Contacts of the helix formed by residues 668 - 690 (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 LEU 668 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B THR 5.8 1.8 - - - +
471B GLU* 3.1 29.2 - - + +
472B THR* 3.4 9.9 + - - +
476B LEU* 4.4 11.4 - - + -
663B ALA* 3.6 27.1 - - + -
667B SER* 1.3 75.6 + - - +
669B ASP* 1.3 60.1 + - - +
670B ASP 3.3 0.2 - - - -
671B ALA* 3.1 20.4 - - - +
672B ARG* 3.1 33.8 + - - +
722B ALA 3.8 16.6 - - - +
723B PHE* 4.7 6.4 - - + +
733B ARG* 3.1 35.2 - - - +
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Residues in contact with ASP 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B THR* 4.9 5.0 - - - +
469B SER 4.6 9.7 - - - +
667B SER* 3.3 9.2 + - - +
668B LEU* 1.3 76.6 - - - +
670B ASP* 1.3 58.2 + - - +
671B ALA 2.9 1.8 - - - -
672B ARG* 2.8 47.5 + - + +
673B VAL* 2.6 43.0 + - + +
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Residues in contact with ASP 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LYS* 3.8 28.4 + - + +
666B SER* 3.3 12.5 + - - +
667B SER* 3.1 32.3 + - - +
668B LEU 3.3 0.2 - - - -
669B ASP* 1.3 78.9 - - - +
671B ALA* 1.3 56.6 + - - +
673B VAL* 3.8 8.3 - - - +
674B LEU* 3.1 26.3 + - - +
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Residues in contact with ALA 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B ALA* 3.7 23.8 - - + +
662B LYS* 3.8 13.4 - - + +
663B ALA* 4.0 6.3 - - - +
667B SER 3.7 1.2 + - - +
668B LEU 3.1 15.0 + - - +
669B ASP 2.9 0.4 - - - -
670B ASP* 1.3 75.9 - - - +
672B ARG* 1.3 57.8 + - - +
673B VAL 3.1 1.3 - - - -
674B LEU* 2.7 25.1 + - - +
675B ILE* 3.0 18.8 + - - +
723B PHE* 3.8 18.2 - - + -
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Residues in contact with ARG 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B THR* 5.6 3.2 + - - +
471B GLU* 5.0 2.6 + - - -
668B LEU* 3.1 47.2 + - - +
669B ASP* 2.8 36.7 + - - +
671B ALA* 1.3 78.2 - - - +
673B VAL* 1.3 57.4 + - + +
675B ILE* 3.5 10.4 + - - +
676B ASN* 2.7 38.0 + - - +
718B THR* 4.3 17.7 - - + +
723B PHE* 2.9 30.9 + - + +
724B ARG 3.6 6.3 + - - -
725B SER* 2.9 36.3 - - - +
726B GLY 4.7 0.6 - - - +
733B ARG* 4.7 0.4 - - - +
910B ASN* 5.9 2.2 - - - +
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B ASP* 2.6 28.9 + - + +
670B ASP* 3.8 8.1 - - - +
672B ARG* 1.3 71.8 - - + +
674B LEU* 1.3 61.7 + - - +
676B ASN* 3.5 7.0 + - - +
677B LYS* 2.9 35.7 + - + +
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B TYR* 4.1 34.1 - - + +
658B LYS* 3.9 32.8 - - + +
659B ALA* 4.4 6.5 - - + +
662B LYS* 4.2 24.5 - - + -
670B ASP 3.1 12.2 + - - +
671B ALA* 2.7 10.4 + - - +
673B VAL* 1.3 79.7 - - - +
675B ILE* 1.3 64.8 + - - +
677B LYS* 3.4 7.5 + - - +
678B SER* 3.0 24.6 + - - -
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Residues in contact with ILE 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B TYR* 5.1 2.0 - - - +
659B ALA* 3.9 23.1 - - + -
671B ALA 3.0 14.6 + - - +
672B ARG* 3.9 6.1 - - - +
673B VAL 3.4 0.2 - - - -
674B LEU* 1.3 79.5 - - + +
676B ASN* 1.3 59.7 + - - +
678B SER* 2.6 23.5 + - - -
679B VAL* 3.5 7.8 + - - +
714B MET* 3.2 49.1 - - + +
717B LEU* 3.7 28.9 - - + -
718B THR* 4.0 14.8 - - + -
723B PHE* 4.1 18.6 - - + -
