Contacts of the helix formed by residues 631 - 638 (chain G) in PDB entry 5JLH
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 ASP 631 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367G ARG* 5.2 9.8 + - - -
402G ARG 4.9 2.3 - - - +
403G LEU 4.0 17.8 - - - +
404G LEU* 4.1 12.1 - - - +
405G GLY 4.9 0.4 - - - +
629G SER* 3.5 1.6 - - - -
630G THR* 1.3 98.8 - - - +
632G ARG* 1.3 65.3 + - - +
633G LEU* 3.5 6.0 + - + +
634G THR* 3.9 14.9 - - + +
635G ALA* 3.4 21.8 + - - +
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Residues in contact with ARG 632 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360G GLU* 3.2 42.9 + - - +
361G GLU* 5.5 5.3 - - - +
364G SER* 4.6 10.1 + - - -
630G THR 3.6 3.1 + - - +
631G ASP* 1.3 72.8 - - - +
633G LEU* 1.3 67.8 + - + +
635G ALA* 4.0 2.1 - - - +
636G GLU* 2.9 29.1 + - + +
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Residues in contact with LEU 633 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G GLU* 5.4 2.5 - - + +
364G SER* 3.4 53.2 - - - +
365G MET* 3.6 12.3 - - + +
368G MET* 4.4 15.7 - - + -
451G LEU* 5.8 0.7 - - + -
454G TRP* 3.6 42.4 - - + +
631G ASP* 3.3 4.3 - - + +
632G ARG* 1.3 82.6 - - - +
634G THR* 1.3 60.0 + - - +
636G GLU* 3.2 6.0 + - - +
637G ILE* 2.9 38.3 + - + +
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Residues in contact with THR 634 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G MET* 5.1 10.9 - - - +
404G LEU* 3.8 32.1 - - + +
405G GLY 4.9 0.7 - - - +
626G LEU* 4.6 3.9 - - - +
629G SER* 3.3 28.7 + - - +
631G ASP* 3.9 15.0 - - + +
633G LEU* 1.3 79.6 - - - +
635G ALA* 1.3 74.9 + - - +
637G ILE* 3.0 19.6 + - - +
638G TRP* 3.1 38.6 + - - -
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Residues in contact with ALA 635 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626G LEU 3.6 14.8 - - - +
627G HIS* 4.3 13.8 + - - +
629G SER* 3.4 24.5 - - - +
631G ASP 3.4 17.7 + - - +
632G ARG* 3.6 2.4 + - - +
633G LEU 3.3 0.6 - - - -
634G THR* 1.3 81.3 - - - +
636G GLU* 1.3 63.8 + - - +
638G TRP* 3.3 16.6 + - - +
639G LYS* 4.0 4.3 + - - +
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Residues in contact with GLU 636 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454G TRP* 2.9 44.3 + - - -
632G ARG* 2.9 21.9 + - + +
633G LEU* 3.4 8.7 - - - +
635G ALA* 1.3 77.4 - - - +
637G ILE* 1.3 73.6 + - - +
639G LYS* 3.3 32.3 - - + +
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Residues in contact with ILE 637 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G MET* 3.4 35.4 - - + -
450G ARG* 3.2 46.6 + - + +
451G LEU* 4.2 10.8 - - + +
454G TRP* 4.0 19.3 - - + -
633G LEU* 2.9 32.2 + - + +
634G THR* 3.0 10.3 + - - +
636G GLU* 1.3 87.5 - - - +
638G TRP* 1.3 64.8 + - + +
639G LYS* 2.9 6.9 + - - +
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Residues in contact with TRP 638 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368G MET* 5.4 1.8 - - - +
443G LEU* 4.4 12.1 - - + -
446G ALA* 4.0 24.0 - - + -
447G THR* 3.4 32.6 + - - +
450G ARG* 3.1 48.9 - - + +
618G LEU* 4.6 11.4 - - + -
623G ALA* 4.7 16.4 - - + +
626G LEU* 3.2 47.2 - - + +
627G HIS* 3.2 25.1 + - + +
634G THR* 3.1 39.7 + - - +
635G ALA 3.3 7.1 + - - +
636G GLU 3.3 1.0 - - - -
637G ILE* 1.3 80.0 - - + +
639G LYS* 1.3 55.5 + - - +
640G ASP* 3.1 15.6 + - + +
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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