Contacts of the helix formed by residues 729 - 743 (chain B) 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 PRO 729 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B GLU* 4.2 4.5 - - - +
727B ILE* 4.6 5.2 - - + +
728B VAL* 1.3 88.7 - - + +
730B SER* 1.3 69.1 + - - +
731B ASP* 3.0 3.6 - - + +
732B HIS* 2.7 47.0 + - + +
733B ARG 3.1 9.4 + - - -
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Residues in contact with SER 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLU* 2.9 39.2 + - - -
475B LEU* 3.0 37.9 + - - +
476B LEU* 4.1 4.2 - - - +
506B TYR* 3.8 18.7 + - - -
510B ALA* 4.5 3.2 - - - +
728B VAL 3.3 4.8 + - - -
729B PRO* 1.3 68.4 - - - +
731B ASP* 1.3 57.7 + - - +
733B ARG* 3.6 5.7 + - - +
734B ALA* 3.0 29.6 + - - +
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Residues in contact with ASP 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP 4.3 0.9 - - - +
506B TYR* 3.3 20.0 - - - -
507B MET 3.1 19.8 + - - -
508B ASP* 3.0 10.5 + - - -
509B VAL* 2.6 44.4 + - + +
510B ALA 4.3 0.2 + - - -
525B PHE* 3.5 28.1 - - + -
729B PRO* 2.7 6.3 + - + +
730B SER* 1.3 74.1 - - - +
732B HIS* 1.3 56.8 + - + +
734B ALA* 3.2 1.6 + - - +
735B SER* 2.7 37.1 + - - -
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Residues in contact with HIS 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B PHE* 4.4 6.9 - + - -
527B PRO* 3.4 40.2 - - + +
721B MET* 4.1 21.0 - - - +
728B VAL* 4.0 14.1 - - + -
729B PRO* 2.7 43.7 + - + +
731B ASP* 1.3 75.8 - - + +
733B ARG* 1.3 57.2 + - - +
735B SER* 3.5 5.8 + - - -
736B ALA* 2.9 29.5 + - - +
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Residues in contact with ARG 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLU* 2.7 40.4 + - - -
476B LEU* 4.1 17.5 - - + -
668B LEU* 3.1 24.8 - - - +
672B ARG* 4.7 0.2 - - - +
721B MET 3.2 15.3 + - - +
722B ALA 3.9 8.9 + - - +
724B ARG* 2.9 39.9 + - - +
726B GLY 4.4 7.3 + - - +
728B VAL* 2.9 46.7 - - + +
729B PRO 3.1 8.3 + - - +
730B SER* 3.9 8.7 - - - +
732B HIS* 1.3 74.5 - - - +
734B ALA* 1.3 65.8 + - - +
736B ALA* 3.2 6.6 + - - +
737B LEU* 3.0 38.2 + - + +
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Residues in contact with ALA 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 3.9 10.3 - - + +
509B VAL* 4.0 5.1 - - + +
510B ALA* 3.4 41.7 - - + +
513B SER* 4.9 1.9 + - - +
517B ARG* 5.2 1.7 + - - -
664B LEU* 5.5 4.4 - - + +
730B SER 3.0 19.3 + - - +
731B ASP 3.2 3.6 + - - +
733B ARG* 1.3 77.2 - - - +
735B SER* 1.3 63.3 + - - +
737B LEU* 3.5 6.1 + - - +
738B ASN* 3.0 23.7 + - - +
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Residues in contact with SER 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B VAL* 4.0 10.7 - - - +
523B THR 5.3 3.7 + - - -
525B PHE* 3.5 38.2 + - - +
731B ASP 2.7 20.0 + - - -
732B HIS* 3.8 4.5 - - - -
734B ALA* 1.3 70.4 - - - +
736B ALA* 1.3 65.6 + - - +
738B ASN* 3.4 7.3 + - - +
739B ASN* 3.0 33.1 + - - +
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Residues in contact with ALA 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720B HIS* 3.9 12.6 - - + -
721B MET* 4.1 10.5 - - + -
722B ALA* 3.6 28.7 - - + +
732B HIS 2.9 18.8 + - - +
733B ARG 3.4 4.9 - - - +
734B ALA 3.2 0.2 - - - -
735B SER* 1.3 76.5 - - - +
737B LEU* 1.3 65.3 + - - +
739B ASN* 2.9 19.4 + - - +
740B LEU* 2.9 17.1 + - - +
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Residues in contact with LEU 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 3.7 31.6 - - + -
517B ARG* 5.3 0.4 - - - -
