Contacts of the helix formed by residues 745 - 749 (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 GLY 745 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TRP* 3.5 22.4 - - - -
366A ILE* 4.0 2.9 - - - +
399A FAD 2.9 51.0 + - - +
743B LEU 3.4 0.4 + - - -
744B GLY* 1.3 70.6 - - - -
746B MET* 1.3 61.6 + - - +
747B GLY 3.1 1.2 + - - -
748B TYR* 3.1 17.3 + - - +
749B VAL 4.0 1.4 + - - -
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Residues in contact with MET 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TRP* 3.7 25.2 - - + -
399A FAD 4.6 0.4 + - - -
669B TYR* 3.6 26.7 - - + +
673B ARG* 6.3 0.2 - - - +
743B LEU* 3.4 14.9 + - + +
744B GLY 3.2 1.0 - - - -
745B GLY* 1.3 76.0 - - - +
747B GLY* 1.3 59.4 + - - +
748B TYR 3.3 0.4 - - - -
749B VAL* 3.4 17.5 + - - +
751B GLU* 3.8 26.5 - - + +
752B MET* 3.5 50.5 - - + +
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Residues in contact with GLY 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B ILE* 3.6 35.9 - - - +
743B LEU* 3.6 22.5 - - - +
744B GLY 2.9 11.2 + - - -
746B MET* 1.3 79.5 - - - +
748B TYR* 1.3 59.3 + - - +
749B VAL 3.4 1.6 - - - -
754B ALA* 4.4 4.0 - - - -
755B GLU* 3.7 16.5 + - - +
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Residues in contact with TYR 748 (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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206A LYS* 3.3 19.4 - - + +
207A LEU* 2.8 49.7 + - + +
208A GLY* 2.8 40.2 - - - -
209A ILE* 3.9 2.8 + - + -
359A ARG 2.7 29.0 + - - -
360A ASP* 3.9 1.7 - - - -
362A ARG* 3.9 14.6 - - + -
363A ILE* 3.5 51.8 - - + +
366A ILE* 4.6 9.6 - - + -
399A FAD 4.1 16.6 - - + -
740B ILE* 5.3 0.7 - - + -
744B GLY 3.9 0.8 + - - -
745B GLY 3.1 11.4 + - - +
747B GLY* 1.3 79.5 - - - +
749B VAL* 1.3 62.0 + - + +
755B GLU* 4.7 1.5 - - - +
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Residues in contact with VAL 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TRP* 3.7 25.6 - - + -
204A GLU* 4.3 17.3 - - + +
205A ASP 3.3 13.2 - - - +
206A LYS* 4.3 6.7 - - + -
399A FAD 5.8 1.1 - - + -
745B GLY 4.3 1.6 - - - +
746B MET* 3.4 32.0 - - - +
747B GLY 4.6 1.2 - - - -
748B TYR* 1.3 86.9 - - + +
750B THR* 1.3 61.3 + - - +
751B GLU* 3.1 37.0 + - + +
752B MET* 3.3 14.2 + - - +
755B GLU* 3.9 7.1 - - - +
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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