Contacts of the helix formed by residues 173 - 186 (chain D) in PDB entry 2I62
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 ASP 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D CYS* 3.3 2.5 + - - +
172D PRO* 1.3 86.5 - - - +
174D LEU* 1.3 58.8 + - - +
175D PRO* 3.4 17.6 - - + +
176D ALA* 2.9 32.8 + - - +
177D TYR 3.0 22.7 + - - -
215D LEU* 3.5 20.1 - - - +
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Residues in contact with LEU 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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173D ASP* 1.3 73.6 - - - +
175D PRO* 1.4 74.1 - - + +
177D TYR* 3.1 25.5 + - + +
178D ARG* 2.9 53.0 + - + +
215D LEU* 4.3 3.9 - - - +
217D LEU* 4.3 12.6 - - + -
221D THR* 3.8 32.8 - - + -
225D ALA* 4.3 12.1 - - + -
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Residues in contact with PRO 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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173D ASP* 3.4 19.3 - - + +
174D LEU* 1.4 92.7 - - + +
176D ALA* 1.3 61.1 + - - +
178D ARG* 3.3 21.2 + - + +
179D THR* 3.1 25.7 + - - -
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Residues in contact with ALA 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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171D CYS* 3.6 8.5 - - + -
172D PRO* 3.5 29.2 - - + -
173D ASP* 2.9 21.9 + - - +
175D PRO* 1.3 76.0 - - - +
177D TYR* 1.3 58.0 + - - +
179D THR* 3.3 7.9 + - - -
180D ALA* 3.0 28.9 + - - +
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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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167D LEU* 3.7 35.6 - - + +
168D ASP* 3.3 23.0 + - - -
171D CYS* 3.6 8.0 - - - -
173D ASP 3.0 12.8 + - - +
174D LEU* 3.4 13.0 - - + +
176D ALA* 1.3 76.5 - - - +
178D ARG* 1.3 63.4 + - - +
180D ALA* 3.3 4.2 + - - +
181D LEU* 3.1 48.7 + - + +
196D MET* 3.6 22.8 - - + +
198D ASP* 4.9 0.9 + - - -
215D LEU* 4.0 11.7 - - + -
217D LEU* 3.8 25.1 - - + -
222D VAL* 3.7 19.7 - - + +
225D ALA* 4.1 18.4 - - + -
226D VAL* 5.3 0.2 - - + -
254D PHE* 4.1 6.6 - - - -
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Residues in contact with ARG 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 LEU* 2.9 48.1 + - + +
175D PRO* 3.3 27.3 + - + +
177D TYR* 1.3 77.4 - - - +
179D THR* 1.3 60.1 + - - +
181D LEU* 3.3 12.2 + - + +
182D ARG* 3.1 22.0 + - - +
225D ALA* 4.7 21.7 - - + +
228D GLU* 4.0 24.1 + - - -
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Residues in contact with THR 179 (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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145D THR* 4.8 6.5 - - - +
175D PRO 3.1 14.3 + - - -
176D ALA* 3.7 9.8 - - - -
177D TYR 3.3 0.4 - - - -
178D ARG* 1.3 72.7 - - - +
180D ALA* 1.3 60.4 + - - +
182D ARG* 3.1 12.3 + - - +
183D ASN* 2.9 53.6 + - - +
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Residues in contact with ALA 180 (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 VAL* 3.7 25.6 - - + +
145D THR* 5.6 2.0 - - + +
167D LEU* 4.2 19.1 - - + -
171D CYS* 3.9 17.3 - - - -
176D ALA 3.0 16.4 + - - +
177D TYR 3.6 5.4 - - - +
179D THR* 1.3 77.1 - - - +
181D LEU* 1.3 57.2 + - - +
183D ASN* 3.2 2.1 + - - +
184D LEU* 2.9 35.7 + - - +
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Residues in contact with LEU 181 (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 LEU* 3.7 22.2 - - + -
177D TYR* 3.1 41.2 + - + +
178D ARG* 3.5 12.1 - - - +
179D THR 3.3 0.2 - - - -
180D ALA* 1.3 76.0 - - - +
182D ARG* 1.3 63.4 + - - +
184D LEU* 3.4 8.0 + - + +
185D GLY* 3.0 19.6 + - - -
194D LEU* 4.6 12.4 - - + +
196D MET* 3.8 23.1 - - + -
225D ALA* 3.7 30.5 - - + +
226D VAL* 4.2 8.5 - - + +
229D ALA* 4.6 14.1 - - + -
231D TYR* 4.5 8.0 + - + -
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Residues in contact with ARG 182 (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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178D ARG 3.1 10.5 + - - +
179D THR* 3.4 13.2 - - - +
181D LEU* 1.3 76.3 - - - +
183D ASN* 1.3 75.9 + - - +
185D GLY* 3.1 12.7 + - - +
186D SER* 3.3 10.2 + - - -
229D ALA* 5.5 5.3 - - + +
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Residues in contact with ASN 183 (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 VAL* 3.0 22.5 + - - +
145D THR* 3.3 16.2 + - - +
146D GLN 3.1 26.3 + - - +
147D SER* 3.4 18.5 - - - +
149D PRO* 3.5 11.4 - - + +
179D THR* 2.9 32.7 + - - +
180D ALA 3.2 7.2 + - - +
182D ARG* 1.3 86.5 - - - +
184D LEU* 1.3 58.5 + - - +
186D SER* 2.6 30.2 + - - -
187D LEU 4.3 0.2 + - - -
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Residues in contact with LEU 184 (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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63D ILE* 3.6 38.8 - - + -
144D VAL* 4.3 9.4 - - + -
149D PRO* 4.6 10.5 - - + -
161D LEU* 2.8 39.5 - - + +
163D SER* 4.3 23.6 - - - -
167D LEU* 4.4 19.7 - - + -
180D ALA 2.9 19.2 + - - +
181D LEU* 3.6 8.3 - - + +
183D ASN* 1.3 77.0 - - - +
185D GLY* 1.3 60.4 + - - +
187D LEU* 3.1 14.1 + - + +
188D LEU 3.9 0.2 + - - -
194D LEU* 4.7 14.8 - - + -
196D MET* 5.6 0.7 - - - -
231D TYR* 5.8 0.2 - - - +
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Residues in contact with GLY 185 (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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181D LEU 3.0 11.8 + - - -
182D ARG* 3.1 8.8 + - - -
184D LEU* 1.3 75.0 - - - +
186D SER* 1.3 58.9 + - - +
188D LEU* 3.1 11.1 + - - +
231D TYR* 3.7 20.6 + - - -
260D LYS* 2.7 31.9 + - - -
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Residues in contact with SER 186 (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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147D SER 3.5 17.6 + - - -
148D GLN* 4.9 1.7 - - - +
149D PRO* 3.7 8.7 - - - +
182D ARG 3.3 6.6 + - - -
183D ASN* 2.6 22.8 + - - -
184D LEU 3.1 0.2 - - - -
185D GLY* 1.3 75.1 - - - +
187D LEU* 1.3 64.5 + - - +
188D LEU 3.3 1.5 - - - +
260D LYS* 4.9 0.7 - - - +
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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