660B VAL* 3.2 27.2 - - + +
663B ALA* 3.5 28.9 - - + -
664B LEU* 4.0 19.5 - - + -
722B ALA* 3.4 27.6 - - + +
723B PHE* 3.7 13.7 - - + -
733B ARG* 3.0 27.1 + - + +
734B ALA* 3.8 4.5 - - - +
736B ALA* 1.3 76.2 - - - +
738B ASN* 1.3 61.3 + - - +
740B LEU* 3.7 2.9 + - - -
741B GLU* 3.1 18.2 + - - +
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Residues in contact with ASN 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B VAL* 5.7 0.4 - - + -
513B SER* 4.4 8.3 - - - +
516B SER* 5.0 0.5 + - - -
517B ARG* 3.4 16.9 + - - +
522B GLN* 2.8 25.2 + - - -
523B THR* 3.3 31.0 + - - -
574B HIS* 3.0 25.1 + - - -
734B ALA 3.0 18.1 + - - +
735B SER* 3.6 8.5 + - - +
737B LEU* 1.3 73.8 - - - +
739B ASN* 1.3 66.6 + - - +
741B GLU* 3.1 21.4 - - - +
742B SER* 2.9 20.6 + - - -
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Residues in contact with ASN 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B GLN* 5.7 3.3 + - - +
720B HIS* 6.1 0.4 - - + -
735B SER* 3.0 25.9 + - - +
736B ALA* 2.9 13.8 + - - +
738B ASN* 1.3 76.7 - - - +
740B LEU* 1.3 70.1 + - + +
742B SER* 3.0 6.2 + - - -
743B LEU* 2.9 55.8 + - + +
751B ASN* 5.5 1.3 - - - +
806B ASN* 4.2 18.1 + - - +
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Residues in contact with LEU 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B ASN* 3.1 39.6 + - - +
657B SER* 5.5 0.2 + - - -
660B VAL* 4.1 8.3 - - + -
717B LEU* 4.0 6.5 - - + -
720B HIS* 3.5 46.0 - - + +
722B ALA* 4.0 3.4 - - + -
723B PHE* 3.8 20.9 - - + -
736B ALA 2.9 13.7 + - - +
737B LEU 4.6 0.2 - - - -
739B ASN* 1.3 81.7 - - + +
741B GLU* 1.3 60.9 + - - +
742B SER 3.2 1.2 + - - -
743B LEU* 3.7 8.0 + - + +
748B LEU* 3.5 23.8 - - + +
751B ASN* 3.9 19.5 - - + +
752B ILE* 5.1 2.2 - - + -
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Residues in contact with GLU 741 (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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517B ARG* 2.6 44.9 + - - -
572B TYR* 5.9 0.9 - - - +
573B GLY* 4.4 22.3 + - - +
574B HIS* 2.7 28.7 + - - +
593B SER 4.5 3.1 - - - +
656B ASN* 4.7 2.2 - - - +
657B SER* 5.1 10.6 + - - +
660B VAL* 3.4 24.5 - - + +
664B LEU* 5.1 1.8 - - - +
737B LEU 3.1 15.5 + - - +
738B ASN* 3.1 16.8 - - - +
739B ASN 3.1 0.4 + - - -
740B LEU* 1.3 76.5 - - - +
742B SER* 1.3 56.1 + - - +
743B LEU 5.5 0.2 - - - -
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Residues in contact with SER 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B GLN* 3.1 21.7 + - - -
573B GLY* 5.8 0.2 - - - -
574B HIS* 3.6 17.1 - - - -
591B ASP 4.2 0.5 - - - +
592B GLN* 3.3 33.6 - - - +
593B SER 3.3 24.8 + - - -
738B ASN 2.9 15.4 + - - -
739B ASN 3.0 3.7 + - - -
741B GLU* 1.3 77.4 - - - +
743B LEU* 1.3 67.9 - - - +
744B PRO* 4.1 0.3 - - - +
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Residues in contact with LEU 743 (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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522B GLN* 6.1 2.5 - - - +
591B ASP 5.9 0.2 - - - +
593B SER* 3.5 8.7 - - - -
739B ASN* 2.9 40.7 + - + +
740B LEU* 3.7 12.2 + - + +
742B SER* 1.3 81.0 - - - +
744B PRO* 1.4 75.9 - - + +
745B LEU* 3.6 0.5 + - - -
747B TYR* 4.0 18.6 - - + +
748B LEU* 4.1 18.6 - - + +
751B ASN* 3.2 40.4 - - + +
865B VAL* 6.0 2.5 - - + -
867B THR* 5.7 4.5 - - - +
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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
------------------------------------------------------------
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