GLN* 4.5 3.1 - - - +
665B SER* 3.0 21.9 + - - +
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Residues in contact with LEU 653 (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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649B TRP 3.0 8.3 + - - +
650B GLN* 3.0 11.2 + - - +
652B GLN* 1.3 77.6 - - - +
654B ARG* 1.3 62.0 + - - +
655B TYR* 4.3 0.8 - - - -
662B GLN* 3.3 41.5 - - + +
665B SER* 3.7 19.1 - - - -
666B ILE* 4.1 4.9 - - + +
669B LEU* 3.7 20.4 - - + -
678B ARG* 3.4 33.2 - - - +
681B LEU* 4.8 6.1 - - + +
685B LEU* 3.3 47.5 - - + +
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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