Contacts of the helix formed by residues 639 - 657 (chain C) in PDB entry 3H52
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 MET 639 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C 486 2.7 61.5 - - + +
638C ASP* 1.3 76.2 - - + +
640C TYR* 1.3 56.6 + - - +
641C ASP* 3.3 7.7 + - - +
642C GLN* 3.3 19.6 + - + +
643C CYS* 3.2 28.1 + - - -
646C MET* 4.8 0.2 - - - +
735C TYR* 3.3 32.8 - - + -
739C THR* 3.4 31.2 - - - -
740C PHE* 4.0 3.8 - - + +
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Residues in contact with TYR 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C ARG 4.5 2.2 - - - +
634C MET* 3.1 34.3 - - - +
635C THR* 4.9 2.2 - - - -
636C LEU 3.3 29.6 - - - +
637C PRO* 5.2 1.8 - - + -
638C ASP 2.7 10.8 + - - +
639C MET* 1.3 71.2 - - - +
641C ASP* 1.3 84.0 + - - +
642C GLN 3.1 1.3 - - - -
643C CYS* 3.5 10.8 - - + +
644C LYS* 3.0 38.3 + - + +
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Residues in contact with ASP 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C PRO 5.8 0.5 - - - -
638C ASP* 4.9 2.4 - - - -
639C MET* 3.3 6.8 + - - -
640C TYR* 1.3 106.4 + - - +
642C GLN* 1.3 68.8 + - - +
644C LYS* 3.8 8.0 - - - +
645C HIS* 3.1 33.2 + - + -
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Residues in contact with GLN 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C 486 4.1 4.3 - - + -
639C MET* 3.3 32.6 - - + +
640C TYR 3.1 0.2 - - - -
641C ASP* 1.3 85.8 - - - +
643C CYS* 1.3 59.3 + - - +
645C HIS* 3.2 9.7 + - - +
646C MET* 2.9 39.2 + - + +
731C ASN 3.0 26.2 + - - +
732C LEU* 3.6 16.0 - - + +
734C ASN* 4.7 2.2 - - - +
735C TYR* 3.1 39.6 - - + +
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Residues in contact with CYS 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C 486 6.1 3.6 - - - -
621C LEU* 3.5 25.5 - - + +
629C ILE* 4.3 13.0 - - - -
633C ARG 5.2 1.6 - - - -
634C MET* 3.9 22.4 - - + +
639C MET* 3.2 17.2 + - - -
640C TYR* 3.2 15.9 + - + +
642C GLN* 1.3 76.9 - - - +
644C LYS* 1.3 59.4 + - - +
646C MET* 3.6 15.1 - - - +
647C LEU* 2.8 35.5 + - - +
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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
----------------------------------------------------------
640C TYR* 3.0 27.8 + - + +
641C ASP* 3.8 8.7 - - - +
643C CYS* 1.3 78.2 - - - +
645C HIS* 1.3 75.8 + - + +
647C LEU* 3.4 5.2 + - - +
648C TYR* 3.2 19.6 + - - +
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Residues in contact with HIS 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641C ASP* 3.1 23.2 + - + -
642C GLN* 3.2 12.9 + - - +
644C LYS* 1.3 89.1 - - + +
646C MET* 1.3 61.5 + - - +
648C TYR* 3.4 18.6 + - - +
649C VAL* 3.8 2.6 + - - +
727C GLU* 5.5 6.7 + - + -
728C VAL* 3.3 33.4 - - + +
731C ASN* 3.2 45.1 + - + +
732C LEU* 4.5 4.3 - - + -
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Residues in contact with MET 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C 486 3.7 32.8 - - + -
605C ALA* 5.2 5.8 - - + +
608C LEU* 3.5 28.7 - - + +
609C GLY* 4.8 3.6 - - - -
621C LEU* 3.7 20.4 - - + +
623C PHE* 4.1 9.6 - - + -
642C GLN* 2.9 40.5 + - + +
643C CYS* 3.6 22.2 - - - +
645C HIS* 1.3 77.2 - - - +
647C LEU* 1.3 61.6 + - - +
648C TYR 3.3 0.7 + - - -
649C VAL* 3.3 21.6 + - - +
650C SER* 3.8 4.2 + - - -
728C VAL* 4.6 3.1 - - - -
732C LEU* 3.6 20.2 - - + -
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Residues in contact with LEU 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ALA 3.3 25.1 - - - +
619C ASN* 4.4 7.0 - - - +
620C LEU 3.8 15.9 - - - +
621C LEU* 3.7 23.6 - - + -
634C MET* 3.1 37.7 - - + -
643C CYS 2.8 20.1 + - - +
644C LYS* 3.9 4.7 - - - +
646C MET* 1.3 70.0 - - - +
648C TYR* 1.3 65.3 + - - +
650C SER* 3.3 10.0 + - - +
651C SER* 2.9 24.4 + - - -
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Residues in contact with TYR 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644C LYS 3.2 12.5 + - - +
