Contacts of the helix formed by residues 432 - 440 (chain B) in PDB entry 1JQI
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 ILE 432 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428B GLU 3.3 21.5 - - - +
429B LEU* 3.0 15.3 + - + +
431B PRO* 1.3 87.1 - - + +
433B ALA* 1.3 67.0 + - - +
434B ALA 3.2 2.9 - - - -
435B GLN* 3.1 23.3 + - - +
436B LEU* 3.0 45.1 + - + +
446B GLN* 3.6 33.0 - - + +
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Residues in contact with ALA 433 (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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429B LEU 2.9 9.6 + - - +
430B VAL* 3.5 8.4 + - - +
432B ILE* 1.3 77.5 - - - +
434B ALA* 1.3 62.8 + - - +
436B LEU* 3.4 12.4 + - - +
437B ASP* 3.1 23.4 + - - +
484B GLY 3.5 19.7 - - - +
485B CYS* 4.4 9.3 - - + -
756B ARG* 3.5 32.6 - - - +
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Residues in contact with ALA 434 (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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430B VAL 4.8 1.4 + - - -
431B PRO 5.3 2.4 + - - +
432B ILE 3.2 1.2 - - - -
433B ALA* 1.3 79.0 - - - +
435B GLN* 1.3 58.0 + - - +
437B ASP* 3.4 5.6 + - - +
438B LYS* 3.0 30.1 + - - +
750B THR 5.9 3.1 - - - +
756B ARG* 4.0 14.1 - - - +
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Residues in contact with GLN 435 (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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432B ILE* 3.1 26.2 + - - +
434B ALA* 1.3 76.0 - - - +
436B LEU* 1.3 64.4 + - + +
438B LYS* 4.4 5.2 - - - -
439B GLU* 2.8 64.1 + - - +
441B LEU* 4.2 14.1 - - + +
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Residues in contact with LEU 436 (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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429B LEU* 5.6 1.6 - - + -
432B ILE* 3.0 42.3 + - + +
433B ALA* 3.7 7.4 - - - +
435B GLN* 1.3 78.3 - - + +
437B ASP* 1.3 57.9 + - - +
440B HIS* 2.8 27.9 + - - -
441B LEU* 3.0 43.4 + - + +
443B PRO* 3.9 32.5 - - + -
446B GLN* 5.7 0.2 - - - +
485B CYS* 4.0 26.0 - - + -
488B THR* 4.5 1.6 - - - +
611B ALA* 3.9 16.5 - - + +
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Residues in contact with ASP 437 (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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433B ALA 3.1 14.4 + - - +
434B ALA* 3.7 5.4 - - - +
436B LEU* 1.3 78.6 - - - +
438B LYS* 1.3 66.0 + - - +
440B HIS* 3.0 26.0 - - - -
610B ARG* 3.5 35.5 + - - +
611B ALA* 4.7 4.2 - - - +
756B ARG* 3.9 19.8 - - - +
759B ARG* 3.0 43.3 + - - -
760B ASP* 4.7 2.6 - - - +
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Residues in contact with LYS 438 (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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40A HIS* 6.1 0.6 - - - -
205A ASP* 3.8 31.5 + - - -
210A ARG* 5.7 5.1 - - - +
434B ALA 3.0 18.8 + - - +
435B GLN* 3.8 5.6 - - - +
437B ASP* 1.3 86.9 + - - +
439B GLU* 1.3 63.8 + - + +
440B HIS* 3.6 10.7 + - - -
610B ARG* 3.9 17.2 + - - +
750B THR* 4.0 15.9 - - + +
759B ARG* 6.1 0.6 - - - +
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Residues in contact with GLU 439 (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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435B GLN* 2.8 53.3 + - + +
438B LYS* 1.3 76.0 - - + +
440B HIS* 1.3 74.5 + - - +
441B LEU* 3.2 21.1 + - + +
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Residues in contact with HIS 440 (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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38A LYS* 5.8 3.8 - - - -
436B LEU 2.8 10.8 + - - -
437B ASP 3.0 18.6 - - - -
438B LYS 3.6 7.6 + - - -
439B GLU* 1.3 80.3 - - - +
441B LEU* 1.3 60.7 + - - +
442B PHE 3.8 1.6 + - - -
603B LYS* 5.1 9.5 + - + +
605B ASP* 3.6 25.2 + - - -
606B LYS 6.0 0.2 - - - -
610B ARG* 2.6 62.1 + - + +
611B ALA* 4.2 1.8 - - - +
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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