Contacts of the helix formed by residues 170 - 184 (chain A) in PDB entry 4ID7
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 ALA 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A PRO* 3.1 11.3 + - + +
169A GLU* 1.3 75.8 - - - +
171A MET* 1.3 62.4 + - - +
172A ASP 3.3 2.0 - - - -
173A ASP* 3.4 25.6 + - + +
174A PHE* 3.4 10.6 + - - +
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Residues in contact with MET 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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168A PRO* 5.2 5.1 - - + +
169A GLU* 3.4 5.0 - - - +
170A ALA* 1.3 76.4 - - - +
172A ASP* 1.3 57.2 + - - +
174A PHE* 2.9 40.1 + - + +
175A ILE* 2.6 55.7 + - + +
201A MET* 4.0 18.8 - - + +
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Residues in contact with ASP 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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169A GLU* 4.5 12.2 - - - +
170A ALA* 3.3 0.6 - - - +
171A MET* 1.3 79.1 - - - +
173A ASP* 1.3 60.4 + - - +
175A ILE* 3.7 17.6 - - - +
176A ARG* 2.9 40.5 + - - +
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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 GLU 5.4 0.9 - - - +
170A ALA* 3.4 20.2 + - + +
171A MET 3.2 0.2 - - - -
172A ASP* 1.3 80.5 - - - +
174A PHE* 1.3 58.6 + - - +
176A ARG* 3.8 9.2 - - - +
177A GLU* 3.2 31.2 + - - +
272A GLY 5.4 9.2 - - - +
275A ARG* 4.6 9.6 + - - +
290A ARG* 2.7 33.1 + - - -
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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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160A LEU* 4.3 27.1 - - + -
170A ALA 3.4 6.9 + - - +
171A MET* 2.9 38.7 + - + +
173A ASP* 1.3 78.0 - - - +
175A ILE* 1.3 64.6 + - + +
177A GLU* 4.0 5.6 - - - +
178A VAL* 3.0 42.6 + - + +
195A VAL* 3.7 18.2 - - + -
197A LEU* 5.7 0.4 - - + -
201A MET* 3.7 38.6 - - + -
202A LYS 5.0 5.2 - - - -
203A MET* 3.4 32.5 - - + -
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Residues in contact with ILE 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 MET* 2.6 42.6 + - + +
172A ASP* 3.7 19.3 - - - +
174A PHE* 1.3 77.2 - - + +
176A ARG* 1.3 65.0 - - - +
178A VAL* 4.0 2.9 - - - +
179A ASN* 2.8 52.0 + - - +
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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
----------------------------------------------------------
172A ASP* 2.9 25.9 + - - +
173A ASP* 3.8 9.6 - - - +
174A PHE 3.4 0.2 - - - -
175A ILE* 1.3 78.4 - - - +
177A GLU* 1.3 57.5 + - - +
179A ASN* 3.9 2.8 - - - +
180A ALA* 2.9 34.3 + - - +
274A MET 4.9 4.7 - - - +
275A ARG* 3.4 46.2 - - - +
276A ALA 6.0 0.4 - - - +
284A TYR* 4.7 9.8 + - - -
402A SO4 6.1 0.4 - - - -
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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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158A LYS* 5.2 5.5 + - - -
173A ASP 3.2 15.9 + - - +
174A PHE* 4.0 6.2 - - - +
175A ILE 3.4 0.2 - - - -
176A ARG* 1.3 77.9 - - - +
178A VAL* 1.3 63.1 + - - +
180A ALA* 3.8 3.5 - - - +
181A MET* 3.0 42.1 + - + +
203A MET* 4.5 18.2 - - + +
270A ASP* 4.7 2.4 - - - +
271A PHE* 3.6 30.1 + - - +
272A GLY* 3.7 21.8 + - - +
401A 1G0 3.9 20.7 - - + +
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Residues in contact with VAL 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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119A CYS 5.8 1.8 - - - +
174A PHE* 3.0 38.6 + - + +
175A ILE* 4.0 3.6 - - - +
177A GLU* 1.3 76.8 - - - +
179A ASN* 1.3 67.7 + - - +
181A MET 3.9 0.2 - - - -
182A HIS* 3.0 27.8 + - + +
192A LEU* 3.9 15.1 - - + +
195A VAL* 3.8 20.6 - - + -
203A MET* 3.3 26.7 - - + -
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Residues in contact with ASN 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 ILE* 2.8 43.5 + - - +
176A ARG* 4.0 3.1 - - - +
178A VAL* 1.3 84.3 - - - +
180A ALA* 1.3 63.2 + - - +
182A HIS* 3.7 13.8 + - - +
183A SER* 3.9 8.8 + - - -
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Residues in contact with ALA 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 ARG 2.9 19.1 + - - +
177A GLU* 3.8 5.2 - - - +
179A ASN* 1.3 78.4 - - - +
181A MET* 1.3 65.1 + - + +
182A HIS 3.5 0.3 + - - -
183A SER* 3.6 4.2 + - - -
184A LEU* 3.4 23.4 + - - +
248A PHE* 4.3 17.5 - - + -
274A MET* 3.9 25.6 - - + +
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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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177A GLU* 3.0 26.1 + - + +
180A ALA* 1.3 74.4 - - + +
182A HIS* 1.3 64.7 + - - +
184A LEU* 3.1 46.1 + - + +
189A LEU* 6.1 1.6 - - - -
190A ILE 5.1 2.7 - - - +
192A LEU* 4.0 21.0 + - + +
271A PHE* 3.4 38.8 - - + -
274A MET* 3.2 42.2 - - + -
401A 1G0 3.5 28.9 - - + -
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Residues in contact with HIS 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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117A LEU* 5.0 28.1 - - + +
118A THR 3.6 26.1 + - - -
119A CYS* 4.8 12.1 - - + +
178A VAL* 3.0 23.1 + - + +
179A ASN* 3.9 8.1 + - - +
180A ALA 3.4 0.2 - - - -
181A MET* 1.3 76.4 - - - +
183A SER* 1.3 67.7 + - - +
184A LEU 4.4 1.7 - - - +
192A LEU* 4.6 17.2 - - + +
193A TYR 5.6 1.1 - - - -
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Residues in contact with SER 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 ASN 3.9 6.4 + - - -
180A ALA 3.6 7.4 + - - -
181A MET 3.2 0.6 - - - -
182A HIS* 1.3 84.7 + - - +
184A LEU* 1.3 66.3 + - - +
185A ASP* 3.7 4.9 + - - +
242A TYR* 4.2 3.6 + - - -
246A LYS* 5.8 1.6 + - - -
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Residues in contact with LEU 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 ALA 3.4 11.4 + - - +
181A MET* 3.1 53.3 + - + +
182A HIS 4.4 1.9 - - - +
183A SER* 1.3 79.0 - - - +
185A ASP* 1.3 62.0 + - - +
189A LEU* 4.8 7.9 - - + -
191A ARG* 5.2 8.7 - - - +
242A TYR* 3.5 26.9 - - + +
243A LEU* 3.6 23.1 - - + -
246A LYS* 3.9 22.2 - - + -
248A PHE* 4.1 16.8 - - + -
274A MET* 3.7 9.6 - - + -
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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