Contacts of the helix formed by residues 150 - 156 (chain X) in PDB entry 2W6C
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 VAL 150 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67X CYS* 4.7 7.2 - - + +
68X GLN 3.6 20.4 + - - +
69X GLN* 3.8 11.7 - - + +
116X TYR* 4.2 5.6 - - + +
120X PHE* 3.2 16.2 - - - +
121X TYR 3.5 16.6 - - - +
122X SER* 3.6 25.8 - - - +
123X GLY 5.5 0.2 - - - +
148X TYR* 3.5 27.1 + - + +
149X ARG* 1.3 77.1 - - - +
151X GLY* 1.3 72.5 + - - +
152X ALA 3.5 0.2 + - - -
153X PHE* 3.3 15.3 + - - +
154X GLY 3.0 10.8 + - - -
155X PHE* 4.4 1.6 - - - -
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Residues in contact with GLY 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X GLN 5.8 0.2 - - - -
120X PHE 2.7 17.0 + - - -
121X TYR* 3.6 12.5 - - - +
150X VAL* 1.3 79.9 - - - +
152X ALA* 1.3 62.5 - - - -
153X PHE* 4.9 2.2 - - - -
155X PHE* 3.1 17.8 + - - +
278X GLU* 4.1 16.4 - - - -
292X PHE* 3.5 15.7 - - - +
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Residues in contact with ALA 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X PHE* 3.4 11.5 - - + -
151X GLY* 1.3 70.7 - - - -
153X PHE* 1.3 71.1 + - + +
156X LEU* 3.0 32.9 + - + +
248X LEU* 4.1 16.2 - - + -
274X LEU* 4.8 13.0 - - + +
278X GLU* 5.0 3.3 + - + -
292X PHE* 3.7 38.7 - - + -
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Residues in contact with PHE 153 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X ARG* 3.8 30.7 - - + -
45X PHE* 4.2 15.5 + + - -
68X GLN* 3.9 25.8 - - + +
92X GLU* 3.8 26.5 - - + -
149X ARG* 3.7 31.4 + - + -
150X VAL 3.4 12.8 - - - +
151X GLY* 4.7 1.6 - - - -
152X ALA* 1.3 85.6 - - + +
154X GLY* 1.3 58.8 + - - +
156X LEU 5.3 0.2 + - - -
168X VAL* 3.8 9.0 - - - +
271X PRO* 3.7 35.2 - - + -
274X LEU* 4.3 17.5 - - + -
275X ILE* 4.1 18.2 - - + -
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Residues in contact with GLY 154 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X ARG* 3.4 31.4 - - - +
150X VAL 3.0 9.3 + - - -
153X PHE* 1.3 79.6 - - - +
155X PHE* 1.3 70.0 + - - +
156X LEU 3.9 0.7 - - - -
168X VAL* 3.4 11.6 + - - +
169X GLY 2.9 26.0 + - - -
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Residues in contact with PHE 155 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X PHE* 3.6 35.7 - + + -
148X TYR* 4.4 5.6 - + - -
149X ARG 3.3 20.2 - - - -
150X VAL* 4.4 0.7 - - - -
151X GLY 3.1 8.9 + - - -
152X ALA 3.4 0.2 + - - -
154X GLY* 1.3 96.5 - - - +
156X LEU* 1.3 68.9 + - - +
157X ALA* 3.2 10.6 + - - +
166X GLY* 4.7 1.6 - - - -
167X ASN* 4.1 13.5 - - - +
169X GLY* 3.7 14.8 - - - -
170X LEU* 3.8 20.9 - - + -
173X GLN* 5.5 0.2 - - - -
292X PHE* 3.4 44.3 - - + +
293X VAL 3.7 9.2 - - - +
294X PRO* 3.6 34.3 - - + -
295X VAL* 5.8 0.2 - - - +
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Residues in contact with LEU 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X PHE* 3.9 22.3 - - + +
152X ALA* 3.0 23.4 + - + +
153X PHE 5.3 0.2 + - - -
154X GLY 3.9 0.2 - - - -
155X PHE* 1.3 77.2 - - - +
157X ALA* 1.3 61.3 + - - +
158X LEU* 4.4 11.7 - - + -
164X ALA* 3.9 29.4 - - + +
166X GLY* 3.6 14.2 + - - -
168X VAL* 5.9 0.2 - - - +
245X ALA* 4.1 15.5 - - + -
248X LEU* 3.6 30.7 - - + -
263X ILE* 5.3 0.9 - - + -
266X LEU* 4.0 23.1 - - + -
292X PHE* 3.9 20.4 - - + -
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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