Contacts of the helix formed by residues 632 - 646 (chain C) in PDB entry 3RTR
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 LYS 632 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551C CYS* 4.3 29.4 + - + +
552C THR* 5.3 2.5 - - - +
626C THR* 5.0 2.2 - - - -
630C GLN 3.3 5.3 + - - -
631C ILE* 1.3 72.9 - - - +
633C MET* 1.3 69.6 + - - +
634C ASP* 3.8 36.3 + - + +
635C ILE* 2.8 18.3 + - + +
636C LEU 2.9 8.2 + - - -
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Residues in contact with MET 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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622C VAL* 3.9 15.7 - - + -
623C GLN* 3.3 42.8 - - + +
626C THR* 2.8 41.6 - - + +
631C ILE 3.2 2.4 + - - -
632C LYS* 1.3 68.2 - - - +
634C ASP* 1.3 56.1 + - - +
635C ILE 2.6 17.1 + - - -
636C LEU* 2.7 20.7 + - + -
637C ALA* 2.9 16.8 + - - +
665C PRO* 4.3 12.8 - - + -
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Residues in contact with ASP 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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632C LYS* 3.1 35.6 + - + +
633C MET* 1.3 76.7 - - - +
635C ILE* 1.3 59.0 + - + +
637C ALA* 4.7 3.2 - - - +
638C GLN* 2.7 35.4 + - - +
769E LYS* 5.5 10.4 - - - +
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Residues in contact with ILE 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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551C CYS* 4.4 23.1 - - + -
606C PHE* 4.7 16.2 - - + -
631C ILE* 4.5 8.7 - - + -
632C LYS* 2.8 11.0 + - + +
633C MET 2.6 3.8 + - - -
634C ASP* 1.3 91.0 - - + +
636C LEU* 1.3 62.1 + - - +
637C ALA 2.9 6.4 + - - -
638C GLN* 2.9 22.6 + - - +
639C VAL* 2.8 38.5 + - + +
688C MET* 4.5 18.2 - - + -
694C GLN* 5.0 6.1 - - - +
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Residues in contact with LEU 636 (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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610C ILE* 3.4 33.0 - - + -
622C VAL* 3.6 26.0 - - + +
625C LEU* 4.0 6.3 - - + -
626C THR* 2.8 38.1 - - - +
629C THR* 4.7 1.6 - - - +
631C ILE* 4.2 21.2 - - + +
632C LYS 2.9 7.2 + - - +
633C MET* 2.7 21.1 + - - +
635C ILE* 1.3 73.0 - - - +
637C ALA* 1.3 55.8 + - - +
639C VAL* 3.8 6.7 - - + -
640C LEU* 3.0 42.1 + - + +
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Residues in contact with ALA 637 (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 MET 2.9 12.1 + - - +
634C ASP* 4.7 5.2 - - - +
635C ILE 2.9 0.8 + - - -
636C LEU* 1.3 74.6 - - - +
638C GLN* 1.3 59.1 + - + +
639C VAL 3.0 8.8 + - - -
640C LEU* 3.3 3.9 + - - +
641C GLN* 3.1 27.7 + - - +
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Residues in contact with GLN 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 ASP* 2.7 26.3 + - - +
635C ILE* 2.9 19.8 + - - +
637C ALA* 1.3 77.0 - - + +
639C VAL* 1.3 59.8 + - - +
641C GLN* 4.4 14.1 - - - +
642C ILE* 3.6 21.7 + - - +
688C MET* 3.3 43.6 - - + +
690C THR* 3.2 31.7 + - + +
694C GLN* 4.0 6.8 + - - +
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Residues in contact with VAL 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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606C PHE* 4.1 24.2 - - + +
607C GLN* 4.1 17.0 - - + +
610C ILE* 4.2 20.4 - - + -
631C ILE* 5.5 3.1 - - + -
635C ILE* 2.8 34.1 + - + +
636C LEU* 3.8 9.4 - - + +
