Contacts of the helix formed by residues 633 - 648 (chain C) in PDB entry 6AH0
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 GLY 633 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C ASN* 5.7 3.4 - - - +
588C ILE* 5.9 2.2 - - - +
631C GLY* 3.5 2.8 - - - -
632C THR* 1.3 82.2 + - - +
634C GLU* 1.3 60.8 + - - -
635C LEU 3.5 1.8 - - - -
636C TYR* 3.4 4.9 + - - +
637C LEU* 2.9 26.3 + - - -
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Residues in contact with GLU 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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633C GLY* 1.3 70.0 - - - -
635C LEU* 1.3 57.3 + - - +
637C LEU* 3.1 1.4 + - - +
638C ASP* 2.6 34.7 + - - -
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Residues in contact with LEU 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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633C GLY 3.5 0.2 - - - -
634C GLU* 1.3 75.7 - - - +
636C TYR* 1.3 63.6 + - - +
638C ASP* 5.1 0.9 - - - +
639C CYS* 2.9 21.1 + - - -
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Residues in contact with TYR 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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210C ASN* 5.5 15.0 - - - +
631C GLY* 6.2 0.4 - - - -
632C THR 5.7 2.2 - - - +
633C GLY 3.4 9.8 + - - +
634C GLU 3.1 0.6 - - - -
635C LEU* 1.3 78.5 - - - +
637C LEU* 1.3 57.3 + - - +
639C CYS* 3.2 1.3 + - - +
640C VAL* 2.9 25.8 + - - -
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Residues in contact with LEU 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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631C GLY* 5.7 6.5 - - - -
632C THR 5.6 1.4 - - - +
633C GLY 2.9 15.6 + - - -
634C GLU* 3.6 2.5 - - - +
636C TYR* 1.3 75.3 - - - +
638C ASP* 1.3 65.4 + - - +
640C VAL* 3.2 1.5 + - - +
641C MET* 2.9 21.3 + - - -
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Residues in contact with ASP 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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316A PHE* 5.7 9.2 - - - +
318A TYR* 5.9 0.7 - - - -
319A LEU* 5.7 11.6 + - - +
634C GLU 2.6 20.0 + - - -
635C LEU* 3.9 1.3 - - - +
637C LEU* 1.3 72.2 - - - +
639C CYS* 1.3 63.1 + - - +
641C MET* 3.2 2.2 + - - +
642C HIS* 2.9 21.3 + - - -
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Residues in contact with CYS 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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635C LEU 2.9 17.5 + - - -
636C TYR 3.7 0.9 - - - -
638C ASP* 1.3 76.2 - - - +
640C VAL* 1.3 57.4 + - - +
642C HIS* 3.2 1.8 + - - +
643C ASP* 2.8 27.4 + - - -
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Residues in contact with VAL 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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636C TYR 2.9 14.7 + - - -
637C LEU* 3.2 3.1 + - - +
639C CYS* 1.3 76.3 - - - +
641C MET* 1.3 62.4 + - - +
643C ASP* 3.2 1.6 + - - +
644C LEU* 2.9 21.3 + - - -
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Residues in contact with MET 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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318A TYR* 5.0 14.6 - - - -
319A LEU* 6.2 1.1 - - - +
637C LEU 2.9 13.8 + - - -
638C ASP* 3.7 3.4 - - - +
640C VAL* 1.3 75.7 - - - +
642C HIS* 1.3 64.6 + - - +
644C LEU* 3.2 0.9 + - - -
645C ARG* 2.9 21.1 + - - -
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Residues in contact with HIS 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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318A TYR* 5.5 7.4 - - - +
638C ASP 2.9 13.7 + - - -
639C CYS* 3.7 2.7 - - - +
641C MET* 1.3 76.4 - - - +
643C ASP* 1.3 63.2 + - - +
645C ARG* 3.2 1.7 + - - +
646C LYS* 2.9 22.3 + - - -
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Residues in contact with ASP 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 CYS 2.8 16.1 + - - -
640C VAL 3.7 1.1 - - - -
642C HIS* 1.3 74.9 - - - +
644C LEU* 1.3 57.3 + - - +
647C MET* 2.8 32.4 + - - -
648C TYR 3.8 0.3 + - - -
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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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606C GLY* 5.7 7.0 - - - -
640C VAL 2.9 15.0 + - - -
641C MET* 3.8 2.7 - - - +
643C ASP* 1.3 75.3 - - - +
645C ARG* 1.3 62.8 + - - +
648C TYR* 2.9 27.5 + - - +
649C SER* 3.1 10.8 + - - -
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Residues in contact with ARG 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 MET 2.9 14.1 + - - -
642C HIS* 3.7 2.5 - - - +
644C LEU* 1.3 77.4 - - - +
646C LYS* 1.3 58.1 + - - +
649C SER 3.0 21.4 - - - +
650C GLU* 4.8 4.0 - - - +
651C ILE 5.4 4.4 - - - +
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Residues in contact with LYS 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 HIS 2.9 14.7 + - - -
643C ASP* 5.4 0.2 - - - +
645C ARG* 1.3 77.3 - - - +
647C MET* 1.3 56.5 + - - +
649C SER 5.4 0.7 - - - -
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Residues in contact with MET 647 (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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485C ASP 4.7 9.9 - - - +
487C GLY 6.0 2.1 - - - -
643C ASP 2.8 14.5 + - - -
646C LYS* 1.3 80.7 - - - +
648C TYR* 1.3 57.2 + - - +
649C SER 4.0 0.2 - - - -
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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
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488C VAL* 6.5 1.6 - - - +
602C LYS 5.5 0.2 - - - +
606C GLY* 4.6 17.2 + - - -
643C ASP 3.8 2.0 + - - -
644C LEU* 2.9 11.1 + - - +
647C MET* 1.3 79.4 - - - +
649C SER* 1.3 60.0 + - - +
650C GLU 4.3 0.4 + - - -
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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