Contacts of the helix formed by residues 170 - 178 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASP* 5.5 1.6 - - - -
138B PRO* 4.2 2.1 - - - +
144B TRP 3.1 23.5 + - - +
145B HIS* 4.3 0.6 - - - +
147B HIS* 3.1 22.8 + - - +
148B GLN* 2.9 38.1 + - - +
169B CYS* 1.3 75.5 - - - +
171B LEU* 1.3 57.6 + - - +
172B THR* 3.6 8.0 + - - -
173B SER* 3.0 26.2 + - - -
174B TRP* 2.8 41.6 + - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP* 4.2 2.7 - - + -
46B GLU* 3.6 35.9 - - + +
49B TYR* 3.4 29.6 - - + -
135B ASP* 5.5 1.0 + - - +
169B CYS* 3.6 20.1 - - + -
170B ASN* 1.3 70.8 - - - +
172B THR* 1.4 59.6 + - - +
174B TRP* 4.3 4.9 - - + +
175B GLY* 2.7 31.7 + - - -
222B TYR* 3.6 24.6 - - + +
223B TYR* 3.6 19.0 - - + -
228B MET* 3.6 24.0 - - + -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.3 19.8 - - + +
10B PHE* 3.7 24.7 - - + -
40B PRO 4.8 0.5 + - - -
137B TYR* 3.4 23.6 + - - +
138B PRO* 4.1 10.5 - - + +
144B TRP* 2.8 32.8 + - + +
170B ASN* 3.4 7.5 + - - -
171B LEU* 1.4 77.6 - - - +
173B SER* 1.3 61.7 + - - +
176B GLU* 3.5 11.8 + - - +
222B TYR* 4.3 19.9 - - - +
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.6 9.6 - - - +
145B HIS* 2.7 36.2 + - - +
148B GLN* 5.3 0.4 + - - -
170B ASN* 3.0 34.2 + - - -
172B THR* 1.3 75.8 - - - +
174B TRP* 1.3 74.0 + - - +
176B GLU* 3.0 6.4 + - - +
177B LEU* 3.0 33.3 + - - +
193B GLN* 5.1 1.0 + - - -
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Residues in contact with TRP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 3.4 25.4 - + - -
148B GLN* 4.2 6.2 - - - +
168B TYR* 3.6 33.0 - + - -
169B CYS* 3.7 18.6 - - + -
170B ASN 2.8 31.7 + - - +
171B LEU* 5.1 4.9 - - + -
173B SER* 1.3 84.8 - - - +
175B GLY* 1.3 56.6 + - - +
177B LEU* 3.3 6.6 + - + +
178B MET* 2.9 37.3 + - + +
185B ILE* 5.7 2.9 - - + -
188B MET* 3.9 22.0 - - - -
189B PHE* 4.2 13.0 - + - -
193B GLN* 3.2 34.1 + - + +
223B TYR* 4.1 17.5 - + + +
228B MET* 6.4 0.7 - - + -
229B ILE* 3.6 24.9 - - + -
231B PRO* 4.3 3.1 - - + -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU 2.7 15.8 + - - -
174B TRP* 1.3 72.1 - - - +
176B GLU* 1.3 59.2 + - - +
178B MET* 3.6 5.4 + - - +
179B LYS* 3.4 28.8 + - - +
222B TYR 3.3 23.8 - - - -
223B TYR* 3.4 20.8 - - - -
224B ALA 5.0 2.2 + - - -
225B PHE 5.7 0.6 + - - -
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TRP* 3.8 30.8 - - + +
145B HIS* 4.1 13.5 - - + +
172B THR 3.5 16.3 + - - +
173B SER 3.0 9.7 + - - +
175B GLY* 1.3 74.0 - - - +
177B LEU* 1.4 64.3 + - + +
179B LYS* 3.2 35.3 + - - +
180B SER* 3.4 17.4 + - - +
222B TYR 4.0 1.4 + - - -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS* 3.9 22.4 - - + +
173B SER* 3.0 32.6 + - - +
174B TRP* 3.9 8.1 - - + +
176B GLU* 1.4 75.5 - - + +
178B MET* 1.3 60.9 + - - +
180B SER* 4.5 3.6 - - - +
181B LYS* 3.2 33.5 + - + -
182B TYR* 2.9 31.3 + - + -
188B MET* 3.9 35.9 - - + -
192B THR* 4.1 18.6 - - + +
193B GLN* 5.0 1.6 - - - +
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 6.1 1.7 - - - +
174B TRP* 2.9 23.3 + - + +
175B GLY* 4.0 6.1 - - - +
176B GLU 3.3 0.4 - - - -
177B LEU* 1.3 75.1 - - - +
179B LYS* 1.4 60.7 + - - +
182B TYR* 3.1 34.6 - - - +
183B SER* 5.2 0.2 - - - -
184B ASP 3.6 9.4 - - - +
185B ILE* 3.6 38.8 - - + +
188B MET* 3.7 31.2 - - + -
223B TYR* 4.8 1.3 - - - +
225B PHE* 3.6 58.5 - - + +
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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
------------------------------------------------------------
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