Contacts of the helix formed by residues 172 - 184 (chain A) in PDB entry 3P3W
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 GLN 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASP* 3.3 17.4 + - - +
171A VAL* 1.3 80.1 - - + +
173A GLU* 1.3 65.4 + - + +
174A PHE 3.2 0.7 - - - -
175A ARG* 3.1 55.3 + - - +
176A ARG* 3.4 12.9 + - - +
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Residues in contact with GLU 173 (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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168A ILE* 3.4 31.4 - - + +
169A LYS 4.9 1.7 + - - -
170A ASP* 3.4 38.0 + - + +
171A VAL 3.2 0.2 - - - -
172A GLN* 1.3 78.6 - - - +
174A PHE* 1.3 59.0 + - - +
176A ARG* 3.4 5.9 + - - +
177A ILE* 3.0 36.2 + - + +
151C GLU* 4.8 12.1 - - - +
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Residues in contact with PHE 174 (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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165A VAL* 3.8 38.6 - - + -
168A ILE* 3.7 34.1 - - + -
169A LYS 5.3 2.2 - - - -
170A ASP 3.6 16.8 - - - -
171A VAL* 3.2 22.5 + - + +
172A GLN 3.2 0.4 - - - -
173A GLU* 1.3 79.5 - - - +
175A ARG* 1.3 57.5 + - - +
176A ARG 3.4 0.2 - - - -
177A ILE* 4.1 8.5 + - + +
178A ILE* 3.3 28.6 - - - +
197A ARG* 4.7 13.7 - - + -
200A THR* 5.1 9.6 - - - -
201A ILE* 3.3 30.2 - - + +
204A GLN* 4.1 16.2 - - + +
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Residues in contact with ARG 175 (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 VAL* 3.6 7.0 + - - +
172A GLN* 3.1 48.1 + - - +
174A PHE* 1.3 79.5 - - - +
176A ARG* 1.3 60.8 + - - +
177A ILE 3.4 0.2 - - - -
178A ILE* 4.1 8.5 + - + +
179A GLU* 3.9 15.4 + - - +
204A GLN* 3.7 35.7 + - + +
207A ILE* 3.7 32.1 - - - +
208A LEU* 4.9 27.1 - - + +
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Residues in contact with ARG 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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172A GLN* 3.4 12.1 + - - +
173A GLU* 3.4 7.8 + - - +
175A ARG* 1.3 78.6 - - - +
177A ILE* 1.3 69.4 + - + +
178A ILE 3.4 0.2 - - - -
179A GLU* 3.4 15.9 + - - +
180A GLU* 3.5 19.2 + - - +
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Residues in contact with ILE 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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136A LEU* 4.7 11.2 - - + -
163A ARG* 3.6 42.6 - - + +
165A VAL* 5.8 7.6 - - + -
168A ILE* 6.1 5.6 - - + -
173A GLU* 3.0 26.1 + - + +
174A PHE* 4.1 11.0 + - + +
175A ARG 3.4 0.6 - - - -
176A ARG* 1.3 80.0 - - + +
178A ILE* 1.3 62.4 + - + +
180A GLU* 3.4 36.4 + - - +
181A MET* 3.7 11.7 + - + +
154C VAL* 6.0 4.0 - - + -
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Residues in contact with ILE 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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136A LEU* 5.9 6.1 - - + -
174A PHE 3.3 22.4 - - - +
175A ARG* 4.3 7.4 - - + +
176A ARG 3.4 0.2 - - - -
177A ILE* 1.3 76.3 - - + +
179A GLU* 1.3 63.0 - - - +
181A MET* 3.2 13.8 + - - +
182A ASP* 3.3 16.1 + - - +
189A TYR* 3.6 27.4 - - + +
201A ILE* 4.9 11.4 - - + +
204A GLN* 4.7 18.2 - - + +
205A VAL* 5.0 10.8 - - + -
208A LEU* 4.8 7.6 - - + -
211A HIS* 4.0 28.7 - - + +
217A TYR* 5.5 2.2 - - - +
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Residues in contact with GLU 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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175A ARG 3.9 11.3 + - - +
176A ARG* 3.4 13.5 + - - +
178A ILE* 1.3 78.1 - - - +
180A GLU* 1.3 61.8 + - + +
182A ASP* 3.4 21.4 + - - +
183A ARG* 3.4 12.0 + - - +
208A LEU* 5.6 4.8 - - + +
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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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163A ARG* 2.8 32.2 + - - +
176A ARG* 3.5 13.4 - - - +
177A ILE* 3.5 29.9 - - - +
178A ILE 3.2 0.6 - - - -
179A GLU* 1.3 78.3 - - + +
181A MET* 1.3 63.2 + - + +
183A ARG* 3.4 16.9 + - - +
184A ARG* 3.5 15.6 + - - +
154C VAL* 4.9 11.9 - - - +
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Residues in contact with MET 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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134A VAL* 3.7 39.7 - - + -
136A LEU* 5.8 0.4 - - + -
161A THR* 4.1 21.5 - - + -
163A ARG* 3.6 32.5 - - + +
177A ILE* 3.7 12.5 + - + +
178A ILE* 3.2 4.5 + - - +
180A GLU* 1.3 80.8 - - + +
182A ASP* 1.3 61.8 + - - +
183A ARG 3.2 1.6 - - - -
184A ARG* 3.1 19.0 + - - +
185A GLN 3.0 8.8 + - - -
186A GLU* 2.9 37.3 + - + +
189A TYR* 3.3 25.8 - - + +
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Residues in contact with ASP 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 ILE 3.3 16.8 + - - +
179A GLU* 3.6 14.2 - - - +
180A GLU 3.3 0.2 - - - -
181A MET* 1.3 76.0 - - - +
183A ARG* 1.3 61.2 + - - +
185A GLN* 3.2 24.2 + - - +
186A GLU 4.1 5.8 - - - +
189A TYR* 3.7 10.0 + - - -
208A LEU* 4.7 4.0 - - - +
211A HIS* 3.8 19.5 + - - -
215A TYR* 3.4 22.8 + - - -
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Residues in contact with ARG 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 GLU 3.4 9.8 + - - +
180A GLU* 3.5 13.2 - - - +
181A MET 3.2 0.4 - - - -
182A ASP* 1.3 77.2 - - - +
184A ARG* 1.3 60.0 + - + +
185A GLN* 3.2 7.0 + - - +
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Residues in contact with ARG 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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161A THR* 4.0 28.9 + - - +
180A GLU 3.5 10.9 + - - +
181A MET* 3.1 25.2 + - - +
183A ARG* 1.3 77.8 - - + +
185A GLN* 1.3 69.5 + - - +
186A GLU* 3.4 19.9 + - + +
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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