Contacts of the helix formed by residues 168 - 171 (chain A) in PDB entry 7JDW
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 PRO 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.8 11.9 - - + +
80A VAL 4.0 1.6 - - - -
81A GLY* 3.4 19.3 - - - +
166A ALA 3.1 13.9 - - - +
167A MET* 1.3 82.4 - - - +
169A ARG* 1.3 56.4 + - - +
171A ILE* 3.2 2.8 + - - +
172A LEU* 2.9 33.2 + - + +
196A TYR* 3.4 32.1 - - + +
407A CYS 3.5 0.9 - - - +
408A TRP 3.2 22.2 - - - +
409A THR 3.8 2.2 - - - -
410A CYS* 3.7 22.2 - - + -
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Residues in contact with ARG 169 (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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71A GLU* 3.7 7.7 + - - -
167A MET 3.1 0.8 + - - -
168A PRO* 1.3 79.1 - - - +
170A ASP* 1.3 62.8 + - - +
171A ILE 3.5 0.2 + - - -
172A LEU 3.8 11.6 + - - +
255A ALA* 3.6 9.0 - - - +
256A ALA* 3.2 29.1 + - + +
258A PHE 5.9 2.2 - - - -
260A ARG* 3.8 5.7 - - - +
305A ASP* 3.8 17.5 - - - +
363A LEU* 4.1 8.1 - - - +
406A HIS* 2.8 62.9 + - + +
407A CYS* 3.3 10.7 + - - +
409A THR* 3.1 36.9 + - - +
410A CYS* 4.0 5.3 - - - +
411A ASP* 2.7 32.9 + - - +
414A ARG* 5.4 0.2 - - - +
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Residues in contact with ASP 170 (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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164A TYR* 4.7 1.0 + - - -
167A MET* 3.1 27.2 + - - +
169A ARG* 1.3 79.7 - - - +
171A ILE* 1.3 58.6 + - + +
184A MET* 3.7 8.2 - - + +
189A ARG* 2.8 45.5 + - - +
254A ASP* 3.6 7.8 - - - -
255A ALA 2.8 22.2 + - - -
256A ALA* 3.7 10.9 - - - +
302A MET* 5.4 0.5 - - - +
303A HIS* 3.1 32.9 + - + +
407A CYS* 4.9 0.3 - - - +
500A DAV 3.7 8.1 + - - -
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Residues in contact with ILE 171 (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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167A MET 4.0 8.3 - - - +
168A PRO 3.6 7.6 - - - +
170A ASP* 1.3 80.3 - - - +
172A LEU* 1.3 70.5 + - + +
180A ILE 3.4 0.5 - - - +
181A GLU* 3.4 4.8 - - + -
182A ALA* 2.7 41.9 + - - +
184A MET* 3.9 25.1 - - + -
192A GLU* 4.0 17.9 - - + +
193A TYR* 3.5 43.7 - - + +
196A TYR* 3.7 26.2 - - + +
215A LYS* 5.6 0.9 - - - +
255A ALA* 4.1 3.1 - - - -
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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