Contacts of the helix formed by residues 635 - 648 (chain C) in PDB entry 3HR4
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 CYS 635 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592C THR* 3.4 13.9 - - - -
625C GLY 3.3 32.3 - - - -
626C LEU 3.8 11.2 - - - -
627C GLY 4.1 2.7 - - - -
634C PHE* 1.3 94.9 - - - +
636C ALA* 1.3 52.7 + - - +
637C PHE 3.2 2.7 - - - -
638C ALA* 2.9 7.0 + - + -
639C HIS* 2.7 44.1 + - + +
656C MET* 3.8 11.4 - - + -
658C GLU* 4.1 9.9 - - - +
659C GLY 4.5 0.4 - - - -
999C FMN 2.5 14.1 + - - -
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Residues in contact with ALA 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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592C THR* 3.6 1.4 + - - -
596C GLY* 3.3 27.8 - - - +
633C ARG* 3.3 23.4 + - + -
634C PHE 3.1 3.0 - - - -
635C CYS* 1.3 75.9 - - - +
637C PHE* 1.3 58.8 + - - +
639C HIS* 2.9 12.5 + - - +
640C ASP* 2.7 35.6 + - - +
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Residues in contact with PHE 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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544C ALA* 4.5 3.8 - - + -
572C MET* 4.1 26.5 - - + -
590C THR* 3.2 36.3 - - + -
591C SER 3.5 10.5 - - - +
592C THR* 3.2 12.9 + - - +
596C GLY 3.7 11.4 + - - +
597C ASP 4.1 7.2 - - - +
598C CYS* 3.2 42.0 - - + -
602C GLY* 4.8 5.6 - - - -
605C LEU* 6.2 0.2 - - + -
606C LYS* 4.3 18.4 - - + -
609C LEU* 5.6 4.7 - - + -
610C PHE* 6.2 0.7 - + - -
635C CYS 3.2 0.8 - - - -
636C ALA* 1.3 76.9 - - - +
638C ALA* 1.3 59.8 + - - +
640C ASP* 3.1 17.6 + - + +
641C ILE* 2.8 36.5 + - + +
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Residues in contact with ALA 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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590C THR* 3.9 14.1 - - + +
592C THR* 3.9 2.2 + - - +
623C VAL* 3.7 7.2 - - + +
625C GLY* 3.3 35.2 - - - +
635C CYS* 2.9 6.8 + - - +
637C PHE* 1.3 79.4 - - - +
639C HIS* 1.3 58.7 + - - +
641C ILE* 3.0 11.2 - - - +
642C ASP* 2.9 30.0 + - - +
656C MET* 3.3 15.5 - - + +
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Residues in contact with HIS 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C PHE 3.2 21.4 + - - -
635C CYS 2.7 22.4 + - - -
636C ALA* 2.9 13.7 + - - +
638C ALA* 1.3 75.8 - - - +
640C ASP* 1.3 58.0 + - - +
642C ASP* 3.7 3.0 + - - +
643C GLN* 3.0 48.2 + - - +
656C MET* 3.3 32.5 - - + +
658C GLU* 3.6 20.5 + - - -
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Residues in contact with ASP 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLY* 5.2 6.2 - - - -
595A ASN* 3.7 25.0 + - - +
596C GLY 3.8 10.4 - - - +
606C LYS* 4.5 7.7 + - - -
610C PHE* 4.4 25.5 - - + -
636C ALA* 2.7 23.9 + - - +
637C PHE* 3.1 23.3 + - + +
639C HIS* 1.3 73.0 - - - +
641C ILE* 1.3 63.4 + - - +
643C GLN* 3.0 8.7 + - - +
644C LYS* 3.0 24.3 + - - +
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Residues in contact with ILE 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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572C MET* 5.0 6.7 - - + -
586C LEU* 6.0 0.7 - - + -
588C VAL* 4.5 24.0 - - + -
590C THR* 4.5 9.2 - - + -
605C LEU* 6.5 0.2 - - + -
609C LEU* 4.3 26.7 - - + -
610C PHE* 5.7 0.4 - - - -
623C VAL* 4.5 7.6 - - + -
637C PHE* 2.8 31.4 - - + +
