Contacts of the helix formed by residues 611 - 621 (chain M) in PDB entry 5MQF
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 HIS 611 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603M GLU* 4.8 8.6 - - + +
608M LEU* 4.2 14.6 + - + +
610M ARG* 1.3 78.7 - - - +
612M ALA* 1.3 56.1 + - - +
614M ALA* 3.8 10.4 - - + +
615M VAL* 2.9 30.7 + - - +
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Residues in contact with ALA 612 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600M ALA* 5.6 1.7 - - - +
603M GLU* 4.8 6.8 + - - -
604M GLU* 3.9 28.9 - - + +
608M LEU 3.4 19.9 + - - +
609M ALA* 4.2 9.2 - - - +
610M ARG 3.0 1.2 - - - -
611M HIS* 1.3 78.1 - - - +
613M MET* 1.3 57.6 + - - +
615M VAL* 3.5 6.6 + - - +
616M TYR* 2.9 26.3 + - - +
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Residues in contact with MET 613 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609M ALA 4.1 7.5 + - - +
610M ARG* 3.0 10.2 + - - +
612M ALA* 1.3 76.0 - - - +
614M ALA* 1.3 61.3 + - - +
616M TYR* 3.0 9.1 + - - +
617M GLU* 2.9 28.6 + - - +
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Residues in contact with ALA 614 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610M ARG 3.4 5.0 + - - +
611M HIS* 3.8 15.3 - - + +
612M ALA 3.4 0.4 - - - -
613M MET* 1.3 79.2 - - - +
615M VAL* 1.3 56.9 + - - +
617M GLU* 3.3 5.0 + - - +
618M ARG* 2.9 32.0 + - - +
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Residues in contact with VAL 615 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599M TYR 5.1 1.3 - - - +
600M ALA* 4.6 15.2 - - - +
603M GLU* 4.5 17.0 - - + -
611M HIS 2.9 19.4 + - - +
612M ALA* 3.7 4.7 - - - +
614M ALA* 1.3 76.7 - - - +
616M TYR* 1.3 49.3 + - - +
618M ARG* 4.6 4.0 - - - -
619M ALA* 2.6 41.0 + - - +
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Residues in contact with TYR 616 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600M ALA* 5.7 2.7 - - - -
612M ALA 2.9 15.5 + - - +
613M MET* 3.0 15.2 + - - +
615M VAL* 1.3 77.1 - - - +
617M GLU* 1.3 59.6 + - - +
619M ALA* 3.8 3.7 - - - +
620M THR* 2.9 27.2 + - - -
635M TYR* 5.4 2.8 - - - +
638M ARG* 4.9 17.7 - - + -
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Residues in contact with GLU 617 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613M MET 2.9 13.6 + - - +
614M ALA* 3.9 4.9 - - - +
616M TYR* 1.3 75.1 - - - +
618M ARG* 1.3 60.6 + - - +
620M THR* 2.9 22.7 + - - -
621M ARG* 2.9 14.6 + - - +
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Residues in contact with ARG 618 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614M ALA 2.9 17.9 + - - +
615M VAL* 4.6 3.8 - - - -
617M GLU* 1.3 76.2 - - - +
619M ALA* 1.3 61.1 + - - +
620M THR 3.5 0.3 + - - -
621M ARG* 3.6 13.3 + - - +
622M ALA* 3.7 11.6 + - - +
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Residues in contact with ALA 619 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595M LEU* 4.9 6.4 - - - +
596M TYR* 3.6 32.5 - - + +
600M ALA* 4.6 5.2 - - + -
615M VAL 2.6 25.9 + - - +
616M TYR* 4.0 4.9 - - - +
618M ARG* 1.3 75.7 - - - +
620M THR* 1.3 58.3 + - - +
621M ARG 3.4 0.2 - - - -
622M ALA* 3.7 4.5 - - - +
623M VAL* 2.9 27.9 + - - +
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Residues in contact with THR 620 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616M TYR 2.9 20.6 + - - -
617M GLU* 2.9 12.6 + - - -
619M ALA* 1.3 77.0 - - - +
621M ARG* 1.3 64.0 + - - +
623M VAL* 3.3 19.5 + - - +
624M GLU 5.0 0.2 + - - -
635M TYR* 4.6 17.9 - - - -
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Residues in contact with ARG 621 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617M GLU 2.9 10.5 + - - +
618M ARG* 3.8 11.9 - - - +
619M ALA 3.4 0.4 - - - -
620M THR* 1.3 80.4 - - - +
622M ALA* 1.3 58.4 + - + +
623M VAL 3.3 0.4 + - - -
624M GLU 5.2 1.2 + - - -
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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