638C GLN* 1.3 78.9 - - - +
640C LEU* 1.3 65.2 + - - +
641C GLN 3.3 0.2 - - - -
642C ILE* 3.1 14.4 + - - +
643C LEU* 2.9 34.8 - - + +
688C MET* 5.0 5.2 - - - -
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Residues in contact with LEU 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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610C ILE* 4.0 26.5 - - + -
622C VAL* 4.3 21.1 - - + -
625C LEU* 4.1 22.7 - - + -
636C LEU* 3.0 35.7 + - + +
637C ALA* 3.3 4.2 + - - +
639C VAL* 1.3 75.8 - - - +
641C GLN* 1.3 51.1 + - - +
643C LEU* 2.7 22.6 + - - +
644C LEU* 2.7 27.7 + - + +
649C LEU* 3.7 28.5 - - + -
669C ILE* 4.3 14.4 - - + -
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Residues in contact with GLN 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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637C ALA 3.1 18.1 + - - +
638C GLN* 4.6 12.1 - - - +
640C LEU* 1.3 76.6 - - - +
642C ILE* 1.3 63.5 + - + +
644C LEU* 3.7 12.9 + - + +
645C LYS* 2.9 52.7 + - - +
658C VAL 4.4 5.8 - - - +
659C ASP* 4.3 17.4 + - - +
688C MET* 6.6 0.4 - - - -
689C LYS* 4.7 19.7 - - - +
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Residues in contact with ILE 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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607C GLN* 4.2 12.8 - - - +
638C GLN 3.6 12.3 - - - +
639C VAL* 3.1 9.7 + - - +
640C LEU 3.1 0.6 - - - -
641C GLN* 1.3 80.6 - - + +
643C LEU* 1.3 64.4 + - + +
645C LYS* 3.5 15.1 - - + +
646C SER* 3.3 15.8 + - - +
684C ILE* 3.9 14.3 - - + +
686C VAL* 3.3 48.0 - - + +
688C MET* 3.4 35.0 - - + +
689C LYS 5.6 0.2 - - - +
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Residues in contact with LEU 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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607C GLN* 3.5 28.9 - - + -
610C ILE* 3.4 18.4 - - + -
611C LEU* 3.8 26.2 - - + -
639C VAL* 2.9 32.1 - - + +
640C LEU* 2.7 16.5 + - - +
642C ILE* 1.3 74.4 - - + +
644C LEU* 1.3 51.9 + - - +
646C SER* 2.8 26.5 + - - +
648C LEU* 3.8 24.3 + - + +
649C LEU* 3.5 30.7 + - + -
684C ILE* 4.1 13.7 - - + -
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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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640C LEU* 2.7 25.7 + - + +
641C GLN* 3.9 14.4 - - + +
642C ILE 3.5 0.2 - - - -
643C LEU* 1.3 68.8 - - - +
645C LYS* 1.3 62.8 + - - +
646C SER 2.5 15.8 - - - +
647C LYS* 4.4 1.6 - - - -
649C LEU* 3.8 36.5 - - + +
658C VAL* 4.3 37.3 - - + +
669C ILE* 4.9 17.7 - - + -
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Residues in contact with LYS 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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641C GLN* 2.9 37.0 - - - +
642C ILE* 3.5 15.5 - - + +
644C LEU* 1.3 79.7 - - + +
646C SER* 1.3 64.6 + - - +
647C LYS* 3.6 14.7 + - - +
658C VAL* 3.3 21.9 - - + +
659C ASP* 2.7 38.8 + - - +
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Residues in contact with SER 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 ILE 3.3 14.6 + - - -
643C LEU* 2.8 11.3 + - - +
644C LEU 2.5 22.2 - - - +
645C LYS* 1.3 78.2 - - - +
647C LYS* 1.3 54.7 + - - +
648C LEU* 2.7 28.5 + - - +
675C TYR* 4.5 8.3 - - - -
684C ILE* 3.8 28.4 - - - +
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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