Contacts of the helix formed by residues 161 - 166 (chain J) in PDB entry 7C97
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 LEU 161 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J ILE* 3.4 28.9 - - + -
110J TRP* 4.6 9.6 - - + -
149J PHE* 4.9 22.7 - - + -
157J VAL* 3.1 29.2 - - + +
158J ASP* 2.9 9.6 + - - +
160J TYR* 1.3 78.3 - - - +
162J ALA* 1.3 55.9 + - - +
164J LEU* 2.7 22.6 + - + -
165J LEU* 2.5 53.5 + - + +
186J TYR* 4.3 15.9 - - + +
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Residues in contact with ALA 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ILE* 5.6 4.0 - - + -
154J PHE* 5.4 5.2 - - + -
158J ASP 3.1 12.2 + - - +
159J CYS* 5.3 1.1 - - - -
161J LEU* 1.3 77.8 - - - +
163J PRO* 1.3 67.7 - - + +
165J LEU* 3.7 1.1 + - - -
166J TRP* 3.3 21.3 + - - +
186J TYR* 5.2 2.8 + - - +
190J VAL* 4.6 21.1 - - + -
191J PHE* 3.9 24.4 - - + -
196J PHE* 4.1 18.7 - - + -
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Residues in contact with PRO 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 3.2 30.6 - - + +
23J HIS* 3.8 47.5 + - + +
24J GLN* 4.2 2.7 - - + +
27J ILE* 4.0 13.0 - - + -
159J CYS 3.0 28.3 - - - +
160J TYR 4.3 0.4 - - - -
161J LEU 3.8 0.7 - - - +
162J ALA* 1.3 92.6 - - + +
164J LEU* 1.3 56.7 + - - +
166J TRP* 4.0 4.2 + - + +
167J ARG* 3.2 23.2 + - - +
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Residues in contact with LEU 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ILE* 3.3 10.3 - - + +
106J ILE* 4.2 4.9 - - + -
110J TRP* 3.4 38.1 - - + -
111J TYR* 4.1 7.2 - - + +
114J MET* 3.4 38.8 - - + -
160J TYR 3.1 19.0 + - - +
161J LEU* 2.7 32.5 + - + +
163J PRO* 1.3 71.8 - - - +
165J LEU* 1.3 73.1 + - + +
167J ARG* 3.1 17.3 + - + +
168J LEU* 4.2 8.5 + - + +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J TRP* 6.2 2.5 - - + -
136J LEU* 6.5 1.1 - - + -
161J LEU* 2.5 58.1 + - + +
162J ALA* 4.9 0.2 - - - -
164J LEU* 1.3 78.5 - - + +
166J TRP* 1.3 49.7 + - - +
167J ARG 3.0 1.6 + - - -
168J LEU* 3.0 40.0 - - + +
175J PHE* 5.2 3.4 - - + -
183J LEU* 4.9 12.3 - - + -
186J TYR* 4.6 11.2 - - + -
187J MET* 3.8 21.8 - - + -
191J PHE* 3.8 20.9 - - + -
208J ARG* 2.3 30.0 + - - -
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Residues in contact with TRP 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J HIS* 4.6 6.5 - + + -
162J ALA 3.3 15.3 + - - +
163J PRO* 4.1 9.0 - - + +
164J LEU 3.1 1.2 - - - -
165J LEU* 1.3 76.9 - - - +
167J ARG* 1.3 60.8 + - - +
168J LEU 3.4 0.7 - - - -
169J PRO* 4.2 3.8 - - - +
191J PHE* 3.4 37.6 - + + -
196J PHE* 3.3 28.7 - + + -
200J LEU* 3.3 26.9 - - + +
204J GLU* 2.3 39.8 + - + +
205J ARG* 4.1 19.8 + - + +
207J MET* 4.2 19.7 - - - +
208J ARG* 3.4 26.1 + - + +
210J GLY* 4.2 27.6 - - - -
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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