Contacts of the helix formed by residues 174 - 185 (chain A) in PDB entry 4O8M
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 SER 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.5 25.0 + - - -
93A GLY* 3.6 11.7 - - - -
94A ALA* 4.0 3.4 - - - +
172A GLN* 2.8 22.9 + - - +
173A HIS* 1.3 75.2 - - - +
175A ARG* 1.3 57.8 + - - +
176A LEU* 3.2 6.8 + - - +
177A PHE* 3.2 23.9 + - - +
178A LEU* 2.9 32.4 + - - +
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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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93A GLY 4.0 3.8 + - - +
96A MET* 4.0 17.3 - - + -
97A ASP* 4.4 14.3 + - - +
174A SER* 1.3 72.5 + - - +
176A LEU* 1.3 63.0 + - - +
178A LEU* 3.8 6.5 - - - +
179A GLN* 3.0 51.8 + - + +
309A GLY 3.6 6.9 + - - -
310A PHE* 4.0 13.6 - - + +
311A PRO* 3.6 20.8 - - - +
312A GLU* 2.5 41.8 + - - +
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Residues in contact with LEU 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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91A ASP* 6.1 0.2 - - - +
93A GLY* 3.8 18.4 - - - +
96A MET* 3.9 7.1 - - - -
103A GLY 3.2 25.6 - - - +
106A ASN* 3.5 34.5 - - + +
107A ALA* 3.9 17.7 - - + -
108A PRO* 4.4 0.9 - - + -
174A SER* 3.2 8.6 + - - +
175A ARG* 1.3 80.3 - - - +
177A PHE* 1.3 70.8 + - + +
179A GLN 3.6 0.3 + - - -
180A THR* 2.8 37.1 + - - +
310A PHE* 3.8 29.7 - - + -
313A TRP* 4.4 4.7 - - + -
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Residues in contact with PHE 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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91A ASP* 4.3 7.2 - - - -
106A ASN* 4.3 2.5 - - + -
108A PRO* 6.4 0.4 - - + -
150A ARG* 3.6 29.4 - - - -
171A VAL* 4.0 20.9 - - + -
172A GLN* 3.4 34.5 - - + -
174A SER* 3.2 16.4 + - - +
176A LEU* 1.3 97.8 - - + +
178A LEU* 1.3 67.4 + - - +
180A THR* 4.1 11.9 - - + -
181A ILE* 2.8 30.9 + - + +
209A GLU* 4.3 15.5 - - - +
232A HIS* 5.5 1.6 - + - -
233A THR* 3.7 22.4 - - + -
235A HIS* 3.7 18.6 - + - -
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Residues in contact with LEU 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 VAL* 4.1 8.5 - - + +
174A SER 2.9 17.6 + - - +
175A ARG* 3.8 7.2 - - - +
177A PHE* 1.3 76.7 - - - +
179A GLN* 1.3 87.3 + - - +
182A ASN* 3.0 25.6 + - + +
188A PRO* 3.5 32.9 - - + +
190A PRO* 3.9 27.4 - - + -
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Residues in contact with GLN 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* 3.0 43.0 + - - +
178A LEU* 1.3 101.0 - - - +
180A THR* 1.4 55.7 + - - +
182A ASN* 3.4 16.3 + - - +
183A ALA* 3.0 29.3 + - - +
305A VAL* 3.9 15.8 - - + +
309A GLY* 4.5 8.2 - - - +
310A PHE* 3.6 27.6 - - + -
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Residues in contact with THR 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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108A PRO* 3.5 42.6 - - + +
176A LEU* 2.8 27.3 + - - +
177A PHE* 3.3 12.5 + - + -
179A GLN* 1.4 72.5 - - - +
181A ILE* 1.3 62.9 + - + +
183A ALA* 3.2 6.9 + - - +
184A MET* 2.9 49.6 + - + +
232A HIS* 4.9 10.5 - - + -
233A THR* 5.8 0.7 - - - +
302A VAL* 4.5 1.5 - - + +
305A VAL* 4.9 4.8 - - - +
310A PHE* 4.9 2.3 - - - -
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Residues in contact with ILE 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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152A LEU* 4.1 23.8 - - + -
164A LEU* 5.5 3.1 - - + -
169A VAL* 3.8 27.8 - - + -
171A VAL* 3.5 24.5 - - + -
177A PHE* 2.8 16.7 + - + +
180A THR* 1.3 75.9 - - + +
182A ASN* 1.3 62.0 + - - +
184A MET* 3.3 23.3 + - + +
185A GLY 3.3 5.2 + - - -
186A GLY* 3.1 24.6 + - - +
188A PRO* 4.1 23.6 - - + -
209A GLU* 4.3 13.0 - - + -
232A HIS* 5.1 4.3 - - - +
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Residues in contact with ASN 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 LEU* 3.0 21.2 + - + +
179A GLN* 3.7 17.9 + - - +
180A THR 3.2 0.2 - - - -
181A ILE* 1.3 77.8 - - - +
183A ALA* 1.3 63.6 + - - +
185A GLY* 3.3 13.0 + - - -
186A GLY 3.7 15.9 - - - +
188A PRO* 4.1 14.2 - - + +
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Residues in contact with ALA 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 GLN 3.0 17.0 + - - +
180A THR 3.7 3.6 - - - +
182A ASN* 1.3 75.4 - - - +
184A MET* 1.3 61.9 + - - +
185A GLY* 3.1 7.4 + - - -
301A SER* 3.3 32.8 - - - +
302A VAL* 4.3 3.1 - - + -
305A VAL* 3.6 28.0 - - + -
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Residues in contact with MET 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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109A TYR* 4.9 2.2 - - - +
152A LEU* 4.4 10.3 - - + -
161A PRO* 3.2 30.8 - - - +
164A LEU* 3.5 11.8 - - + +
180A THR* 2.9 37.0 + - - +
181A ILE* 3.7 22.0 - - + +
182A ASN 3.3 0.2 - - - -
183A ALA* 1.3 75.9 - - - +
185A GLY* 1.3 57.1 + - - +
186A GLY 3.7 1.1 - - - -
230A THR* 4.0 18.6 - - + -
232A HIS* 4.1 25.4 - - + +
298A PHE* 3.6 30.5 - - + +
301A SER* 3.5 17.3 - - - +
302A VAL* 4.0 10.8 - - + -
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Residues in contact with GLY 185 (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 PRO* 4.3 8.0 - - - +
164A LEU* 3.3 21.3 - - - +
165A LYS* 3.9 7.1 + - - -
166A GLY 4.5 1.4 + - - -
181A ILE 3.3 1.2 + - - -
182A ASN 3.3 6.7 + - - -
183A ALA 3.1 5.6 - - - -
184A MET* 1.3 79.6 - - - +
186A GLY* 1.3 64.1 + - - +
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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