Contacts of the helix formed by residues 689 - 708 (chain B) in PDB entry 1S0V
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 VAL 689 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B ILE* 3.4 37.0 - - + -
547B SER* 4.9 0.4 - - - +
552B ASP* 3.7 1.8 - - - -
555B GLY* 3.9 12.3 - - - -
558B ALA* 4.7 2.5 - - + -
570B ILE* 3.9 25.8 - - + -
634B VAL* 5.9 0.9 - - + -
637B LEU* 4.5 7.6 - - + -
685B VAL* 3.2 13.3 + - + +
688B THR* 1.3 83.4 - - + +
690B VAL* 1.3 67.4 + - - +
691B ALA* 2.6 6.6 + - - +
692B ALA* 2.9 26.2 + - + -
693B VAL* 3.4 10.0 - - + +
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Residues in contact with VAL 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B ASP* 3.5 9.6 - - - +
554B VAL* 4.9 8.3 - - + -
686B SER 4.0 12.6 - - - +
687B VAL* 3.6 21.3 - - - +
688B THR 3.4 17.5 - - - +
689B VAL* 1.3 74.9 - - - +
691B ALA* 1.3 67.9 + - - +
693B VAL* 2.8 27.8 + - + +
694B GLU* 2.9 24.1 + - + +
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Residues in contact with ALA 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B PHE* 4.2 0.4 - - - +
547B SER* 3.8 22.7 - - - +
550B LEU* 3.5 24.9 - - + +
552B ASP* 3.0 32.4 + - + +
689B VAL 2.6 5.6 + - - +
690B VAL* 1.3 73.7 - - - +
692B ALA* 1.3 52.2 + - - +
694B GLU* 2.7 31.3 - - - +
695B ALA 2.9 12.8 + - - -
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Residues in contact with ALA 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ILE* 4.2 16.2 - - + -
546B PHE* 3.6 34.3 - - + +
637B LEU* 4.4 2.7 - - + -
689B VAL* 2.9 24.0 + - + +
691B ALA* 1.3 75.8 - - - +
693B VAL* 1.3 65.7 + - - +
694B GLU 2.8 2.1 + - - -
695B ALA* 3.0 1.4 + - - -
696B MET* 2.9 35.9 + - - +
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Residues in contact with VAL 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B LEU* 5.1 8.5 - - + +
682B TRP* 3.6 37.2 - - + -
685B VAL* 5.1 5.2 - - + -
686B SER* 4.2 22.2 - - - +
689B VAL* 3.4 13.5 - - + +
690B VAL* 2.8 35.0 - - + +
692B ALA* 1.3 74.6 - - - +
694B GLU* 1.3 58.5 + - + +
696B MET* 4.4 11.5 - - + +
697B ASN* 3.5 25.9 + - - +
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Residues in contact with GLU 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 4.7 1.1 - - + -
690B VAL* 2.9 33.8 + - + +
691B ALA* 2.7 15.2 + - - +
692B ALA 2.8 0.4 + - - -
693B VAL* 1.3 72.7 - - + +
695B ALA* 1.3 54.0 - - - +
696B MET 3.2 1.6 - - - -
697B ASN* 2.7 28.8 + - - +
698B TRP* 3.1 12.1 + - - +
865B PRO* 4.0 28.9 - - + +
866B ALA* 4.7 7.3 + - - +
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Residues in contact with ALA 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B PHE* 4.3 24.7 - - + -
549B MET* 5.3 0.2 - - - -
550B LEU* 3.7 18.8 - - + +
691B ALA 2.9 13.4 + - - +
692B ALA 3.6 3.1 - - - +
694B GLU* 1.3 73.4 - - - +
696B MET* 1.3 60.6 + - - +
698B TRP* 4.1 6.3 - - - -
699B LEU* 2.5 38.4 + - + +
842B LEU* 4.5 9.9 - - + -
865B PRO* 4.6 4.9 - - - -
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Residues in contact with MET 696 (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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546B PHE* 3.2 30.3 - - + -
