Contacts of the helix formed by residues 165 - 182 (chain A) in PDB entry 4I2C
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 ASN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ASN* 2.9 10.3 + - - +
164A TYR* 1.3 83.6 - - - +
166A GLN* 1.3 59.1 + - - +
167A LEU* 3.2 3.4 - - - -
168A PHE* 3.0 22.0 + - + -
169A THR* 3.0 30.2 + - + +
198A LEU* 3.5 27.7 + - + +
201A LEU* 3.7 10.2 + - - +
203A PHE 3.1 23.4 + - - -
204A PRO* 3.5 0.3 - - - +
205A ILE* 2.8 38.4 + - - +
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Residues in contact with GLN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 3.7 25.6 + - + +
164A TYR 3.7 2.2 - - - -
165A ASN* 1.3 75.3 - - - +
167A LEU* 1.3 57.0 + - - +
169A THR* 3.5 6.7 - - - -
170A ASP* 2.8 68.4 + - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASN* 3.2 1.0 - - - -
166A GLN* 1.3 79.3 - - - +
168A PHE* 1.3 71.1 + - + +
170A ASP* 4.6 2.1 - - - +
171A ALA* 3.8 16.3 + - - +
228A ILE* 3.7 28.2 - - + +
232A GLY* 3.7 30.3 - - - +
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Residues in contact with PHE 168 (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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164A TYR 5.8 0.2 - - - -
165A ASN* 3.0 28.4 + - + +
167A LEU* 1.3 83.3 - - + +
169A THR* 1.4 59.2 + - - +
171A ALA* 3.4 5.5 + - - +
172A LEU* 3.0 33.3 + - + +
198A LEU* 3.9 20.6 - - + -
204A PRO* 6.0 0.7 - - + -
205A ILE* 3.4 42.6 - - + -
225A ILE* 3.6 40.2 - - + -
228A ILE* 3.7 35.2 - - + +
229A ILE* 3.9 15.3 - - + -
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Residues in contact with THR 169 (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 ASN* 3.0 23.6 + - - +
165A ASN* 3.0 16.3 + - + +
166A GLN* 3.5 5.5 - - - -
168A PHE* 1.4 71.2 - - - +
170A ASP* 1.4 65.6 + - - +
172A LEU* 4.3 3.8 - - - -
173A ASP* 2.8 37.5 + - - +
195A SER* 3.4 35.4 - - - +
198A LEU* 3.7 20.6 - - + -
199A LYS* 3.8 19.4 - - + +
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Residues in contact with ASP 170 (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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166A GLN* 2.8 61.0 + - - +
167A LEU* 4.6 2.5 - - - +
169A THR* 1.4 74.1 + - - +
171A ALA* 1.4 60.8 + - - +
173A ASP* 3.4 9.9 + - - +
174A ILE* 3.1 34.8 + - + +
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Residues in contact with ALA 171 (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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167A LEU 3.8 6.3 + - - +
168A PHE 3.4 9.2 + - - +
169A THR 3.2 0.2 - - - -
170A ASP* 1.4 79.1 - - - +
172A LEU* 1.4 59.8 + - - +
174A ILE* 3.2 6.2 + - - +
175A LEU* 3.1 29.1 + - - +
224A ILE* 4.8 3.1 - - + -
228A ILE* 3.8 12.8 - - + -
234A SER* 3.7 30.5 - - - +
237A ALA* 3.8 12.4 - - + +
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Residues in contact with LEU 172 (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 PHE* 3.0 21.4 + - + +
169A THR 3.9 0.9 - - - +
171A ALA* 1.4 74.2 - - - +
173A ASP* 1.4 58.0 + - - +
175A LEU* 3.4 4.7 + - + +
176A ALA* 2.9 30.0 + - - +
191A PHE* 3.7 34.1 - - + +
194A ALA* 4.1 7.0 - - + -
195A SER* 3.8 34.3 - - - +
198A LEU* 3.7 29.6 - - + -
221A VAL* 4.3 17.5 - - + -
224A ILE* 4.1 24.0 - - + -
225A ILE* 5.2 2.9 - - + -
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Residues in contact with ASP 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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169A THR* 2.8 27.4 + - - +
170A ASP* 3.7 11.2 - - - +
172A LEU* 1.4 67.9 - - - +
174A ILE* 1.3 62.3 + - + +
176A ALA* 3.5 7.5 + - - +
177A GLU* 3.0 29.8 + - - +
192A MET* 5.7 1.9 - - - +
195A SER* 2.6 26.5 + - - -
199A LYS* 3.1 26.1 + - - -
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Residues in contact with ILE 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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170A ASP* 3.1 27.3 + - + +
