Contacts of the helix formed by residues 624 - 633 (chain B) 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 ASP 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B VAL* 5.8 3.5 - - - +
587B ARG* 5.4 4.9 + - - -
591B ARG* 2.8 34.8 + - - -
621B LEU 3.4 11.5 + - - +
622B ALA 3.0 11.2 - - - +
623B GLN* 1.3 84.9 - - - +
625B LYS* 1.3 63.0 + - - +
626B GLU* 4.3 2.2 + - - +
627B ALA* 4.1 16.2 - - + +
628B ALA* 3.2 12.6 - - - +
661B ARG 4.8 0.7 - - - +
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Residues in contact with LYS 625 (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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624B ASP* 1.3 77.3 + - - +
626B GLU* 1.3 66.8 + - + +
628B ALA* 4.2 1.5 - - - +
629B GLU* 3.1 38.3 + - - +
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Residues in contact with GLU 626 (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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591B ARG* 5.4 10.2 + - - +
624B ASP* 4.3 2.8 + - + +
625B LYS* 1.3 78.7 - - + +
627B ALA* 1.3 60.6 + - - +
629B GLU* 3.1 7.3 + - - +
630B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 627 (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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591B ARG* 4.0 27.2 - - + +
596B ILE* 3.8 16.2 - - + +
621B LEU* 3.5 26.0 - - + +
624B ASP* 4.1 10.0 - - + +
626B GLU* 1.3 78.5 - - - +
628B ALA* 1.3 63.3 + - - +
630B ALA* 3.0 5.1 + - - +
631B ILE* 2.9 29.7 + - - +
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Residues in contact with ALA 628 (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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622B ALA* 3.1 40.5 - - + +
624B ASP 3.2 12.7 + - - +
625B LYS* 4.2 3.1 - - - +
626B GLU 3.3 0.4 - - - -
627B ALA* 1.3 78.9 - - - +
629B GLU* 1.3 64.1 + - + +
631B ILE* 3.5 4.2 + - - +
632B GLU 3.3 15.8 + - - -
661B ARG 3.4 15.9 - - - +
662B MET* 3.6 22.7 - - - +
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Residues in contact with GLU 629 (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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625B LYS* 3.1 27.3 + - - +
626B GLU* 3.1 7.3 + - - +
628B ALA* 1.3 78.4 - - + +
630B ALA* 1.3 60.4 + - - +
631B ILE 3.3 0.2 - - - -
632B GLU* 3.6 9.5 - - + +
633B ALA* 3.1 24.3 + - - +
662B MET* 5.3 7.9 - - - +
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Residues in contact with ALA 630 (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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596B ILE* 4.5 13.3 - - + +
626B GLU 2.9 12.7 + - - +
627B ALA* 3.0 12.1 + - - +
629B GLU* 1.3 76.0 - - - +
631B ILE* 1.3 60.5 + - - +
633B ALA* 3.4 8.1 + - - +
634B GLU* 3.0 26.5 + - - +
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Residues in contact with ILE 631 (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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596B ILE* 3.6 24.9 - - + -
600B VAL* 3.9 11.0 - - + -
618B LEU* 3.5 30.3 - - + +
621B LEU* 5.0 1.3 - - + -
622B ALA* 3.6 34.8 - - + +
627B ALA 2.9 15.0 - - - +
628B ALA* 3.6 2.2 - - - +
630B ALA* 1.3 75.3 - - - +
632B GLU* 1.3 61.1 + - - +
634B GLU* 2.8 22.1 + - - +
635B GLY 3.2 4.9 + - - -
636B ALA* 3.3 28.7 + - + -
658B VAL* 4.7 0.9 - - + -
662B MET* 3.4 17.0 - - + -
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Residues in contact with GLU 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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628B ALA 3.3 11.1 + - - +
629B GLU* 3.6 13.9 - - + +
631B ILE* 1.3 79.0 - - - +
633B ALA* 1.3 61.8 + - - +
634B GLU 2.8 6.4 + - - -
635B GLY* 2.9 16.1 + - - -
636B ALA 4.9 0.2 - - - +
637B THR* 3.7 21.7 + - - +
662B MET* 4.0 21.2 - - + +
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Residues in contact with ALA 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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629B GLU 3.1 13.9 + - - +
630B ALA* 3.6 10.3 - - - +
631B ILE 3.3 0.4 - - - -
632B GLU* 1.3 84.4 - - - +
634B GLU* 1.3 60.0 + - - +
635B GLY 3.4 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