Contacts of the helix formed by residues 170 - 178 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASP* 5.6 0.7 - - - -
136D THR 6.1 0.7 - - - -
138D PRO* 4.7 0.3 - - - +
144D TRP 2.9 23.1 + - - +
145D HIS* 4.0 1.0 - - - +
147D HIS* 3.5 17.2 + - - +
148D GLN* 2.8 40.3 + - - +
169D CYS* 1.3 75.5 - - - +
171D LEU* 1.3 57.7 + - - +
172D THR* 3.6 13.9 - - - +
173D SER* 3.1 25.2 + - - -
174D TRP* 2.9 41.1 + - - +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D TRP* 4.7 3.1 - - + -
46D GLU* 3.5 38.6 - - + +
49D TYR* 3.7 20.4 - - + -
50D MET* 5.0 0.4 - - + -
135D ASP* 5.6 0.6 + - - +
169D CYS* 4.0 9.2 - - + -
170D ASN* 1.3 71.4 - - - +
172D THR* 1.3 60.6 + - - +
174D TRP* 4.3 15.0 - - + +
175D GLY* 2.8 29.5 + - - -
222D TYR* 3.7 18.9 - - + +
223D TYR* 3.6 19.1 - - + +
228D MET* 3.6 34.1 - - + -
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D TYR* 4.3 21.6 + - + -
138D PRO* 3.5 39.7 - - + -
144D TRP* 3.0 37.3 + - + +
170D ASN* 3.6 7.2 - - - +
171D LEU* 1.3 78.5 - - - +
173D SER* 1.3 63.7 + - - +
176D GLU* 3.7 8.3 + - - +
222D TYR* 4.5 23.5 - - - +
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TRP* 3.6 9.0 - - - +
145D HIS* 2.8 36.0 + - - +
148D GLN* 5.1 0.3 + - - -
170D ASN* 3.1 36.8 + - - -
172D THR* 1.3 76.3 - - - +
174D TRP* 1.4 69.8 + - - +
176D GLU* 3.3 6.8 + - - +
177D LEU* 3.1 32.1 + - - +
193D GLN* 5.2 1.2 + - - -
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Residues in contact with TRP 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D TYR* 3.4 24.0 - + - -
148D GLN* 4.3 5.3 - - - +
168D TYR* 3.6 33.0 - + - -
169D CYS* 3.7 18.2 - - - -
170D ASN* 2.9 31.1 + - + +
171D LEU* 4.3 9.2 - - + -
173D SER* 1.4 79.3 - - - +
175D GLY* 1.3 65.3 + - - +
177D LEU* 3.3 6.5 + - + +
178D MET* 3.0 30.1 + - + +
185D ILE* 5.8 0.2 - - + -
188D MET* 3.6 29.4 - - + -
189D PHE* 4.3 6.1 - + - -
193D GLN* 3.2 33.4 + - + +
223D TYR* 4.1 15.9 - - + +
229D ILE* 3.6 23.8 - - + -
231D PRO* 4.3 9.4 - - + -
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Residues in contact with GLY 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU 2.8 15.4 + - - -
174D TRP* 1.3 71.5 - - - +
176D GLU* 1.4 58.6 + - - +
178D MET* 3.5 5.4 + - - +
179D LYS* 3.3 30.2 + - - +
222D TYR 3.3 23.6 - - - -
223D TYR* 3.4 21.3 - - - -
224D ALA 5.0 2.6 + - - -
225D PHE 5.6 0.7 + - - -
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D TRP* 3.4 33.1 - - + -
145D HIS* 4.3 11.0 - - + +
172D THR 3.7 14.1 + - - +
173D SER 3.3 9.8 + - - +
174D TRP 3.3 0.2 - - - -
175D GLY* 1.4 71.5 - - - +
177D LEU* 1.3 66.6 + - + +
178D MET 3.2 0.2 - - - -
179D LYS* 3.1 33.2 + - - +
180D SER* 3.7 10.6 + - - +
222D TYR 4.2 1.0 + - - -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D HIS* 4.3 18.2 - - + +
173D SER* 3.1 32.9 + - - +
174D TRP* 3.3 8.7 + - + +
176D GLU* 1.3 76.9 - - + +
178D MET* 1.3 58.3 - - - +
181D LYS* 3.3 32.3 + - + +
182D TYR* 2.9 34.5 + - + -
188D MET* 4.0 32.3 - - + -
192D THR* 4.2 18.8 - - + +
193D GLN* 5.0 1.6 - - - +
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Residues in contact with MET 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D TRP* 3.0 22.7 + - + +
175D GLY* 3.9 5.2 - - - +
176D GLU 3.2 0.4 - - - -
177D LEU* 1.3 75.3 - - - +
179D LYS* 1.3 59.2 + - - +
182D TYR* 3.1 36.0 - - - +
184D ASP 3.6 7.9 - - - +
185D ILE* 3.6 39.7 - - + +
188D MET* 3.7 33.2 - - + -
223D TYR* 4.8 1.1 - - - +
225D PHE* 3.6 60.4 - - + +
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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