Contacts of the helix formed by residues 603 - 608 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B MET* 4.1 17.4 - - + +
566B GLU* 3.5 25.9 + - + +
567B ARG* 5.4 4.6 - - + +
602B SER* 1.3 77.5 - - - +
604B SER* 1.3 59.7 + - - +
605B GLY 3.3 0.4 - - - -
606B LYS* 2.7 51.2 + - - +
607B ASP* 3.4 6.6 + - - +
772B LEU 4.8 0.6 - - - +
773B ARG* 4.3 16.2 + - - -
774B ALA* 3.7 21.1 + - - -
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Residues in contact with SER 604 (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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566B GLU* 2.9 19.7 + - - +
568B LEU* 4.9 2.3 + - - +
571B LEU* 3.1 32.2 - - - +
600B GLY 3.0 25.5 + - - -
601B TYR* 3.7 6.3 - - - -
603B ASP* 1.3 78.9 - - - +
605B GLY* 1.3 58.4 + - - +
606B LYS 3.1 1.2 + - - -
607B ASP* 2.8 23.8 - - - +
608B ALA* 3.8 2.3 + - - +
613B ALA* 3.7 12.2 - - - +
617B LEU* 4.3 8.6 - - - +
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Residues in contact with GLY 605 (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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601B TYR 3.1 14.0 + - - -
602B SER 4.3 2.7 - - - -
604B SER* 1.3 75.1 - - - +
606B LYS* 1.3 55.3 + - - +
608B ALA 2.7 25.2 - - - +
609B GLY 4.3 5.4 - - - -
610B ARG* 4.1 14.7 + - - -
613B ALA* 3.6 13.8 - - - +
646B GLY 5.2 2.2 - - - -
728B TYR* 3.8 6.9 + - - -
777B TRP* 5.3 1.8 + - - -
789B PRO* 4.9 5.9 - - - +
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Residues in contact with LYS 606 (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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602B SER 3.8 13.4 + - - +
603B ASP* 2.7 38.3 + - - +
604B SER 3.0 0.6 - - - -
605B GLY* 1.3 77.2 - - - +
607B ASP* 1.3 61.4 + - - +
728B TYR* 2.7 24.7 + - - -
732B VAL* 5.5 0.9 - - - +
769B ILE 5.4 1.6 - - - -
770B THR* 4.2 27.4 + - - +
772B LEU* 3.7 27.1 + - - -
773B ARG 4.2 7.2 - - - -
774B ALA* 4.5 4.7 - - - -
777B TRP* 3.1 41.0 + - + +
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Residues in contact with ASP 607 (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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567B ARG* 3.8 13.0 - - + +
568B LEU* 2.9 36.5 + - - +
569B ALA* 4.4 1.0 + - - +
603B ASP 3.4 4.0 + - - +
604B SER 2.8 20.8 - - - +
606B LYS* 1.3 77.2 - - - +
608B ALA* 1.3 79.6 + - - +
728B TYR* 3.0 17.7 - - - -
729B ARG* 3.5 21.0 - - - +
733B VAL* 5.3 3.3 - - - +
770B THR* 6.0 7.4 - - + -
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Residues in contact with ALA 608 (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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568B LEU* 3.3 37.5 - - + -
604B SER 4.4 2.7 - - - +
605B GLY* 2.7 30.3 - - - +
607B ASP* 1.3 87.3 + - - +
609B GLY* 1.3 65.8 + - - +
612B SER* 4.1 13.0 - - - -
613B ALA* 4.5 2.7 - - + +
725B THR* 4.2 9.4 - - + +
728B TYR* 3.4 4.5 - - - -
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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