Contacts of the helix formed by residues 175 - 184 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A HIS* 2.8 51.0 + + + +
174A ASP* 1.3 89.2 - - + +
176A ALA* 1.3 54.7 + - - +
177A PRO* 3.1 4.5 - - - -
178A GLN* 2.8 46.4 + - - +
179A VAL* 2.9 11.8 + - - +
114B PHE* 3.9 7.2 - + - -
115B CYS* 3.8 34.8 - - + -
118B MSE 3.7 22.7 - - + -
170B GLN* 3.7 17.7 - - + -
174B ASP* 4.1 8.1 - - - -
212B URA 3.7 16.4 - - - -
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ARG* 3.7 12.1 - - - +
172A TYR 3.5 16.5 + - - +
173A ALA* 3.2 18.2 + - - +
175A PHE* 1.3 75.6 - - - +
177A PRO* 1.3 70.1 - - + +
179A VAL* 3.8 6.4 - - - +
180A GLU* 2.9 27.6 + - - +
185A ALA 5.1 0.3 - - - +
186A THR* 5.4 9.2 - - + +
188A ARG* 5.9 3.8 - - - +
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Residues in contact with PRO 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ARG* 5.1 4.3 - - - +
173A ALA 4.8 0.7 - - - +
174A ASP 4.3 1.8 - - - +
175A PHE* 3.2 1.1 - - - -
176A ALA* 1.3 94.9 - - + +
178A GLN* 1.3 55.4 + - - +
180A GLU* 3.8 6.3 - - + +
181A ALA* 2.9 29.4 + - - +
118B MSE 3.0 42.6 - - + +
121B GLY* 4.0 15.5 - - - +
122B ALA* 4.0 11.0 - - + -
126B MSE 3.9 28.5 - - + +
129B LEU* 4.7 0.4 - - - -
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A HIS* 4.6 1.6 + - - -
175A PHE* 2.8 23.5 + - + +
177A PRO* 1.3 77.1 - - - +
179A VAL* 1.3 68.1 + - + +
181A ALA* 3.4 6.6 - - + +
182A VAL* 3.1 23.2 + - + +
114B PHE* 3.5 19.5 - - - -
118B MSE 3.3 14.0 - - + +
129B LEU* 3.9 9.1 - - + +
133B LEU* 3.2 29.0 - - + +
163B PHE* 5.5 1.6 - - + -
166B TRP* 3.4 18.6 - - + -
212B URA 2.8 42.5 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A HIS* 4.1 20.0 - - + +
172A TYR* 4.0 25.8 - - + +
175A PHE 2.9 16.8 + - - +
176A ALA* 3.8 8.1 - - - +
178A GLN* 1.3 79.6 - - + +
180A GLU* 1.3 52.5 + - - +
182A VAL* 3.2 2.1 + - - +
183A THR* 2.8 36.9 + - - -
185A ALA 4.0 6.1 - - - +
186A THR* 5.5 1.6 - - - -
192A PHE* 3.6 35.7 - - + -
163B PHE* 4.0 24.9 - - + -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA 2.9 18.8 + - - +
177A PRO* 3.8 4.4 - - - +
179A VAL* 1.3 78.1 - - - +
181A ALA* 1.3 60.6 + - - +
184A GLY* 2.4 45.3 + - - +
185A ALA 3.2 21.5 + - - +
186A THR* 3.8 22.5 - - + +
126B MSE 4.7 14.6 - - + +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO 2.9 22.2 + - - +
178A GLN 3.4 7.6 - - - +
180A GLU* 1.3 75.0 - - - +
182A VAL* 1.3 60.1 + - + +
184A GLY 4.6 0.7 + - - -
126B MSE 4.4 3.7 - - - +
129B LEU* 3.6 31.4 - - + +
130B THR* 4.0 28.5 - - + +
134B LYS* 3.7 14.8 - - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLN* 3.1 13.5 + - + +
179A VAL 3.4 3.8 - - - +
181A ALA* 1.3 78.3 - - + +
183A THR* 1.3 67.8 + - - +
184A GLY 3.7 0.2 - - - -
133B LEU* 4.3 20.4 - - + -
134B LYS* 3.8 25.5 - - + +
137B ILE* 4.3 28.5 - - + -
138B ASP* 4.7 4.0 - - - +
159B GLN* 3.4 20.8 + - - +
163B PHE* 3.1 39.7 - - + -
166B TRP* 5.2 0.7 - - + -
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 2.8 17.1 + - - -
182A VAL* 1.3 88.4 - - - +
184A GLY* 1.3 57.8 + - - +
185A ALA* 3.0 25.1 - - + +
192A PHE* 3.0 41.4 - - + -
159B GLN* 4.0 15.6 + - - +
163B PHE* 4.1 7.6 - - - -
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 2.4 34.4 + - - +
181A ALA 4.6 0.6 + - - -
182A VAL 3.7 0.4 - - - -
183A THR* 1.3 71.5 - - - +
185A ALA* 1.3 56.3 + - - +
189A ASP* 4.9 1.7 - - - +
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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