Contacts of the helix formed by residues 174 - 186 (chain B) in PDB entry 3ESF
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 ASP 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B TYR* 4.7 0.2 - - - -
171B TYR* 2.9 27.5 + - + +
172B LYS 3.2 0.8 - - - -
173B ASN* 1.3 82.4 - - - +
175B ARG* 1.3 61.2 + - - +
176B PRO* 3.5 15.2 - - - +
177B ALA* 3.3 36.9 + - + +
178B TYR 3.3 8.3 + - - -
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Residues in contact with ARG 175 (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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163A TRP* 6.0 2.6 - - - -
117B ALA 2.8 29.0 + - - -
118B VAL* 3.4 18.3 + - - +
120B HIS* 2.7 36.9 + - - +
122B GLY 3.6 17.2 + - - +
162B VAL* 3.8 22.2 + - - +
164B GLU* 5.3 3.8 + - - +
167B TYR* 3.1 46.7 + - + +
173B ASN 2.9 11.4 + - - +
174B ASP* 1.3 68.3 - - - +
176B PRO* 1.4 73.8 - - + +
178B TYR* 3.1 10.8 + - + +
179B VAL* 2.8 31.1 + - + +
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Residues in contact with PRO 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 4.0 35.2 - - + -
173B ASN 4.7 1.3 - - - +
174B ASP* 3.5 14.8 - - - +
175B ARG* 1.4 91.7 - - + +
177B ALA* 1.3 55.2 + - - +
179B VAL* 3.4 2.9 + - - +
180B GLN* 3.0 33.9 + - + +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 3.8 18.6 - - + -
174B ASP* 3.3 31.3 + - - +
175B ARG 3.2 0.6 - - - -
176B PRO* 1.3 75.3 - - - +
178B TYR* 1.3 60.5 - - - +
180B GLN* 3.3 9.0 + - - +
181B THR* 3.0 28.8 + - - -
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Residues in contact with TYR 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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20B ILE* 4.8 15.3 - - + -
79B TYR* 2.8 30.7 + + - -
160B CYS* 3.5 21.9 - - - -
161B ASP 2.6 31.2 + - - -
162B VAL* 4.4 4.7 - - + -
166B ALA* 3.8 11.4 - - + +
167B TYR* 3.3 45.3 - + + -
171B TYR* 3.8 26.8 - + + -
174B ASP 3.3 7.8 + - - +
175B ARG* 3.4 16.6 - - + +
177B ALA* 1.3 75.7 - - - +
179B VAL* 1.3 58.0 + - + +
181B THR* 3.1 6.2 + - - -
182B PHE* 2.8 34.9 + + + +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 5.4 2.9 - - + -
114B THR* 4.1 20.0 - - + -
117B ALA* 3.7 33.0 - - + -
118B VAL* 3.9 12.3 - - + -
160B CYS* 4.9 2.7 - - - -
162B VAL* 4.8 1.1 - - + -
175B ARG* 2.8 37.1 + - + +
176B PRO 3.7 4.3 - - - +
178B TYR* 1.3 81.1 - - + +
180B GLN* 1.3 62.3 + - - +
182B PHE* 3.1 12.6 + - + +
183B TRP* 3.1 45.0 + - + +
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Residues in contact with GLN 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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110B LYS* 4.7 11.2 + - - +
114B THR* 4.1 20.8 + - - +
176B PRO 3.0 21.4 + - - +
177B ALA* 3.5 10.5 - - - +
178B TYR 3.2 0.2 - - - -
179B VAL* 1.3 75.6 - - - +
181B THR* 1.3 61.1 + - - +
183B TRP* 3.2 34.6 + - - +
184B ASN* 3.4 17.8 + - - +
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Residues in contact with THR 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 LYS 3.5 21.6 + - - +
19B GLY* 3.7 10.0 - - - +
20B ILE* 3.7 20.6 - - + -
171B TYR* 2.5 32.6 + - + +
177B ALA 3.0 9.2 + - - -
178B TYR* 3.3 9.6 - - + +
180B GLN* 1.3 72.8 - - - +
182B PHE* 1.3 64.4 + - - +
184B ASN* 2.9 21.7 + - - +
185B VAL* 3.2 11.8 + - + +
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Residues in contact with PHE 182 (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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20B ILE* 5.6 1.5 - - - +
79B TYR* 4.6 1.8 - + - -
82B SER* 4.3 5.4 - - - -
83B MET* 3.9 34.3 - - + -
113B PHE* 3.8 28.9 - + - -
158B LEU* 4.1 10.8 - - + -
159B THR 3.5 29.2 - - - -
160B CYS* 3.7 26.0 - - + -
178B TYR* 2.8 18.8 + + + +
179B VAL* 3.1 16.5 + - + +
181B THR* 1.3 73.2 - - - +
183B TRP* 1.3 70.6 + + - +
185B VAL* 3.0 8.5 + - - +
186B VAL* 2.8 51.0 + - + +
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Residues in contact with TRP 183 (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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88B GLY* 3.2 19.2 - - - -
89B GLY 3.9 6.4 + - - +
106B PHE* 4.5 6.3 - + - -
109B PHE* 3.7 31.4 - + - -
110B LYS* 3.5 50.8 - - + +
113B PHE* 3.4 36.3 - + + -
114B THR* 2.7 27.4 + - - -
158B LEU* 5.8 1.3 - - + -
179B VAL* 3.1 26.5 + - + +
180B GLN* 3.4 25.1 - - - +
181B THR 3.2 0.4 - - - -
182B PHE* 1.3 86.2 - + - +
184B ASN* 1.3 61.7 + - - +
186B VAL* 3.7 21.0 - - + +
188B TRP* 4.5 11.7 - + - -
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Residues in contact with ASN 184 (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 LYS* 3.2 36.8 + - + +
87B GLY 3.3 12.6 - - - +
88B GLY* 3.4 6.3 - - - -
89B GLY 5.7 0.7 + - - -
180B GLN 3.4 13.4 + - - +
181B THR* 2.9 16.8 + - - +
183B TRP* 1.3 84.0 - - - +
185B VAL* 1.3 59.1 + - - +
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Residues in contact with VAL 185 (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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15B LEU* 4.1 15.7 - - + -
18B LYS* 3.6 38.6 - - + +
20B ILE* 4.2 9.4 - - + -
83B MET* 3.1 36.4 - - + -
84B SER 2.8 42.6 + - - +
87B GLY* 3.7 0.9 - - - -
88B GLY 3.7 2.0 - - - +
181B THR 3.5 8.1 - - - +
182B PHE* 3.0 16.5 + - - +
184B ASN* 1.3 76.6 - - - +
186B VAL* 1.3 69.3 + - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER 3.5 10.5 - - - +
87B GLY* 3.1 3.8 - - - -
88B GLY* 2.8 27.0 + - - +
89B GLY 4.4 0.7 - - - +
158B LEU* 3.7 30.1 - - + -
182B PHE* 2.8 32.0 + - + +
183B TRP* 3.7 28.0 - - + +
185B VAL* 1.3 75.4 - - - +
187B ASN* 1.3 62.6 + - - +
188B TRP* 3.5 43.3 + - + +
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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