Contacts of the helix formed by residues 167 - 177 (chain D) in PDB entry 2OFJ
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 THR 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D TRP* 1.3 77.7 - - - +
168D PRO* 1.4 71.1 - - + +
169D LEU* 3.6 7.6 + - - +
170D LYS* 3.5 28.3 + - + +
171D GLY* 2.8 25.3 + - - -
193D CYS* 3.9 3.5 - - - -
194D LYS* 4.1 27.3 - - + +
198D ASP* 5.2 1.1 - - - -
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Residues in contact with PRO 168 (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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167D THR* 1.4 87.5 - - - +
169D LEU* 1.3 53.5 + - - +
171D GLY* 3.0 2.7 + - - +
172D GLN* 2.8 37.5 + - - +
193D CYS* 4.6 7.0 - - - -
198D ASP* 3.6 35.9 - - + +
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Residues in contact with LEU 169 (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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167D THR* 3.3 10.3 + - - +
168D PRO* 1.3 78.6 - - - +
170D LYS* 1.3 79.8 + - - +
172D GLN* 3.1 4.6 + - + +
173D GLN* 2.8 49.3 + - + +
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Residues in contact with LYS 170 (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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138D GLU* 5.0 11.1 + - - +
139D ALA* 3.5 17.3 - - + +
166D TRP* 3.6 34.2 - - + -
167D THR* 3.4 17.1 + - + +
168D PRO 3.3 0.4 - - - -
169D LEU* 1.3 100.8 - - - +
171D GLY* 1.3 66.1 + - - +
173D GLN* 2.8 34.4 + - - +
174D PHE* 3.0 21.3 + - - +
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Residues in contact with GLY 171 (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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166D TRP* 3.7 18.7 - - - +
167D THR 2.8 16.6 + - - -
168D PRO* 3.0 5.6 + - - -
170D LYS* 1.3 78.9 - - - +
172D GLN* 1.3 55.9 + - - +
174D PHE* 3.2 5.5 + - - +
175D ALA 3.1 19.1 + - - -
193D CYS* 4.8 2.2 - - - -
202D PHE* 3.4 25.7 - - - -
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Residues in contact with GLN 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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168D PRO 2.8 17.5 + - - +
169D LEU* 4.0 4.5 - - + +
171D GLY* 1.3 69.3 - - - -
173D GLN* 1.3 61.6 + - - +
175D ALA* 3.7 9.0 - - + -
176D LYS* 3.0 25.5 + - - +
202D PHE* 4.4 8.5 + - - +
205D GLU* 3.4 34.6 - - - +
206D THR* 3.2 30.7 - - - +
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Residues in contact with GLN 173 (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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139D ALA* 4.6 10.0 - - + +
140D VAL* 4.2 13.9 + - + +
169D LEU* 2.8 36.1 + - + +
170D LYS* 2.8 43.4 + - - +
172D GLN* 1.3 76.7 - - - +
174D PHE* 1.3 68.1 + - - +
176D LYS* 3.4 21.2 + - + +
177D TYR* 3.9 11.5 - - + -
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Residues in contact with PHE 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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134D VAL* 4.0 10.3 - - + -
139D ALA* 3.7 11.0 - - - +
142D ASP* 3.4 36.3 - - + -
143D GLY* 3.5 29.2 - - - -
146D VAL* 4.0 8.5 - - + -
160D LEU* 3.6 27.1 - - + -
166D TRP* 3.4 29.6 - + + -
170D LYS 3.0 9.6 + - - +
171D GLY 3.3 8.3 - - - +
173D GLN* 1.3 77.8 - - - +
175D ALA* 1.3 67.4 + - - +
177D TYR 3.4 7.4 + - - -
178D VAL* 3.6 20.0 - - + +
186D ILE* 4.5 0.9 - - + -
189D LEU* 4.0 18.6 - - + -
202D PHE* 4.3 7.0 - + - -
208D ILE* 4.2 11.0 - - + -
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Residues in contact with ALA 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 GLY 3.1 6.9 + - - +
172D GLN* 3.7 13.5 - - + +
173D GLN 3.2 0.2 - - - -
174D PHE* 1.3 87.8 - - - +
176D LYS* 1.3 64.6 + - - +
178D VAL* 2.9 16.3 + - - -
183D ARG* 3.1 25.5 + - - +
202D PHE* 4.8 0.4 - - + -
206D THR* 3.7 33.4 - - + -
208D ILE* 4.5 4.3 - - + -
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Residues in contact with LYS 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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172D GLN 3.0 19.0 + - - +
173D GLN* 3.5 15.7 - - + +
174D PHE 3.2 0.4 - - - -
175D ALA* 1.3 76.2 - - - +
177D TYR* 1.3 93.3 + - + +
178D VAL 3.7 4.5 + - - +
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Residues in contact with TYR 177 (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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148A LEU* 3.4 39.9 - - + +
140D VAL* 3.3 29.3 - - + +
143D GLY* 2.9 24.6 - - - +
144D MET* 3.4 32.0 - - + -
147D ASN* 3.2 16.0 - - - +
173D GLN* 3.9 6.1 - - - -
174D PHE 3.4 2.8 + - - +
175D ALA 3.1 1.0 - - - -
176D LYS* 1.3 117.8 + - + +
178D VAL* 1.3 58.8 + - - +
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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