Contacts of the helix formed by residues 170 - 178 (chain A) in PDB entry 3ORH
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASP* 5.7 0.2 - - - -
138A PRO* 4.5 0.7 - - - +
144A TRP 2.9 22.2 + - - -
145A HIS 4.1 0.8 - - - -
147A HIS* 3.4 19.5 + - - +
148A GLN* 2.8 38.7 + - - +
169A CYS* 1.3 75.9 - - - +
171A LEU* 1.3 58.1 + - - +
172A THR* 2.8 26.9 + - - -
173A SER* 3.1 14.3 + - - -
174A TRP* 3.0 40.6 + - - +
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Residues in contact with LEU 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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45A TRP* 4.6 6.7 - - + -
46A GLU* 3.5 39.5 - - + +
49A TYR* 3.7 20.6 - - + -
135A ASP* 5.9 0.2 + - - -
169A CYS* 4.1 8.8 - - + -
170A ASN* 1.3 73.2 - - - +
172A THR* 1.3 57.4 + - + +
174A TRP* 4.3 12.1 - - + +
175A GLY* 2.8 31.5 + - - -
222A TYR* 3.7 16.4 - - + +
223A TYR* 3.6 20.3 - - + -
228A MET* 3.6 34.3 - - + -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.8 5.4 - - + -
137A TYR* 3.6 39.7 - - + +
138A PRO* 3.4 18.5 - - + +
144A TRP* 3.4 43.3 + - + -
170A ASN* 2.8 20.8 + - - -
171A LEU* 1.3 76.3 - - + +
173A SER* 1.3 61.3 + - - +
175A GLY* 4.4 0.3 - - - -
176A GLU* 3.6 13.9 + - - +
222A TYR* 4.4 18.9 - - + +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 3.8 8.3 - - - +
145A HIS* 2.8 37.9 + - - +
148A GLN* 5.3 0.2 - - - -
170A ASN* 3.1 29.9 + - - -
172A THR* 1.3 80.1 + - - +
174A TRP* 1.3 67.3 + - - +
176A GLU* 3.3 4.7 + - - +
177A LEU* 3.0 40.1 + - - +
193A GLN* 5.0 1.2 + - - -
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Residues in contact with TRP 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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49A TYR* 3.4 24.2 - - - -
148A GLN* 4.3 5.4 - - - +
168A TYR* 3.6 32.8 - + - -
169A CYS* 3.7 17.7 - - - -
170A ASN 3.0 25.1 + - - +
171A LEU* 4.3 9.6 - - + -
173A SER* 1.3 83.3 - - - +
175A GLY* 1.3 62.7 + - - +
177A LEU* 3.4 1.1 + - - +
178A MET* 3.0 31.7 + - + +
185A ILE* 5.9 2.2 - - + -
188A MET* 3.1 32.5 - - + +
189A PHE* 4.3 6.5 - + - -
193A GLN* 3.2 30.8 + - + +
223A TYR* 4.1 16.8 - - + +
229A ILE* 3.6 24.5 - - + -
231A PRO* 4.2 9.9 - - + -
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Residues in contact with GLY 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 LEU 2.8 16.7 + - - -
174A TRP* 1.3 72.0 - - - +
176A GLU* 1.3 60.4 + - - +
178A MET* 3.5 6.1 + - - +
179A LYS* 3.3 29.4 + - - +
222A TYR 3.3 24.0 - - - -
223A TYR* 3.4 19.2 - - - -
224A ALA 4.9 3.0 + - - -
225A PHE 5.6 0.4 + - - -
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Residues in contact with GLU 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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144A TRP* 4.3 20.7 - - - +
145A HIS* 4.6 9.4 - - + +
172A THR 3.6 14.4 + - - +
173A SER 3.3 8.7 + - - +
174A TRP 3.3 0.2 - - - -
175A GLY* 1.3 73.7 - - - +
177A LEU* 1.3 65.4 + - + +
178A MET 3.2 0.2 - - - -
179A LYS* 3.1 33.8 + - - +
180A SER* 3.7 8.7 + - - -
222A TYR 4.1 1.8 + - - -
183B SER* 5.4 3.3 + - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 3.8 22.0 - - + +
173A SER* 3.0 35.6 + - - +
174A TRP 4.0 4.0 - - - +
176A GLU* 1.3 76.2 - - + +
178A MET* 1.4 58.5 + - - +
181A LYS* 3.4 28.5 + - + -
182A TYR* 2.9 39.2 + - + -
188A MET* 3.3 39.7 - - + -
192A THR* 4.5 12.6 - - + +
193A GLN* 5.2 0.9 - - - +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A TRP* 3.0 21.9 + - + +
175A GLY* 3.9 6.1 - - - +
176A GLU 3.2 0.4 - - - -
177A LEU* 1.4 74.2 - - - +
179A LYS* 1.3 60.0 + - - +
182A TYR* 3.1 35.9 - - - +
184A ASP 3.6 9.0 - - - +
185A ILE* 3.6 38.4 - - + +
188A MET* 3.6 34.1 - - + +
223A TYR* 4.8 2.0 - - - +
225A PHE* 3.6 58.4 - - + +
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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