645C HIS* 3.5 14.1 - - - +
646C MET 3.2 0.8 - - - -
647C LEU* 1.3 73.8 - - - +
649C VAL* 1.3 74.1 + - + +
651C SER* 3.0 12.3 + - - -
652C GLU* 2.7 54.3 + - - +
721C LEU* 4.1 13.4 - - + +
724C SER* 3.9 29.0 + - - -
725C MET* 6.5 0.2 - - - -
728C VAL* 5.7 5.2 - - + -
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Residues in contact with VAL 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C ALA* 4.0 11.4 - - + +
606C PHE* 4.0 28.3 - - + -
609C GLY* 3.8 17.7 - - - -
645C HIS 4.2 7.9 - - - +
646C MET* 3.3 13.5 + - - +
648C TYR* 1.3 86.1 - - + +
650C SER* 1.3 62.9 + - - +
652C GLU* 3.2 4.3 + - - +
653C LEU* 3.0 28.8 + - + +
721C LEU* 4.9 4.6 - - + +
725C MET* 3.6 26.0 - - + -
728C VAL* 4.2 13.7 - - + -
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Residues in contact with SER 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609C GLY* 2.8 33.8 + - - -
612C SER* 3.2 12.7 - - - -
613C TYR* 3.0 18.4 + - - +
618C ALA* 3.4 16.1 - - - +
621C LEU* 5.8 0.4 - - - -
646C MET 3.8 2.1 + - - -
647C LEU* 3.3 14.6 + - - -
648C TYR 3.2 0.2 - - - -
649C VAL* 1.3 78.2 - - - +
651C SER* 1.3 59.4 + - - +
653C LEU* 3.1 4.4 + - - +
654C HIS* 2.9 28.2 + - - +
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Residues in contact with SER 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ALA* 4.2 14.5 - - - +
647C LEU 2.9 15.2 + - - -
648C TYR* 3.0 19.6 + - - -
650C SER* 1.3 76.4 - - - +
652C GLU* 1.3 57.4 + - - +
654C HIS* 3.3 3.7 + - - +
655C ARG* 2.7 36.3 + - - +
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Residues in contact with GLU 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648C TYR* 2.7 50.3 + - + +
649C VAL 3.7 1.1 - - - +
651C SER* 1.3 78.1 + - - +
653C LEU* 1.3 62.5 + - - +
655C ARG* 2.7 51.9 + - - +
656C LEU* 3.1 43.6 + - + +
721C LEU* 3.5 32.8 - - + -
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Residues in contact with LEU 653 (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* 4.0 20.0 - - + +
609C GLY 3.5 6.5 - - - -
610C TRP* 3.3 47.6 - - + +
613C TYR* 3.8 17.6 - - + -
649C VAL* 3.0 24.4 + - + +
650C SER 3.5 5.4 - - - +
652C GLU* 1.3 75.9 - - - +
654C HIS* 1.3 65.1 + - - +
656C LEU 3.4 0.9 + - - -
657C GLN* 3.0 18.5 + - - -
658C VAL* 3.1 40.5 + - + -
721C LEU* 3.8 19.3 - - + -
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Residues in contact with HIS 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C TYR* 3.8 25.6 - + + -
617C SER* 3.3 41.4 + - - -
618C ALA* 3.6 10.5 - - + -
650C SER 2.9 13.0 + - - +
651C SER* 3.4 9.4 + - - +
653C LEU* 1.3 77.0 - - - +
655C ARG* 1.3 64.4 + - - +
657C GLN* 3.3 26.5 + - - +
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Residues in contact with ARG 655 (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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651C SER 2.7 20.5 + - - +
652C GLU* 2.7 42.1 + - - +
653C LEU 3.2 0.2 - - - -
654C HIS* 1.3 78.1 - - - +
656C LEU* 1.3 76.4 + - - +
657C GLN* 3.3 2.9 + - - +
717C GLN* 3.1 31.3 + - - +
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Residues in contact with LEU 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C GLU* 3.1 36.0 + - + +
654C HIS 3.4 0.2 - - - -
655C ARG* 1.3 103.1 - - - +
657C GLN* 1.3 60.2 + - - +
658C VAL* 3.8 12.6 - - + -
704C ARG* 4.3 0.9 + - - -
714C ARG* 2.7 46.8 + - - +
717C GLN* 3.7 47.8 - - + +
718C LEU* 4.4 13.0 - - + +
721C LEU* 4.5 7.6 - - + -
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Residues in contact with GLN 657 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C TYR* 3.2 32.0 + - - -
653C LEU 3.0 7.6 + - - -
654C HIS* 3.3 23.7 + - - +
655C ARG 3.3 3.6 - - - +
656C LEU* 1.3 78.6 - - - +
658C VAL* 1.3 67.1 + - - +
659C SER* 3.4 2.9 + - - -
704C ARG* 4.0 16.8 + - - +
714C ARG* 3.4 4.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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