Contacts of the helix formed by residues 751 - 764 (chain A) in PDB entry 1M2V
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 751 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A TYR* 3.8 6.5 - - - -
750A VAL* 1.3 93.1 - - - +
752A LEU* 1.3 64.9 + - - +
753A GLN* 3.0 30.1 + - - +
754A ASN* 3.0 23.9 + - - -
755A PHE* 2.9 17.7 + - - +
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Residues in contact with LEU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A GLN* 3.9 40.4 - - + +
588A TYR* 3.5 52.4 + - + -
589A TYR* 4.7 11.4 - - + +
751A SER* 1.3 73.4 - - - +
753A GLN* 1.3 57.5 + - + +
755A PHE* 4.0 1.8 - - + -
756A MET* 2.9 54.3 + - + +
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Residues in contact with GLN 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A SER* 3.1 23.0 + - - +
752A LEU* 1.3 76.5 - - + +
754A ASN* 1.3 70.0 + - - +
756A MET* 3.2 6.6 + - - +
757A THR* 2.9 26.5 + - - -
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Residues in contact with ASN 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A VAL* 3.3 40.5 - - + +
751A SER* 3.0 16.1 + - - +
753A GLN* 1.3 84.4 - - - +
755A PHE* 1.3 65.2 + - - +
757A THR* 3.0 7.5 + - - -
758A HIS* 2.8 27.1 + - - +
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Residues in contact with PHE 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A ASP* 4.2 7.0 - - - -
556A LEU* 3.7 27.4 - - + -
584A PRO 3.6 20.4 - - - -
587A THR* 4.3 0.2 - - + -
588A TYR* 3.7 29.2 - + + -
591A ARG* 3.5 52.3 - - - -
750A VAL 4.6 4.2 + - - +
751A SER 2.9 12.6 + - - +
752A LEU* 3.5 8.3 - - + +
754A ASN* 1.3 77.5 - - - +
756A MET* 1.3 63.0 + - - +
758A HIS* 3.3 5.4 + - + +
759A LEU* 2.8 44.3 + - + +
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Residues in contact with MET 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A PHE* 5.7 7.6 - - + -
576A LEU* 6.0 1.6 - - + -
581A SER 5.2 7.0 - - - +
584A PRO* 3.9 31.2 - - + -
585A GLN* 5.1 2.2 - - + +
752A LEU* 2.9 46.2 + - + +
753A GLN* 3.6 6.1 - - - +
755A PHE* 1.3 79.7 - - + +
757A THR* 1.3 59.1 + - - +
759A LEU* 3.6 12.8 - - + +
760A GLN* 3.0 44.8 + - - +
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Residues in contact with THR 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A GLN* 5.3 11.1 + - - +
753A GLN 2.9 17.4 + - - -
754A ASN* 3.0 7.6 + - - +
756A MET* 1.3 74.7 - - - +
758A HIS* 1.3 67.6 + - - +
759A LEU 3.0 1.3 - - - -
760A GLN* 3.1 19.3 + - - +
761A GLN* 3.0 38.3 + - + +
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Residues in contact with HIS 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ASN 2.8 19.1 + - - +
755A PHE* 3.8 4.7 - - + +
757A THR* 1.3 75.1 - - - +
759A LEU* 1.3 62.9 + - - +
761A GLN* 3.3 27.0 + - + +
762A VAL* 3.2 30.1 + - + +
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Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A LEU* 3.9 24.7 - - + -
557A ILE* 4.1 29.6 - - + -
560A CYS* 4.5 12.8 - - - -
574A PHE* 4.9 8.3 - - + -
584A PRO* 3.8 31.6 - - + -
755A PHE* 2.8 26.2 + - + +
756A MET* 3.6 16.6 - - - +
757A THR 3.0 0.2 - - - -
758A HIS* 1.3 77.6 - - - +
760A GLN* 1.3 63.2 + - + +
762A VAL* 3.4 5.0 + - - +
763A ALA* 3.1 22.0 + - + +
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Residues in contact with GLN 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A PRO* 3.6 21.1 + - + +
572A GLN* 4.1 24.2 + - - +
574A PHE* 3.5 49.1 + - + +
756A MET* 3.0 33.6 + - + +
757A THR* 3.1 12.4 + - - +
759A LEU* 1.3 77.6 - - + +
761A GLN* 1.3 61.8 + - - +
763A ALA* 3.5 0.9 + - - +
764A VAL* 3.3 30.4 + - - +
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Residues in contact with GLN 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A PRO* 3.9 26.4 - - + +
572A GLN* 6.2 0.6 - - - +
757A THR* 3.0 32.9 + - + +
758A HIS* 3.3 25.1 + - + +
760A GLN* 1.3 78.5 - - - +
762A VAL* 1.3 62.1 + - + +
764A VAL* 3.3 13.9 - - - +
765A SER* 3.4 11.6 + - - -
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Residues in contact with VAL 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ILE* 3.6 29.6 - - + -
561A GLN* 3.7 3.6 + - - -
758A HIS* 3.2 35.8 + - + +
759A LEU* 4.0 4.7 - - - +
761A GLN* 1.3 75.6 - - + +
763A ALA* 1.3 60.6 + - - +
764A VAL 3.1 2.0 - - - -
765A SER* 2.7 35.2 + - - +
767A GLN* 3.6 26.0 - - - +
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Residues in contact with ALA 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ILE* 4.5 2.9 - - - +
560A CYS* 4.3 14.8 - - + -
561A GLN* 3.7 21.8 + - + +
566A TYR* 3.3 23.5 + - + -
574A PHE* 3.5 33.2 - - + -
759A LEU* 3.1 20.1 + - + +
760A GLN 3.9 1.1 - - - +
761A GLN 3.4 0.2 - - - -
762A VAL* 1.3 77.4 - - - +
764A VAL* 1.3 59.4 + - - +
765A SER 3.7 0.9 + - - +
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Residues in contact with VAL 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A TYR* 3.4 42.9 - - + -
567A ASN 3.9 1.1 - - - +
568A LYS* 3.5 9.9 - - - +
569A ASP* 2.9 33.0 + - - +
570A ASP 3.8 19.7 - - - +
571A PRO* 3.8 27.1 - - + +
574A PHE* 4.7 4.7 - - + -
760A GLN 3.3 19.1 - - - +
761A GLN 3.3 11.9 - - - +
763A ALA* 1.3 77.0 - - - +
765A SER* 1.3 58.8 + - - +
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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