Contacts of the helix formed by residues 637 - 646 (chain B) in PDB entry 1R0X
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 ARG 637 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625B TYR* 3.2 52.1 + - + +
626B PHE* 3.6 27.8 - - + +
633B LEU* 2.8 23.8 + - + +
636B LEU* 1.3 120.0 + - - +
638B PRO* 1.3 55.9 - - - +
639B ASP 3.3 2.4 + - - -
640B PHE* 3.4 10.7 + - + -
641B SER* 2.4 35.5 + - - -
670B SER 4.1 16.7 + - - -
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Residues in contact with PRO 638 (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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634B GLN 3.9 16.8 - - - +
635B SER 3.9 10.1 - - - +
636B LEU 3.4 9.2 - - - +
637B ARG* 1.3 88.0 - - - +
639B ASP* 1.3 68.8 + - - +
641B SER* 3.9 2.2 - - - +
642B SER* 3.1 31.7 + - - -
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Residues in contact with ASP 639 (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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637B ARG 3.3 0.6 - - - -
638B PRO* 1.3 86.9 - - + +
640B PHE* 1.3 66.1 + - - +
642B SER* 4.8 3.6 + - - -
643B LYS* 3.5 15.4 + - - +
669B PHE* 3.4 53.1 - - + -
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Residues in contact with PHE 640 (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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457B THR* 5.1 0.7 - - + -
607B MET* 4.6 8.7 - - + -
610B LEU* 4.9 1.1 - - + -
618B ILE* 4.0 21.1 - - + -
625B TYR* 3.7 22.4 + + + +
633B LEU* 4.0 22.0 - - + -
637B ARG* 3.4 13.2 + - + +
639B ASP* 1.3 80.4 - - - +
641B SER* 1.3 63.5 + - - +
643B LYS* 3.6 0.5 - - - +
644B LEU* 2.9 52.5 + - + +
645B MET* 6.2 0.4 - - - -
662B LEU* 3.6 29.4 - - + -
665B THR* 4.0 20.2 - - + -
666B LEU* 3.5 35.9 - - + -
669B PHE* 4.3 3.4 - - + -
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Residues in contact with SER 641 (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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630B PHE* 6.3 0.2 - - - -
633B LEU* 3.1 29.3 + - - +
634B GLN* 4.1 20.9 - - - -
637B ARG 2.4 23.9 + - - -
638B PRO* 4.3 3.8 - - - -
640B PHE* 1.3 79.6 - - - +
642B SER* 1.3 60.6 + - - +
644B LEU 4.5 0.2 - - - +
645B MET* 2.8 45.8 + - - +
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Residues in contact with SER 642 (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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638B PRO 3.1 20.6 + - - -
639B ASP* 4.8 3.3 + - - -
640B PHE 3.3 0.2 - - - -
641B SER* 1.3 74.8 - - - +
643B LYS* 1.3 62.0 + - - +
645B MET* 3.8 2.7 - - - -
646B GLY* 2.9 27.0 + - - -
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Residues in contact with LYS 643 (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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639B ASP 3.5 19.8 + - - +
640B PHE 3.4 3.5 + - - +
641B SER 3.4 0.2 - - - -
642B SER* 1.3 79.9 + - - +
644B LEU* 1.3 63.8 + - + +
646B GLY* 3.2 11.1 + - - -
647B TYR* 2.5 49.0 + - + -
661B ILE* 5.1 1.2 - - - +
664B GLU* 4.3 12.9 + - - +
665B THR* 3.5 29.4 - - + +
668B ARG* 3.8 27.3 - - - +
669B PHE* 4.8 2.0 - - + -
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Residues in contact with LEU 644 (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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607B MET* 3.9 23.5 - - - +
640B PHE* 2.9 47.2 + - + +
641B SER 4.2 1.3 - - - +
643B LYS* 1.3 75.0 - - + +
645B MET* 1.3 64.5 + - - +
646B GLY 3.0 8.2 + - - -
647B TYR* 3.5 19.4 + - - +
650B PHE* 3.5 50.7 - - + +
661B ILE* 4.2 7.0 - - + -
662B LEU* 4.2 8.7 - - + -
665B THR* 3.6 33.9 - - + +
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Residues in contact with MET 645 (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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607B MET* 3.5 27.8 - - + +
611B ARG* 3.4 41.5 - - - +
630B PHE* 3.7 25.1 - - + -
633B LEU* 5.9 2.0 - - - -
634B GLN* 5.3 6.7 - - - +
640B PHE* 6.2 0.2 - - - -
641B SER* 2.8 33.9 + - - +
642B SER* 3.8 3.6 - - - +
644B LEU* 1.3 78.9 - - - +
646B GLY* 1.3 60.6 + - - +
647B TYR 3.3 9.2 + - - +
648B ASP* 5.4 0.7 - - - +
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Residues in contact with GLY 646 (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 SER 2.9 17.9 + - - -
643B LYS 3.2 5.3 + - - -
644B LEU 3.0 2.4 - - - -
645B MET* 1.3 76.6 - - - +
647B TYR* 1.3 61.0 + - - +
648B ASP* 4.0 7.8 + - - +
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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