638C ALA* 3.0 20.6 - - - +
640C ASP* 1.3 74.9 - - - +
642C ASP* 1.3 62.7 + - - +
643C GLN 3.2 0.9 + - - -
644C LYS* 3.6 4.4 + - + +
645C LEU* 3.2 49.3 + - + +
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Residues in contact with ASP 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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621C TYR* 3.4 24.9 + - - -
623C VAL* 3.7 19.8 + - + +
638C ALA 2.9 20.0 + - - +
639C HIS* 3.7 6.1 + - - +
641C ILE* 1.3 78.5 - - - +
643C GLN* 1.3 70.1 + - - +
645C LEU 3.8 0.3 + - - -
646C SER* 3.2 19.5 + - - -
652C GLN* 5.5 5.6 - - - +
656C MET* 3.4 36.1 + - - +
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Residues in contact with GLN 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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595A ASN* 6.3 0.7 - - - +
639C HIS* 3.0 32.8 + - - +
640C ASP* 3.0 13.4 + - - +
642C ASP* 1.3 84.6 - - - +
644C LYS* 1.3 58.4 + - - +
645C LEU 3.1 1.3 - - - -
646C SER* 2.8 34.6 + - - -
647C HIS* 3.1 24.3 + - + +
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Residues in contact with LYS 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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609C LEU* 4.5 18.8 - - + -
610C PHE* 4.0 47.4 + - + +
612C LEU 4.0 14.6 + - - -
613C LYS* 5.3 1.6 - - - +
614C GLU* 4.6 3.2 - - - +
640C ASP 3.0 13.2 + - - +
641C ILE* 4.2 4.9 - - + +
643C GLN* 1.3 76.0 - - - +
645C LEU* 1.3 63.6 + - + +
647C HIS* 3.2 26.0 + - + +
648C LEU* 3.2 67.3 + - + +
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Residues in contact with LEU 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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580C LEU* 5.9 7.0 - - + -
586C LEU* 5.1 5.4 - - + -
588C VAL* 5.1 6.5 - - + -
609C LEU* 5.0 10.5 - - + -
619C PHE* 4.7 17.9 - - + -
621C TYR* 3.4 44.0 - - + -
623C VAL* 4.5 4.5 - - + -
641C ILE* 3.2 43.0 + - + +
643C GLN 3.1 0.6 - - - -
644C LYS* 1.3 75.8 - - + +
646C SER* 1.3 66.3 + - - +
647C HIS 3.3 0.3 + - - -
648C LEU* 3.5 16.0 + - + +
650C ALA* 3.1 28.4 + - + +
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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
----------------------------------------------------------
621C TYR* 3.7 17.7 + - - -
642C ASP* 3.2 12.0 + - - -
643C GLN* 2.8 18.7 + - - -
645C LEU* 1.3 80.2 - - - +
647C HIS* 1.3 67.1 + - - +
649C GLY* 4.0 4.5 + - - -
650C ALA 4.1 8.1 - - - +
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Residues in contact with HIS 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C GLN* 3.1 29.5 + - + +
644C LYS* 3.2 32.5 + - + +
646C SER* 1.3 82.9 - - - +
648C LEU* 1.3 63.3 + - + +
649C GLY* 2.6 19.1 + - - -
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Residues in contact with LEU 648 (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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609C LEU* 6.0 2.5 - - + +
612C LEU* 4.2 10.1 - - + +
614C GLU* 3.5 33.7 - - + -
615C LEU* 3.9 21.1 - - + +
616C ASN* 3.8 12.6 - - - +
618C LYS* 5.2 2.1 + - - -
644C LYS* 3.2 54.8 + - + +
645C LEU* 3.5 10.3 + - + +
647C HIS* 1.3 81.0 - - + +
649C GLY* 1.3 49.7 + - - +
650C ALA* 2.6 22.5 + - - +
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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