Contacts of the helix formed by residues 171 - 181 (chain B) in PDB entry 2W7W
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B TYR* 5.0 0.9 - - - -
168B PHE* 3.1 22.7 + - - +
169B ARG* 3.2 2.1 - - + -
170B ASN* 1.3 98.0 - - - +
172B ARG* 1.3 60.5 + - - +
173B PRO* 3.7 18.6 - - + -
174B ASP* 3.2 43.9 + - - +
175B TYR 3.4 7.1 + - - -
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Residues in contact with ARG 172 (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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160A TRP* 5.8 2.8 - - - -
115B ALA 3.1 18.2 + - - -
116B ILE* 3.5 29.7 + - + +
118B ASN 2.8 22.8 + - - -
120B GLY 2.9 31.7 + - - +
159B LEU* 3.2 35.3 + - + +
161B GLU* 5.2 3.8 - - - +
164B TYR* 2.9 38.1 + - + +
170B ASN 3.3 5.7 + - - +
171B VAL* 1.3 69.3 - - - +
173B PRO* 1.4 69.5 - - + +
175B TYR* 2.9 12.5 + - + +
176B MET* 2.8 31.7 + - + +
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 5.6 2.4 - - + +
116B ILE* 3.6 28.2 - - + -
171B VAL* 3.5 15.3 - - + -
172B ARG* 1.4 93.1 - - + +
174B ASP* 1.3 63.2 + - - +
176B MET* 3.4 5.6 + - + +
177B GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.4 30.2 - - + +
171B VAL* 3.2 33.6 + - + +
172B ARG 3.1 1.0 - - - -
173B PRO* 1.3 78.0 - - - +
175B TYR* 1.3 65.7 + - - +
177B GLY* 3.3 3.4 + - - +
178B ALA 3.3 14.7 + - - -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.3 15.0 - - + -
77B TYR* 2.7 31.4 + - - -
157B VAL* 3.6 21.3 - - + +
158B ASP 2.6 29.7 + - - -
159B LEU* 4.1 13.0 - - + -
163B ALA* 3.8 13.9 - - + +
164B TYR* 3.5 42.4 - + + -
168B PHE* 3.8 22.8 - + + -
171B VAL 3.4 2.2 + - - +
172B ARG* 2.9 16.0 + - - +
174B ASP* 1.3 76.6 - - - +
176B MET* 1.3 65.9 + - - +
178B ALA* 3.0 4.5 + - + +
179B PHE* 2.9 29.8 + + + +
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Residues in contact with MET 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 4.1 21.3 - - + -
112B THR* 3.9 21.8 - - + -
115B ALA* 4.0 20.2 - - + -
116B ILE* 3.7 19.5 - - + -
157B VAL* 4.0 20.0 - - + -
159B LEU* 4.3 8.3 - - + -
172B ARG 2.8 18.4 + - - +
173B PRO* 3.7 6.5 - - + +
175B TYR* 1.3 81.5 - - + +
177B GLY* 1.3 58.9 + - - +
179B PHE* 3.4 28.9 + - + +
180B TRP* 2.8 46.6 + - + +
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Residues in contact with GLY 177 (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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173B PRO 3.2 13.0 + - - -
174B ASP* 3.3 5.1 + - - -
175B TYR 3.1 1.0 - - - -
176B MET* 1.3 77.0 - - - +
178B ALA* 1.3 58.2 + - - +
180B TRP* 3.5 7.7 + - - +
181B SER* 3.0 26.2 + - - -
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Residues in contact with ALA 178 (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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18B HIS* 3.6 29.4 - - + +
19B ILE* 4.6 5.6 - - + -
168B PHE* 3.5 31.0 - - + -
174B ASP 3.3 4.8 + - - -
175B TYR* 3.0 10.2 + - + +
177B GLY* 1.3 73.5 - - - +
179B PHE* 1.3 67.1 + - - +
181B SER* 3.1 20.1 + - - -
182B LEU* 3.3 15.8 - - - +
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Residues in contact with PHE 179 (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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19B ILE* 5.7 1.3 - - - +
77B TYR* 4.9 4.3 - + - -
80B CYS* 5.1 1.3 - - + -
81B LEU* 4.1 20.6 - - + -
111B PHE* 3.6 20.2 - + - -
155B LEU* 3.9 23.3 - - + -
156B THR 3.2 28.5 - - - -
157B VAL* 3.6 23.8 - - + -
175B TYR* 2.9 21.4 + + + +
176B MET* 3.5 29.8 - - + +
178B ALA* 1.3 71.9 - - - +
180B TRP* 1.3 74.8 + + - +
182B LEU* 2.9 25.6 + - - +
183B VAL* 3.1 31.2 + - + +
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Residues in contact with TRP 180 (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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86B GLY* 3.3 20.4 - - - -
87B GLY* 3.3 10.6 + - - +
104B PHE* 4.3 21.1 - + + -
107B PHE* 3.9 24.2 - + - -
108B LYS* 3.6 44.5 - - + +
111B PHE* 3.4 39.7 - + + -
112B THR* 3.1 27.4 + - + +
155B LEU* 4.7 1.8 - - + -
176B MET* 2.8 37.0 + - + +
177B GLY* 3.5 7.6 + - - +
178B ALA 3.3 0.4 - - - -
179B PHE* 1.3 91.8 - + - +
181B SER* 1.3 56.4 - - - +
182B LEU 3.2 0.4 - - - -
183B VAL* 3.9 17.5 + - + +
185B TRP* 4.5 6.5 - + - -
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Residues in contact with SER 181 (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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18B HIS* 3.7 36.2 + - - -
82B ALA 4.7 0.3 - - - +
85B ALA 3.8 9.4 + - - +
86B GLY* 3.7 13.4 + - - -
87B GLY 4.8 1.8 - - - +
177B GLY 3.0 13.9 + - - -
178B ALA 3.1 11.4 + - - -
179B PHE 3.1 0.2 - - - -
180B TRP* 1.3 78.5 - - - +
182B LEU* 1.3 60.0 + - - +
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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