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Residues in contact with ASN 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B ARG* 2.7 28.1 + - - +
673B VAL* 3.9 6.7 - - - +
674B LEU 3.3 0.2 - - - -
675B ILE* 1.3 76.0 - - - +
677B LYS* 1.3 66.6 + - - +
679B VAL* 3.0 10.2 + - - +
680B GLN* 2.9 22.6 + - - +
715B HIS* 5.7 0.2 + - - -
718B THR* 3.9 18.8 - - - +
916B PHE* 3.8 24.4 - - + -
920B MET* 4.5 4.1 - - - +
923B ARG* 4.9 15.0 - - - +
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Residues in contact with LYS 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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200B LYS* 5.9 2.7 - - - +
673B VAL* 2.9 25.9 + - + +
674B LEU* 3.8 6.1 - - - +
676B ASN* 1.3 76.8 - - - +
678B SER* 1.3 58.3 + - - +
680B GLN* 4.0 13.7 - - + +
681B ASP* 2.8 66.2 + - - +
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Residues in contact with SER 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B TYR* 3.7 42.1 - - - -
674B LEU 3.0 13.2 + - - -
675B ILE* 2.6 25.3 + - - -
677B LYS* 1.3 76.6 - - - +
679B VAL* 1.3 61.3 + - - +
681B ASP* 4.4 3.2 - - - +
682B ILE* 3.2 30.7 + - - +
710B PHE* 3.7 12.3 - - - -
714B MET* 3.9 6.1 - - - +
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Residues in contact with VAL 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B ILE 4.0 2.0 - - - +
676B ASN 3.0 7.9 + - - +
678B SER* 1.3 79.1 + - - +
680B GLN* 1.3 66.5 + - - +
682B ILE* 4.1 1.0 - - - +
683B LEU* 3.2 29.6 + - + +
710B PHE* 3.8 11.0 - - + -
711B PRO* 3.8 27.4 - - + +
714B MET* 3.3 39.7 - - + -
916B PHE* 3.8 28.5 - - + -
920B MET* 4.1 14.6 - - + -
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Residues in contact with GLN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B ASN* 2.9 12.2 + - - +
677B LYS* 3.0 16.5 + - - +
679B VAL* 1.3 74.5 - - - +
681B ASP* 1.3 66.7 + - - +
682B ILE 3.1 0.3 + - - -
683B LEU* 3.2 3.3 + - - +
684B ALA* 2.8 32.7 + - + +
920B MET* 3.2 26.5 - - + -
923B ARG* 3.0 50.6 + - - +
924B ILE* 3.9 10.2 - - + +
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Residues in contact with ASP 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LYS* 4.2 32.6 + - + +
677B LYS* 2.8 59.1 + - - +
678B SER* 4.4 4.8 - - - +
680B GLN* 1.3 78.7 + - - +
682B ILE* 1.3 52.5 + - + +
684B ALA* 3.5 8.2 + - - +
685B THR* 2.5 39.4 + - - -
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Residues in contact with ILE 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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200B LYS* 3.6 20.4 - - - +
201B LEU* 3.5 26.5 - - + -
643B TYR* 4.0 27.1 + - + +
651B ILE* 5.0 1.8 - - + -
655B TYR* 4.8 8.5 - - + +
678B SER 3.2 20.7 + - - +
679B VAL 4.1 2.5 - - - +
680B GLN 3.1 0.6 - - - -
681B ASP* 1.3 74.8 - - + +
683B LEU* 1.3 69.1 + - + +
685B THR* 3.1 2.0 + - - -
686B TYR* 2.9 23.4 + - - +
703B LEU* 4.1 15.0 - - + -
707B LEU* 4.8 5.2 - - + -
710B PHE* 3.5 31.2 - - + -
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Residues in contact with LEU 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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143B LEU* 3.7 22.2 - - + -
679B VAL* 3.2 24.0 + - + +