637B LEU* 3.6 40.6 - - + +
638B ALA* 4.5 8.5 - - - +
640B GLY* 4.8 13.0 - - - +
641B SER 5.5 0.2 - - - +
642B LYS* 5.8 4.5 - - + -
682B TRP* 6.3 1.1 - - + -
692B ALA* 2.9 35.6 + - - +
693B VAL* 4.1 10.8 - - + +
695B ALA* 1.3 79.3 - - - +
697B ASN* 1.4 54.0 + - - +
699B LEU* 3.8 3.5 - - - +
700B LYS* 2.7 35.0 + - - +
779B ALA* 3.7 28.3 - - + +
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Residues in contact with ASN 697 (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 LYS* 5.6 10.2 + - - +
682B TRP* 5.8 6.9 - - - -
693B VAL* 3.5 15.4 + - - +
694B GLU* 2.7 15.7 + - - +
696B MET* 1.4 76.7 - - - +
698B TRP* 1.3 54.0 + - - +
700B LYS* 3.5 13.8 - - - +
701B SER* 2.8 36.2 + - - -
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Residues in contact with TRP 698 (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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694B GLU 3.1 9.2 + - - +
695B ALA 3.9 6.7 - - - +
697B ASN* 1.3 74.5 - - - +
699B LEU* 1.3 81.4 + - + +
700B LYS 2.9 0.4 - - - -
701B SER* 2.3 30.9 + - - -
702B ALA* 2.8 12.6 + - + -
842B LEU* 4.2 22.2 - - + -
845B PHE* 4.1 22.7 - + - -
846B TYR* 3.5 26.9 - + + -
849B PHE* 4.1 12.6 - + - -
861B MET* 3.1 19.9 - - + +
862B PRO* 2.8 36.6 + - + -
863B ALA 3.6 3.1 - - - -
864B LEU* 3.4 37.4 - - + +
865B PRO* 3.4 28.3 - - + -
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Residues in contact with LEU 699 (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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546B PHE* 5.3 3.6 - - + -
695B ALA* 2.5 30.2 + - + +
696B MET* 3.8 4.7 - - - +
698B TRP* 1.3 90.9 - - + +
700B LYS* 1.3 63.3 + - - +
702B ALA* 3.4 4.3 + - - +
703B ALA* 2.9 22.7 + - - +
778B ILE* 3.6 36.9 - - + +
779B ALA 4.6 5.2 - - - +
782B PHE* 3.6 35.0 - - + -
842B LEU* 3.5 26.5 - - + -
845B PHE* 4.3 16.0 - - + -
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Residues in contact with LYS 700 (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 LYS* 5.5 11.1 - - - +
696B MET 2.7 24.2 + - - +
697B ASN* 3.5 17.5 - - - +
699B LEU* 1.3 69.9 - - - +
701B SER* 1.3 71.2 + - - +
703B ALA* 3.3 3.1 + - - +
704B LYS* 3.2 17.0 + - - +
775B GLU* 2.8 61.0 + - + +
776B SER* 5.2 9.4 + - - +
778B ILE* 4.1 8.7 - - - +
779B ALA* 5.7 3.4 - - + -
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Residues in contact with SER 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B ASN* 2.8 19.4 + - - -
698B TRP 2.3 23.3 + - - -
700B LYS* 1.3 67.9 - - - +
702B ALA* 1.3 67.3 + - - +
704B LYS* 2.6 28.3 + - - +
705B LEU* 3.3 6.7 + - - +
860B LYS* 3.4 22.4 + - - +
861B MET* 4.3 1.8 - - - -
862B PRO* 3.3 33.6 - - - +
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Residues in contact with ALA 702 (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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698B TRP* 2.8 7.6 + - + +
699B LEU* 4.0 8.5 - - - +
701B SER* 1.3 76.8 - - - +
703B ALA* 1.3 66.6 + - - +
705B LEU* 3.1 7.6 + - - +
706B LEU* 2.9 24.6 + - + +
845B PHE* 5.0 7.2 - - + -
849B PHE* 2.8 41.3 - - + -
861B MET* 3.6 19.0 - - + -
