Contacts of the helix formed by residues 637 - 646 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C TYR* 2.9 58.8 + - + -
626C PHE* 3.8 27.9 - - + +
633C LEU* 3.0 26.0 + - + +
636C LEU* 1.3 115.6 + - - +
638C PRO* 1.3 60.3 - - - +
639C ASP 3.2 3.0 + - - -
640C PHE* 3.4 11.0 + - + -
641C SER* 2.9 27.5 + - - -
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Residues in contact with PRO 638 (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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634C GLN 3.4 17.5 - - - +
635C SER* 4.1 8.7 - - - +
636C LEU* 3.3 11.0 - - - +
637C ARG* 1.3 90.4 - - - +
639C ASP* 1.3 67.5 + - - +
641C SER* 3.9 2.1 - - - -
642C SER* 3.0 30.5 + - - -
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Residues in contact with ASP 639 (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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637C ARG 3.2 0.8 - - - -
638C PRO* 1.3 86.5 - - - +
640C PHE* 1.3 68.1 + - - +
642C SER* 3.5 4.2 + - - -
643C LYS* 3.2 21.8 + - - +
669C PHE* 3.7 41.9 - - + -
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Residues in contact with PHE 640 (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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457C THR* 5.4 0.9 - - + -
607C MET* 4.9 8.3 - - + -
610C LEU* 5.0 2.0 - - + -
618C ILE* 4.0 24.5 - - + -
625C TYR* 3.5 22.9 + + - +
633C LEU* 4.2 19.7 - - + -
637C ARG* 3.4 11.9 + - + +
639C ASP* 1.3 77.1 - - - +
641C SER* 1.3 73.1 - - - +
643C LYS* 3.3 2.6 + - - +
644C LEU* 3.1 49.4 + - + +
645C MET* 6.4 0.4 - - - -
662C LEU* 3.8 19.7 - - + -
665C THR* 3.8 22.9 - - + -
666C LEU* 3.5 36.3 - - + -
669C PHE* 3.9 3.9 - - - -
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Residues in contact with SER 641 (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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633C LEU* 3.0 30.9 + - - +
634C GLN* 3.4 26.0 - - - -
637C ARG 2.9 18.4 + - - -
638C PRO* 3.9 4.9 - - - -
640C PHE* 1.3 80.7 - - - +
642C SER* 1.3 57.4 + - - +
644C LEU 3.3 1.6 + - - +
645C MET* 3.0 42.4 + - - +
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Residues in contact with SER 642 (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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638C PRO 3.0 19.9 + - - -
639C ASP* 4.1 4.8 + - - -
640C PHE 3.3 0.2 - - - -
641C SER* 1.3 76.2 - - - +
643C LYS* 1.3 62.4 + - - +
645C MET* 4.1 3.7 - - - +
646C GLY* 3.2 20.8 + - - -
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Residues in contact with LYS 643 (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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639C ASP 3.2 17.6 + - - +
640C PHE 3.7 3.1 - - - +
642C SER* 1.3 80.6 + - - +
644C LEU* 1.3 65.3 + - + +
645C MET 3.4 0.7 + - - -
646C GLY* 3.5 5.0 + - - -
647C TYR* 2.7 50.4 + - + -
661C ILE* 4.5 5.8 - - + +
664C GLU* 6.4 1.6 - - - -
665C THR* 3.5 34.1 - - + +
668C ARG* 4.8 15.9 - - - +
669C PHE* 4.7 4.5 - - + -
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Residues in contact with LEU 644 (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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607C MET* 3.6 32.1 - - + +
640C PHE* 3.1 53.2 + - + +
643C LYS* 1.3 75.7 - - - +
645C MET* 1.3 68.7 + - - +
646C GLY 3.8 0.2 + - - -
647C TYR* 3.9 13.6 + - - +
650C PHE* 3.4 52.7 - - + +
661C ILE* 4.7 5.2 - - + -
662C LEU* 3.7 13.9 - - + -
665C THR* 4.0 19.7 - - + +
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Residues in contact with MET 645 (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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607C MET* 3.4 28.0 - - + +
611C ARG* 3.3 30.7 - - - +
630C PHE* 3.7 29.4 - - + -
633C LEU* 6.3 1.6 - - + -
634C GLN* 5.4 6.5 - - + +
640C PHE* 6.4 0.4 - - - -
641C SER* 3.0 27.8 + - - +
642C SER* 4.5 3.4 - - - +
644C LEU* 1.3 84.7 - - - +
646C GLY* 1.3 56.6 + - - +
647C TYR 2.8 21.9 - - - +
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Residues in contact with GLY 646 (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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642C SER 3.2 16.9 + - - -
643C LYS 3.5 3.3 + - - -
644C LEU 3.5 0.6 - - - -
645C MET* 1.3 73.6 - - - +
647C TYR* 1.3 64.8 + - - +
648C ASP* 4.0 3.3 + - - +
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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
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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