Contacts of the helix formed by residues 626 - 635 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575C ALA* 4.0 6.5 - - - +
624C GLY* 3.2 18.7 + - - +
625C VAL* 1.3 80.7 - - - +
627C ARG* 1.3 64.8 + - - +
628C SER* 3.0 27.8 + - - -
629C VAL* 3.3 16.5 + - - +
630C THR* 3.5 7.6 + - - -
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Residues in contact with ARG 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LYS* 3.4 8.3 - - - +
569C ASP* 2.7 34.5 + - - -
571C TYR* 3.1 54.1 - - - +
572C GLY* 4.2 6.3 - - - -
575C ALA* 4.5 3.0 - - - +
626C THR* 1.3 78.2 - - - +
628C SER* 1.3 59.3 + - - +
630C THR* 3.1 3.0 + - - -
631C LYS* 2.8 43.5 + - + +
2002C APC 2.5 32.1 + - - -
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Residues in contact with SER 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C THR* 3.1 15.4 + - - -
627C ARG* 1.3 81.3 - - - +
629C VAL* 1.3 67.3 + - - +
630C THR 3.1 2.3 + - - -
631C LYS* 3.7 14.4 + - - +
632C ARG* 4.9 2.9 + - - +
654C THR* 4.1 9.1 + - - -
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Residues in contact with VAL 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C TRP* 4.5 6.5 - - + -
623C TYR* 4.3 8.5 - - + -
624C GLY 4.7 0.2 - - - +
625C VAL* 3.9 13.7 - - + -
626C THR* 3.3 24.2 + - - +
628C SER* 1.3 79.7 - - - +
630C THR* 1.3 61.2 + - + +
633C SER* 4.4 4.0 + - - -
650C VAL* 4.7 6.8 - - + +
654C THR* 3.3 38.1 + - + +
677C MET* 3.5 39.7 - - + -
681C ILE* 3.5 11.1 - - - +
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Residues in contact with THR 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C TYR* 2.9 27.2 + - - -
574C VAL* 4.5 14.6 - - + -
575C ALA* 3.8 7.1 - - - +
578C VAL* 4.1 20.2 - - + -
625C VAL* 4.5 4.0 - - + -
626C THR 3.5 11.4 + - - +
627C ARG 3.1 6.4 + - - -
628C SER 3.1 0.2 - - - -
629C VAL* 1.3 89.1 - - + +
631C LYS* 1.3 70.2 + - - +
632C ARG 3.8 0.2 - - - -
633C SER* 3.5 4.3 + - - -
634C VAL* 3.1 20.3 + - - +
681C ILE* 4.1 25.2 - - + +
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Residues in contact with LYS 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C TYR* 3.4 28.2 - - + +
627C ARG* 2.8 23.1 + - - +
628C SER* 4.1 10.1 - - - +
629C VAL 3.6 1.0 - - - -
630C THR* 1.3 81.6 - - - +
632C ARG* 1.3 81.8 + - + +
633C SER 2.7 0.2 + - - -
634C VAL* 2.8 8.5 + - - +
635C MET* 3.0 26.0 + - - -
2002C APC 2.5 75.6 + - - +
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Residues in contact with ARG 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C SER 4.9 2.8 + - - +
630C THR 3.8 0.2 - - - -
631C LYS* 1.3 89.5 - - + +
633C SER* 1.3 68.0 + - - +
635C MET* 2.6 47.5 + - - +
636C THR* 3.1 8.0 + - - +
649C GLN* 3.5 20.9 - - + +
653C ASP* 4.8 21.1 - - + +
2002C APC 2.8 96.7 + - - +
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Residues in contact with SER 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C VAL 4.4 3.8 + - - -
630C THR 3.5 9.1 + - - -
631C LYS 2.7 2.8 + - - -
632C ARG* 1.3 78.1 - - - +
634C VAL* 1.3 62.8 + - - -
635C MET 3.1 0.2 + - - -
636C THR* 3.1 13.0 + - - -
637C LEU 3.5 3.5 + - - -
646C PHE* 3.3 32.4 + - - +
649C GLN* 3.5 31.1 + - - +
650C VAL* 4.9 1.9 - - - +
681C ILE* 3.8 29.3 - - - +
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Residues in contact with VAL 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C CYS* 6.0 1.6 - - - -
543C ILE* 4.5 22.4 - - + +
570C ILE* 4.5 9.6 - - + -
571C TYR* 3.1 44.2 - - + +
574C VAL* 4.4 11.2 - - + -
630C THR 3.1 7.0 + - - +
631C LYS 2.8 9.4 + - - +
633C SER* 1.3 77.9 - - - +
635C MET* 1.3 58.8 + - - +
636C THR 3.2 3.4 + - - -
637C LEU* 3.3 21.0 + - + +
638C ALA 4.9 0.2 + - - -
646C PHE* 5.1 2.0 - - - -
681C ILE* 5.0 1.9 - - + +
685C VAL* 3.7 30.5 - - + -
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Residues in contact with MET 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C CYS* 5.9 3.4 - - - -
571C TYR* 3.5 26.0 - - + +
631C LYS* 3.0 30.7 + - - +
632C ARG* 2.6 54.1 + - - +
634C VAL* 1.3 72.5 - - - +
636C THR* 1.3 59.2 + - - +
637C LEU 3.6 0.4 - - - -
638C ALA* 5.1 2.3 - - - +
639C TYR* 4.0 2.4 - - - -
2002C APC 3.1 59.9 + - + +
3007C MG 3.8 17.5 - - - -
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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
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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