Contacts of the helix formed by residues 631 - 635 (chain B) in PDB entry 2JED
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 HIS 631 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605B GLU* 3.0 31.2 - - - -
608B ASP* 2.8 26.8 + - + -
609B LEU* 3.3 30.7 + - + +
612B LYS* 4.1 18.8 - - + -
622B LEU* 4.4 6.1 - - + -
627B ASP 3.8 2.1 + - - +
628B ILE* 3.3 18.3 + - - +
629B ARG 3.2 2.6 - - - -
630B GLN* 1.3 79.5 - - - +
632B PRO* 1.4 73.2 - - + +
633B LEU* 3.1 28.6 + - - +
634B PHE* 2.9 32.7 + - + +
635B ARG 3.5 3.1 + - - -
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Residues in contact with PRO 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B GLU* 4.1 14.6 - - + -
608B ASP* 5.2 2.5 - - - +
630B GLN 3.5 5.4 - - - +
631B HIS* 1.4 99.0 - - + +
633B LEU* 1.3 63.5 + - - +
634B PHE 3.1 0.2 - - - -
635B ARG* 3.1 52.4 + - + +
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LEU* 4.3 11.7 - - + -
482B THR* 3.5 38.4 - - + +
485B ALA* 5.5 0.2 - - + -
569B LEU* 4.5 16.2 - - + -
573B LEU* 5.5 1.1 - - + -
603B GLU* 6.2 0.4 - - + -
605B GLU* 4.0 10.4 - - + +
606B ALA* 4.0 34.3 - - + +
609B LEU* 3.6 26.2 - - + -
631B HIS* 3.0 23.3 + - + +
632B PRO* 1.3 77.2 - - - +
634B PHE* 1.3 69.3 + - + +
635B ARG* 3.4 1.1 + - - +
636B GLU* 4.9 2.1 + - - +
637B ILE* 4.7 0.7 - - - +
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Residues in contact with PHE 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B THR* 3.7 34.8 - - + -
485B ALA* 4.1 12.1 - - + -
486B ALA* 3.9 14.8 - - + -
489B ILE* 3.4 30.5 - - + -
565B PHE* 4.9 0.2 - + - -
609B LEU* 3.7 31.0 - - + -
628B ILE* 3.4 24.5 - - + -
629B ARG 3.8 7.0 - - - +
631B HIS* 2.9 15.0 + - + +
633B LEU* 1.3 79.4 - - + +
635B ARG* 1.3 65.0 + - - +
636B GLU 3.1 3.8 - - - -
637B ILE* 2.9 33.8 + - + +
639B TRP* 3.7 22.4 + + + -
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Residues in contact with ARG 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A LYS* 5.3 7.3 - - - +
605B GLU* 3.2 37.4 + - - +
631B HIS 3.5 4.7 + - - -
632B PRO* 3.1 37.8 + - + +
633B LEU 3.4 1.3 - - - +
634B PHE* 1.3 75.3 - - - +
636B GLU* 1.3 68.3 + - + +
637B ILE 3.7 3.1 + - - +
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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