Contacts of the helix formed by residues 636 - 644 (chain C) in PDB entry 1JPW
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 ALA 636 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600C VAL* 3.4 20.2 - - + -
603C LEU* 3.9 9.4 - - + -
618C LEU* 4.7 1.3 - - + -
631C ILE* 3.3 38.2 + - + +
632C GLU 4.2 0.4 + - - -
634C GLU 3.5 1.0 - - - -
635C GLY* 1.3 75.2 - - - +
637C THR* 1.3 59.9 + - - +
639C PRO* 3.4 10.7 - - - +
640C LEU* 2.8 37.2 + - + +
662C MET* 4.8 4.5 - - + -
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Residues in contact with THR 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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632C GLU* 3.8 22.9 + - - +
635C GLY* 3.1 2.6 - - - -
636C ALA* 1.3 76.4 - - - +
638C ALA* 1.3 72.9 + - - +
640C LEU* 3.1 2.9 + - - +
641C THR* 2.9 29.6 + - - +
659C LEU* 4.0 20.7 - - + +
662C MET* 4.2 14.7 - - - -
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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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604C TYR* 4.8 4.7 - - + +
635C GLY* 3.7 4.8 + - - +
637C THR* 1.3 82.6 - - - +
639C PRO* 1.3 71.5 - - + +
641C THR* 3.0 20.6 + - - +
642C GLU* 3.5 6.2 + - - +
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Residues in contact with PRO 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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603C LEU* 3.9 24.9 - - + +
604C TYR* 3.6 39.2 - - + +
635C GLY 2.8 29.6 - - - +
636C ALA* 3.4 15.7 - - - +
637C THR 3.6 0.2 - - - -
638C ALA* 1.3 85.1 - - + +
640C LEU* 1.3 62.2 + - - +
642C GLU* 3.4 7.6 + - + +
643C LEU* 3.1 28.0 + - - +
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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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603C LEU* 4.2 19.3 - - + -
615C ALA* 4.5 9.0 - - + -
618C LEU* 5.5 0.2 - - + -
636C ALA* 2.8 25.8 - - + +
637C THR 3.1 4.3 + - - +
639C PRO* 1.3 79.6 - - - +
641C THR* 1.3 65.4 + - - +
643C LEU* 2.8 9.5 + - + +
644C LEU* 2.8 24.4 + - - +
655C ALA* 3.7 26.1 - - + +
658C VAL* 3.3 42.2 - - + -
659C LEU* 3.4 33.7 - - + +
662C MET* 4.5 2.2 - - + -
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Residues in contact with THR 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 THR* 2.9 23.9 + - - +
638C ALA* 3.0 13.9 + - - +
640C LEU* 1.3 75.5 - - - +
642C GLU* 1.3 59.5 + - - +
644C LEU* 3.1 35.1 - - + +
645C HIS* 3.3 15.9 + - - +
659C LEU* 4.4 5.8 - - - +
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Residues in contact with GLU 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 ALA 3.5 5.5 + - - +
639C PRO* 3.4 9.1 + - + +
640C LEU 3.2 0.6 - - - -
641C THR* 1.3 76.9 - - - +
643C LEU* 1.3 63.8 + - + +
644C LEU 3.0 5.8 + - - -
645C HIS* 3.1 24.4 + - - +
646C SER* 4.1 1.9 + - - -
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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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603C LEU* 3.7 42.2 - - + +
611C GLN* 3.2 41.5 - - + +
615C ALA* 5.5 2.2 - - + -
639C PRO 3.1 18.2 + - - +
640C LEU* 2.8 14.9 + - + +
642C GLU* 1.3 76.0 - - + +
644C LEU* 1.3 63.5 + - - +
645C HIS 3.1 1.2 + - - -
646C SER* 3.2 22.5 + - - +
651C VAL* 3.6 19.5 - - + -
652C ALA* 3.6 11.6 + - - -
655C ALA* 4.0 8.1 - - + -
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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 2.8 7.9 + - - +
641C THR* 3.1 23.3 - - + +
642C GLU 3.0 0.4 - - - -
643C LEU* 1.3 79.7 - - - +
645C HIS* 1.3 70.7 + - + +
646C SER 3.4 1.1 + - - -
652C ALA* 3.8 15.6 - - - +
655C ALA* 4.3 3.6 - - - -
656C ALA* 3.6 40.2 - - + +
659C LEU* 3.5 28.5 - - + -
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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