Contacts of the helix formed by residues 603 - 608 (chain A) in PDB entry 1JQO
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 603 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLU* 3.7 23.5 - - + +
567A ARG* 3.6 32.7 + - - -
602A SER* 1.3 78.4 - - - +
604A SER* 1.3 65.9 + - - +
605A GLY 3.3 0.2 - - - -
606A LYS* 2.9 43.6 + - - +
607A ASP* 2.8 17.9 + - - +
774A ALA* 4.6 8.1 + - - +
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Residues in contact with SER 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLU 3.4 13.8 + - - -
568A LEU* 4.1 9.6 - - - +
571A LEU* 3.6 20.0 - - - -
600A GLY 2.5 31.2 + - - -
601A TYR* 3.5 8.1 - - - -
602A SER 3.3 0.2 - - - -
603A ASP* 1.3 71.9 - - - +
605A GLY* 1.3 57.5 + - - +
607A ASP* 2.5 21.0 - - - +
608A ALA* 3.8 8.5 + - - +
613A ALA* 3.6 18.5 - - - +
617A LEU* 4.0 8.2 - - - +
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Residues in contact with GLY 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A SER 3.8 6.0 + - - -
603A ASP 3.3 0.2 - - - -
604A SER* 1.3 77.9 - - - +
606A LYS* 1.3 56.8 + - - +
608A ALA 2.6 20.5 - - - +
609A GLY 3.4 11.4 - - - +
610A ARG* 4.3 14.3 + - - +
613A ALA* 3.3 20.0 - - - +
646A GLY 5.9 1.1 - - - -
728A TYR* 3.6 10.0 + - - -
777A TRP* 5.3 0.5 + - - -
789A PRO* 5.4 2.3 - - - +
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Residues in contact with LYS 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ARG* 3.7 18.1 - - - +
602A SER 3.8 4.6 + - - +
603A ASP* 2.9 37.8 + - - +
605A GLY* 1.3 79.4 - - - +
607A ASP* 1.3 61.7 + - - +
728A TYR* 3.0 24.5 + - - -
732A VAL* 5.3 0.7 - - - +
770A THR 4.0 6.7 + - - -
771A THR* 3.9 13.3 + - - +
772A LEU 2.9 34.0 + - - +
773A ARG 4.2 8.1 - - - +
774A ALA* 4.0 13.0 - - + -
777A TRP* 3.7 35.0 - - + +
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Residues in contact with ASP 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A ARG* 3.2 32.4 + - - +
568A LEU* 3.2 33.1 + - - +
569A ALA 4.7 0.3 + - - -
603A ASP 2.8 9.2 - - - +
604A SER 2.5 26.0 - - - +
606A LYS* 1.3 74.7 - - - +
608A ALA* 1.3 55.1 + - - +
728A TYR* 4.6 3.5 - - - -
729A ARG* 3.3 29.6 - - - +
732A VAL* 6.2 0.2 - - - -
733A VAL* 5.2 3.8 - - - +
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Residues in contact with ALA 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A LEU* 3.6 26.7 - - + -
604A SER 3.8 8.4 + - - +
605A GLY 2.6 29.0 - - - +
607A ASP* 1.3 80.1 + - - +
609A GLY* 1.3 63.6 + - - +
612A SER* 4.3 5.6 - - - -
613A ALA 5.0 0.9 - - - +
725A THR* 3.6 27.4 - - + +
728A TYR* 3.3 13.3 - - - -
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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