Contacts of the helix formed by residues 175 - 184 (chain B) in PDB entry 3LOC
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 PHE 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.0 6.5 - + - -
115A CYS* 3.8 35.7 - - + -
118A MSE 3.6 23.1 - - + -
167A ALA* 6.4 0.4 - - - -
170A GLN* 3.6 30.1 - - + -
174A ASP* 4.2 7.0 - - - -
212A URA 3.8 7.0 - - - -
171B HIS* 2.8 58.2 + + + +
174B ASP* 1.3 85.7 - - + +
176B ALA* 1.3 66.2 + - - +
177B PRO* 3.2 5.2 - - - -
178B GLN* 2.8 31.2 + - + +
179B VAL* 2.9 10.9 + - - -
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Residues in contact with ALA 176 (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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108B PRO* 6.5 0.2 - - + -
172B TYR 3.4 18.5 + - - +
173B ALA* 3.0 17.6 + - - +
175B PHE* 1.3 75.1 - - - +
177B PRO* 1.3 65.0 - - + +
179B VAL* 3.1 6.4 + - - +
180B GLU* 2.8 34.5 + - - +
185B ALA 5.0 0.2 - - - +
186B THR* 5.6 10.8 - - + +
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Residues in contact with PRO 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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118A MSE 3.4 29.8 - - + +
121A GLY* 3.7 20.0 - - - +
122A ALA* 3.7 23.8 - - + +
126A MSE 4.0 15.3 - - + +
129A LEU* 4.5 1.6 - - - -
112B ARG* 6.5 0.7 - - - -
173B ALA 4.5 1.1 - - - +
174B ASP 4.2 1.8 - - - +
175B PHE* 3.2 7.6 - - - -
176B ALA* 1.3 95.4 - - + +
178B GLN* 1.3 56.4 + - - +
180B GLU* 3.9 7.1 - - + +
181B ALA* 2.9 27.9 + - - +
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Residues in contact with GLN 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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114A PHE* 3.4 19.8 - - - -
118A MSE 3.8 14.8 - - - -
129A LEU* 3.9 7.0 - - + +
133A LEU* 3.7 22.5 - - + +
163A PHE* 5.4 1.3 - - + -
166A TRP* 3.2 29.5 - - + -
212A URA 3.0 35.9 + - - -
171B HIS* 4.4 4.6 + - - -
175B PHE* 2.8 29.0 + - + +
177B PRO* 1.3 73.5 - - - +
179B VAL* 1.3 65.9 + - + +
180B GLU 3.2 0.2 + - - -
181B ALA* 3.2 6.7 + - + +
182B VAL* 3.1 29.6 + - + +
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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
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163A PHE* 4.1 25.8 - - + -
171B HIS* 4.1 21.5 - - + +
172B TYR* 4.1 22.9 - - + +
175B PHE 2.9 18.4 + - - +
176B ALA* 3.6 10.1 - - - +
178B GLN* 1.3 76.2 - - - +
180B GLU* 1.3 58.0 + - - +
182B VAL* 3.9 0.2 - - - -
183B THR* 2.8 36.7 + - - +
185B ALA 4.0 4.9 - - - +
186B THR* 5.5 1.3 - - - -
187B LEU* 5.7 0.9 - - + -
192B PHE* 3.5 36.1 - - + -
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Residues in contact with GLU 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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126A MSE 6.0 3.2 - - + +
176B ALA* 2.8 20.6 + - - +
177B PRO* 3.9 7.5 - - + +
179B VAL* 1.3 71.5 - - - +
181B ALA* 1.3 67.4 + - - +
184B GLY* 2.8 31.6 + - - +
185B ALA 3.3 26.2 - - - +
186B THR* 3.4 23.6 - - + +
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Residues in contact with ALA 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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126A MSE 4.5 3.5 - - - -
129A LEU* 3.6 35.9 - - + +
130A THR* 4.2 20.7 - - + +
134A LYS* 3.4 24.7 - - - +
177B PRO 2.9 20.3 + - - +
178B GLN 3.3 8.1 - - - +
180B GLU* 1.3 77.0 - - - +
182B VAL* 1.3 59.1 + - + +
184B GLY 4.8 0.2 + - - -
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Residues in contact with VAL 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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129A LEU 5.5 0.2 - - - +
133A LEU* 4.7 11.7 - - + -
134A LYS* 3.7 32.9 + - + +
137A ILE* 4.5 20.6 - - + -
138A ASP* 4.5 3.5 - - - +
159A GLN* 3.7 22.6 + - + +
163A PHE* 3.5 24.9 - - + -
166A TRP* 5.3 0.9 - - + -
178B GLN* 3.1 25.9 + - + +
180B GLU 3.1 0.4 - - - -
181B ALA* 1.3 79.8 - - + +
183B THR* 1.3 81.4 + - + +
184B GLY 3.6 0.2 - - - -
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Residues in contact with THR 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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134A LYS* 5.9 0.9 - - - -
159A GLN* 4.1 22.0 - - + +
160A HIS* 5.8 0.2 - - - +
163A PHE* 4.0 15.5 - - + -
179B VAL* 2.8 22.4 + - + +
182B VAL* 1.3 92.7 - - + +
184B GLY* 1.3 58.2 + - - +
185B ALA* 3.0 26.6 + - - +
192B PHE* 3.8 25.8 - - + -
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Residues in contact with GLY 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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134A LYS* 5.8 0.8 - - - +
180B GLU* 2.8 24.5 + - - +
181B ALA 4.7 0.8 + - - -
182B VAL 3.6 1.2 - - - -
183B THR* 1.3 76.0 - - - +
185B ALA* 1.3 57.5 + - - +
189B ASP* 5.0 1.6 - - - +
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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