Contacts of the helix formed by residues 626 - 637 (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 THR 626 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B ALA* 4.3 9.0 - - - -
624B GLY 3.7 8.5 + - - +
625B VAL* 1.4 82.7 - - - +
627B ARG* 1.3 59.6 + - - +
628B SER* 2.3 35.2 + - - -
629B VAL* 2.6 18.5 + - - +
630B THR* 4.1 0.9 + - - +
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Residues in contact with ARG 627 (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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472B LYS* 4.2 17.9 - - - +
569B ASP* 2.5 47.5 + - - +
571B TYR* 4.0 28.2 - - + +
572B GLY* 4.4 2.9 - - - +
575B ALA* 3.9 12.6 - - - +
626B THR* 1.3 75.3 - - - +
628B SER* 1.3 64.8 + - - +
629B VAL 2.6 12.8 + - - -
630B THR* 2.8 23.8 + - - -
631B LYS* 3.0 19.8 + - + +
2001B APC 2.9 28.5 + - - -
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Residues in contact with SER 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B THR* 2.3 27.6 + - - -
627B ARG* 1.3 77.8 - - - +
629B VAL* 1.3 61.2 + - - +
631B LYS* 4.4 13.4 + - - +
632B ARG 5.3 0.7 + - - -
653B ASP* 5.4 6.4 - - - +
654B THR* 5.1 4.3 - - - +
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Residues in contact with VAL 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B TRP* 4.8 4.3 - - + -
623B TYR* 4.3 17.0 - - + +
625B VAL* 4.8 6.5 - - + -
626B THR* 2.6 23.6 + - - +
627B ARG 2.6 1.4 + - - -
628B SER* 1.3 76.5 - - - +
630B THR* 1.3 66.6 + - + +
631B LYS 3.3 1.1 + - - -
632B ARG* 4.8 3.1 + - - +
633B SER* 3.4 9.7 + - - -
650B VAL* 4.5 13.0 - - + +
653B ASP* 5.9 1.6 - - - +
654B THR* 3.9 31.5 - - + +
677B MET* 4.0 35.4 - - + -
681B ILE* 4.5 3.9 - - + +
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Residues in contact with THR 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 2.9 26.9 + - - -
574B VAL* 3.8 22.9 - - + +
575B ALA* 3.7 32.8 - - + -
578B VAL* 5.5 1.1 - - + -
625B VAL* 5.2 4.3 - - + -
626B THR 4.5 4.3 - - - +
627B ARG 2.8 9.4 + - - +
629B VAL* 1.3 82.9 - - + +
631B LYS* 1.3 51.4 + - - -
633B SER* 2.9 10.1 + - - -
634B VAL* 2.7 36.9 + - - +
681B ILE* 4.5 13.4 - - + +
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Residues in contact with LYS 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 3.0 32.7 - - + -
627B ARG* 3.0 16.8 + - + +
628B SER* 4.6 11.2 - - - +
629B VAL 3.3 1.0 - - - -
630B THR* 1.3 75.9 + - - +
632B ARG* 1.3 87.6 + - - +
633B SER 2.8 1.4 + - - -
634B VAL* 2.9 7.4 + - - +
635B MET* 3.0 18.1 + - - +
2001B APC 2.8 80.4 + - - +
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Residues in contact with ARG 632 (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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628B SER 5.3 1.0 + - - -
629B VAL 4.8 2.9 + - - +
630B THR 3.8 0.2 - - - -
631B LYS* 1.3 94.2 - - - +
633B SER* 1.3 58.0 + - - +
635B MET* 3.2 10.3 + - - +
636B THR* 2.7 31.5 + - - +
649B GLN* 3.5 15.3 - - + +
653B ASP* 3.1 45.9 + - + +
2001B APC 2.8 80.3 + - - +
10H T 4.6 0.7 - - - +
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Residues in contact with SER 633 (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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629B VAL 3.4 11.3 + - - -
630B THR* 2.9 21.3 + - - -
632B ARG* 1.3 73.9 - - - +
634B VAL* 1.3 67.5 + - - +
635B MET 2.8 1.9 + - - -
636B THR* 3.0 13.0 + - - -
637B LEU 3.2 6.8 + - - -
646B PHE* 3.1 39.3 - - - -
649B GLN* 2.9 15.3 + - - +
650B VAL* 5.4 3.6 - - - +
681B ILE* 4.1 12.7 - - - +
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Residues in contact with VAL 634 (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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540B CYS* 5.7 2.6 - - - -
543B ILE* 4.2 14.9 - - + +
570B ILE* 3.9 26.0 - - + -
571B TYR* 3.6 40.4 - - + -
574B VAL* 5.4 2.9 - - + -
630B THR* 2.7 22.6 + - - +
631B LYS 2.9 7.4 + - - +
633B SER* 1.3 73.1 - - - +
635B MET* 1.3 64.5 + - - +
637B LEU* 2.8 29.7 - - + +
646B PHE* 4.9 2.7 - - - -
681B ILE* 5.5 1.0 - - - +
685B VAL* 4.8 20.4 - - + -
689B VAL* 5.9 0.9 - - + -
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Residues in contact with MET 635 (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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540B CYS* 5.3 10.1 - - - -
571B TYR* 2.5 37.0 - - + +
631B LYS* 3.0 24.8 + - - +
632B ARG* 3.7 11.9 - - - +
633B SER 2.8 2.4 + - - -
634B VAL* 1.3 80.8 - - - +
636B THR* 1.3 55.4 + - - +
637B LEU 2.8 9.6 + - - -
638B ALA* 3.8 6.8 + - - +
639B TYR* 3.8 18.8 + - + +
2001B APC 3.5 86.6 - - + +
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Residues in contact with THR 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ARG 2.7 19.9 + - - +
633B SER 3.0 7.0 + - - -
635B MET* 1.3 72.4 - - - +
637B LEU* 1.3 68.8 + - - +
638B ALA 3.3 0.7 - - - -
639B TYR* 2.9 24.4 + - - +
640B GLY 3.3 4.9 + - - -
641B SER* 2.4 31.2 + - - -
646B PHE* 4.0 1.0 - - - -
649B GLN* 3.2 23.7 + - - +
2001B APC 3.9 15.0 - - + -
10H T 3.2 28.7 - - - +
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Residues in contact with LEU 637 (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 26.2 - - + -
633B SER 3.2 3.7 + - - +
634B VAL* 2.8 26.3 + - + +
635B MET 2.8 3.0 - - - -
636B THR* 1.3 78.5 - - - +
638B ALA* 1.3 62.1 + - + +
640B GLY* 2.8 25.1 + - - -
641B SER* 4.4 8.5 - - - +
646B PHE* 3.9 23.6 - - + -
682B TRP* 4.9 8.1 - - + -
685B VAL* 4.4 19.3 - - + -
689B VAL* 4.5 7.6 - - + -
692B ALA* 4.4 7.0 - - + -
693B VAL* 5.1 6.1 - - + +
696B MET* 3.6 30.2 - - + +
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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