171A ALA* 3.2 6.9 + - - +
173A ASP* 1.3 75.0 - - + +
175A LEU* 1.3 58.2 + - - +
177A GLU* 3.3 6.0 + - - +
178A ASN* 3.0 27.9 + - - +
237A ALA* 3.9 22.0 - - + +
240A VAL* 3.5 30.3 - - + +
241A LEU* 3.9 32.5 - - + -
246A TYR* 4.1 19.2 - - - +
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Residues in contact with LEU 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 ALA 3.1 22.4 + - - +
172A LEU* 3.8 7.0 - - + +
174A ILE* 1.3 74.6 - - - +
176A ALA* 1.3 61.2 + - - +
178A ASN* 3.5 5.6 + - + +
179A ASP* 3.1 27.7 + - - +
191A PHE* 3.8 24.9 - - + -
224A ILE* 3.8 43.3 - - + -
234A SER* 4.7 0.7 - - - +
236A GLU* 3.8 36.8 - - + +
237A ALA* 4.0 6.5 - - - +
240A VAL* 3.9 13.7 - - + -
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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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172A LEU 2.9 17.2 + - - +
173A ASP* 3.7 8.1 - - - +
174A ILE 3.3 0.2 - - - -
175A LEU* 1.3 76.0 - - - +
177A GLU* 1.3 55.5 + - - +
179A ASP* 3.2 2.6 + - - +
180A GLU 3.0 23.0 + - - -
188A CYS* 3.3 29.7 - - - +
191A PHE* 3.8 20.8 - - + -
192A MET* 3.8 18.6 - - + +
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Residues in contact with GLU 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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173A ASP 3.0 18.5 + - - +
174A ILE* 3.5 6.9 - - - +
176A ALA* 1.3 73.3 - - - +
178A ASN* 1.3 65.0 + - - +
180A GLU* 3.2 14.0 + - - +
181A LEU* 3.1 22.2 + - - +
246A TYR* 3.0 27.7 + - + -
249A PHE* 4.0 16.7 - - + -
250A LYS* 2.7 39.6 + - - +
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Residues in contact with ASN 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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174A ILE 3.0 15.9 + - - +
175A LEU* 3.7 5.8 - - + +
177A GLU* 1.3 75.9 - - - +
179A ASP* 1.3 61.4 + - - +
181A LEU* 3.2 13.4 + - - +
182A ARG* 2.8 49.1 + - - +
240A VAL* 3.6 32.0 - - + +
243A ASP* 4.7 6.5 + - - -
246A TYR* 3.9 27.1 - - - +
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Residues in contact with ASP 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 LEU 3.1 13.5 + - - +
176A ALA 3.2 8.3 + - - +
178A ASN* 1.3 79.7 - - - +
180A GLU* 1.3 58.8 + - - +
182A ARG* 3.5 4.7 + - - +
183A GLU 3.2 2.4 + - - -
184A ASN* 2.7 57.2 + - + +
187A SER* 2.7 33.4 + - - -
188A CYS* 3.6 6.3 - - - +
191A PHE* 3.1 24.8 - - - -
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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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176A ALA 3.0 11.9 + - - +
177A GLU* 3.3 17.0 - - - +
178A ASN 3.2 0.2 - - - -
179A ASP* 1.3 73.0 - - - +
181A LEU* 1.3 62.5 + - - +
183A GLU* 3.2 16.5 + - - +
184A ASN 5.0 0.9 - - - +
185A GLU* 6.2 0.7 - - - +
188A CYS* 4.1 17.7 - - - +
192A MET* 5.9 2.3 - - - +
249A PHE* 4.2 18.4 - - - -
260A LEU* 4.6 20.6 - - + +
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Residues in contact with LEU 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 GLU 3.1 12.8 + - - +
178A ASN* 3.2 20.4 + - - +
180A GLU* 1.3 78.5 + - - +
182A ARG* 1.3 56.9 + - + +
183A GLU* 3.2 9.8 + - - +
243A ASP* 5.3 0.2 - - - +
245A ARG* 3.4 49.2 + - + +
246A TYR* 3.7 33.7 - - + +
249A PHE* 3.6 43.7 - - + -
260A LEU* 4.2 18.0 - - + +
264A GLU* 6.4 1.6 - - + -
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Residues in contact with ARG 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 ASN* 2.8 42.7 + - - +
179A ASP* 4.2 8.3 - - - +
180A GLU 3.4 0.4 - - - -
181A LEU* 1.3 73.7 - - + +
183A GLU* 1.4 67.5 + - - +
184A ASN* 3.2 8.6 + - + +
245A ARG* 5.1 15.5 - - - +
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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