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Residues in contact with ALA 703 (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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699B LEU 2.9 13.8 + - - +
700B LYS 3.4 9.6 - - - +
701B SER 2.7 4.9 + - - -
702B ALA* 1.3 77.8 - - - +
704B LYS* 1.3 68.9 + - - +
705B LEU 2.8 0.5 + - - -
706B LEU* 3.0 16.6 + - - +
707B ALA* 3.3 10.8 + - - +
725B VAL* 5.0 12.8 - - + +
774B GLN* 3.8 5.8 - - - +
775B GLU* 3.7 24.0 - - - +
778B ILE* 3.8 16.2 - - + -
845B PHE* 6.1 0.4 - - - -
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Residues in contact with LYS 704 (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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700B LYS* 3.2 6.4 + - - +
701B SER* 2.6 16.9 + - - +
703B ALA* 1.3 74.4 - - - +
705B LEU* 1.3 72.3 + - + +
707B ALA* 3.1 5.9 + - - +
708B ALA* 2.8 22.2 + - + +
771B ALA* 5.8 1.5 - - - +
775B GLU* 3.0 34.7 + - - +
860B LYS* 3.5 37.3 - - - +
5J A 4.5 17.6 + - - -
6J T 3.1 30.6 + - - +
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Residues in contact with LEU 705 (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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701B SER 4.0 6.5 - - - +
702B ALA* 3.4 8.3 - - - +
703B ALA 2.8 3.6 + - - -
704B LYS* 1.3 77.3 - - + +
706B LEU* 1.3 53.0 + - - +
707B ALA 2.3 20.4 + - - -
708B ALA* 2.7 12.3 + - + +
720B ARG* 3.4 12.9 + - - -
853B LEU* 3.9 23.8 - - + -
857B GLN* 3.4 35.4 - - + +
860B LYS* 4.4 28.5 - - + +
861B MET* 3.7 42.4 - - + +
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Residues in contact with LEU 706 (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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702B ALA* 2.9 29.1 + - + +
703B ALA* 3.0 7.5 + - - +
705B LEU* 1.3 72.7 - - - +
707B ALA* 1.3 53.5 + - - +
720B ARG* 4.4 10.5 - - - +
723B CYS* 2.2 49.5 + - + +
724B ALA 4.4 9.9 - - - +
725B VAL* 4.3 24.9 - - + -
726B HIS 5.8 0.4 - - - +
845B PHE* 5.2 0.2 - - + -
849B PHE* 3.0 53.6 - - + -
852B GLN* 4.2 26.0 - - + +
853B LEU* 4.5 6.9 - - + +
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Residues in contact with ALA 707 (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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703B ALA 3.3 7.8 + - - +
704B LYS* 3.1 8.7 + - - +
705B LEU 2.3 17.0 + - - -
706B LEU* 1.3 70.2 - - - +
708B ALA* 1.3 67.2 + - - +
722B ARG* 3.0 34.8 + - - +
723B CYS 4.3 1.1 - - - +
769B ILE* 4.3 12.8 - - + -
771B ALA* 4.1 26.2 - - + +
774B GLN* 4.5 13.5 - - + -
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Residues in contact with ALA 708 (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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704B LYS* 2.8 15.2 + - + +
705B LEU* 2.7 18.1 + - + +
707B ALA* 1.3 75.0 - - - +
709B GLU* 1.3 60.1 + - - +
710B VAL* 3.3 10.8 + - + +
720B ARG* 3.4 21.0 + - - +
721B LYS 4.4 1.0 - - - +
722B ARG* 4.5 4.4 - - - +
771B ALA* 5.3 2.6 - - - +
857B GLN* 4.9 8.3 - - - +
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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