680B GLN* 3.2 4.1 + - - +
682B ILE* 1.3 80.4 - - + +
684B ALA* 1.3 62.4 + - - +
686B TYR* 3.8 5.4 - - - +
687B LYS* 3.1 25.5 + - - +
701B LEU* 3.7 37.0 - - + -
702B ARG 4.1 7.7 - - - +
703B LEU* 3.8 25.1 - - + -
710B PHE* 6.3 0.4 - - + -
711B PRO* 4.2 8.1 - - + -
917B LEU* 5.3 0.7 - - + -
920B MET* 4.1 18.8 - - + -
924B ILE* 3.9 16.1 - - + +
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Residues in contact with ALA 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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680B GLN* 2.8 19.4 + - + +
681B ASP* 3.6 10.5 - - - +
683B LEU* 1.3 80.0 - - - +
685B THR* 1.3 55.3 + - - +
687B LYS* 3.8 4.3 + - - +
688B LYS* 3.1 29.6 + - - +
924B ILE* 3.9 24.4 - - + +
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Residues in contact with THR 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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198B LYS* 3.2 26.5 - - + +
199B SER* 4.2 2.0 - - - +
200B LYS* 3.0 18.6 - - + +
639B LEU* 5.0 1.8 - - + -
643B TYR* 3.6 21.3 - - + +
681B ASP 2.5 23.2 + - - -
682B ILE 3.7 0.2 - - - -
684B ALA* 1.3 73.7 - - - +
686B TYR* 1.3 60.0 + - - +
688B LYS* 4.7 2.2 - - - -
689B GLU* 2.6 58.3 + - + +
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Residues in contact with TYR 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.3 19.5 - - + +
140B PRO* 4.3 11.4 - - + +
643B TYR* 3.7 16.9 + + + -
682B ILE 2.9 15.2 + - - +
683B LEU 3.8 4.0 - - - +
685B THR* 1.3 75.8 - - - +
687B LYS* 1.3 62.3 + - - +
690B ILE* 2.7 70.7 + - + +
691B VAL* 3.2 19.9 + - + -
702B ARG* 3.7 13.9 - - + +
703B LEU* 3.5 54.3 + - + -
704B CYS* 3.7 27.0 - - - +
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Residues in contact with LYS 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 LEU 3.1 15.2 + - - +
684B ALA* 3.8 4.3 - - - +
686B TYR* 1.3 81.6 - - - +
688B LYS* 1.3 62.5 + - + +
691B VAL* 3.4 34.9 + - + +
702B ARG* 5.0 6.5 + - + +
924B ILE* 3.0 48.2 + - + +
925B SER* 3.1 21.2 - - - +
926B LYS* 3.8 12.8 - - - +
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Residues in contact with LYS 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B ALA 3.1 17.6 + - - +
685B THR* 4.0 2.5 - - - +
687B LYS* 1.3 84.7 - - + +
689B GLU* 1.3 89.3 + - + +
690B ILE 3.7 0.2 - - - -
691B VAL 4.9 3.3 - - - +
926B LYS* 6.6 0.2 - - - -
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Residues in contact with GLU 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 4.1 29.4 + - + +
639B LEU* 3.6 25.0 - - + +
685B THR* 2.6 37.5 + - + +
688B LYS* 1.3 112.6 + - + +
690B ILE* 1.3 61.2 + - - +
691B VAL 4.9 0.7 - - - -
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Residues in contact with ILE 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.5 29.6 - - + -
639B LEU* 4.1 19.3 - - + +
640B ALA* 4.5 5.8 - - + +
643B TYR* 3.8 28.9 - - + -
686B TYR* 2.7 58.2 + - + +
689B GLU* 1.3 79.2 - - - +
691B VAL* 1.3 67.9 + - - +
692B VAL* 3.3 12.3 + - - +
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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
------------------------------------------------------------
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