Contacts of the helix formed by residues 180 - 190 (chain O) in PDB entry 2I2X
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 180 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174O TYR* 4.3 7.5 - - + -
175O ALA* 3.2 27.0 + - + +
178O ARG* 3.0 9.7 + - + +
179O ASN* 1.3 72.7 - - - +
181O ILE* 1.3 62.3 + - - +
182O PRO* 3.5 11.6 - - - +
183O GLY* 3.0 13.8 + - - -
184O LEU* 3.1 20.9 + - - +
446O LYS* 4.0 9.2 - - - -
447O TYR* 2.4 38.1 + - - -
450O GLU* 4.8 0.9 - - - +
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Residues in contact with ILE 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179O ASN* 3.0 19.6 + - + +
180O ASP* 1.3 68.7 - - - +
182O PRO* 1.4 78.6 - - + +
184O LEU* 3.0 15.4 + - + +
185O LEU* 2.9 19.5 + - - +
242O ILE* 4.0 33.2 - - + -
245O ILE* 4.4 15.0 - - + -
424O ASP 5.5 0.4 - - - -
425O ALA* 3.9 29.2 - - + +
428O ALA* 4.6 8.3 - - + -
429O LEU* 4.0 33.7 - - + -
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Residues in contact with PRO 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180O ASP* 3.5 10.3 - - - +
181O ILE* 1.4 91.5 - - + +
183O GLY* 1.3 56.5 + - - +
185O LEU* 3.1 11.2 + - + +
186O TYR* 2.8 29.0 + - - +
428O ALA* 4.4 18.2 - - + +
429O LEU* 5.5 0.4 - - + -
432O LEU* 4.0 33.4 - - + -
439O PHE* 3.5 11.5 - - + -
443O CYS* 5.6 2.0 - - - -
446O LYS* 6.1 1.8 - - - -
447O TYR* 4.0 4.0 - - - +
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Residues in contact with GLY 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O VAL* 4.1 2.6 - - - +
175O ALA* 4.0 9.0 - - - -
180O ASP* 3.0 18.6 + - - -
182O PRO* 1.3 72.3 - - - +
184O LEU* 1.3 54.0 + - - +
186O TYR* 3.5 1.1 - - - +
187O SER* 2.6 42.6 + - - -
447O TYR* 3.0 30.4 + - - -
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Residues in contact with LEU 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 3.7 30.7 - - + -
175O ALA* 4.1 5.4 - - + +
176O VAL* 4.0 26.7 - - + +
179O ASN* 6.0 0.4 - - - -
180O ASP 3.1 7.9 + - - +
181O ILE* 3.0 28.2 + - + +
183O GLY* 1.3 73.3 - - - +
185O LEU* 1.3 66.4 + - - +
187O SER* 3.5 3.4 - - - -
188O ILE* 3.0 41.4 + - + +
242O ILE* 4.0 27.6 - - + +
245O ILE* 5.5 1.6 - - + -
246O ALA* 4.6 14.4 - - + +
249O ILE* 4.1 11.4 - - + +
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Residues in contact with LEU 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181O ILE 2.9 11.6 + - - +
182O PRO* 3.3 11.2 - - + +
184O LEU* 1.3 74.6 - - - +
186O TYR* 1.3 59.1 + - - +
189O GLY* 2.9 31.1 + - - -
190O CYS* 3.5 2.9 + - - -
249O ILE* 3.8 17.6 - - + +
390O TYR* 3.5 35.4 - - + +
393O ALA* 3.5 33.0 - - + +
394O LYS* 3.8 18.8 - - + +
429O LEU* 4.1 13.5 - - + -
432O LEU* 3.8 22.4 - - + -
439O PHE* 4.0 4.3 - - + -
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Residues in contact with TYR 186 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O VAL* 4.3 6.3 - - + -
182O PRO 2.8 15.7 + - - +
183O GLY* 3.5 5.8 - - - +
185O LEU* 1.3 76.2 - - - +
187O SER* 1.3 60.9 + - - +
190O CYS* 3.0 14.2 + - + +
191O LEU* 2.9 62.2 + - + +
439O PHE* 3.9 17.9 - + + -
440O MET* 3.9 28.7 + - + +
443O CYS* 3.5 33.0 - - + -
444O LEU* 4.0 12.7 - - - +
447O TYR* 3.7 23.6 - + + -
454O PHE* 3.7 20.1 - + - -
461O PHE* 4.0 9.9 - - - -
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Residues in contact with SER 187 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLY* 3.3 22.0 - - - -
171O VAL* 3.8 9.6 - - - -
172O PHE* 3.5 25.9 - - - +
183O GLY 2.6 28.2 + - - -
184O LEU* 3.2 9.7 + - - -
186O TYR* 1.3 73.8 - - - +
188O ILE* 1.3 62.0 + - - +
191O LEU* 3.4 15.1 - - - +
192O GLY 2.9 26.3 + - - -
222O GLN* 3.6 9.0 + - - -
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Residues in contact with ILE 188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O PHE* 4.1 15.9 - - + -
184O LEU* 3.0 21.1 + - + +
187O SER* 1.3 80.5 - - - +
189O GLY* 1.3 61.6 + - - +
192O GLY* 3.4 16.3 - - - -
193O SER 3.6 0.2 + - - -
219O ASP* 3.6 12.6 - - - +
222O GLN* 3.5 30.3 - - + +
223O ALA 4.9 0.4 - - - +
246O ALA* 3.8 35.9 - - + +
249O ILE* 3.6 12.1 - - + +
250O SER* 3.6 30.3 - - - -
253O ARG* 3.5 11.9 - - + +
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Residues in contact with GLY 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O LEU 2.9 21.1 + - - -
188O ILE* 1.3 76.3 - - - +
190O CYS* 1.3 58.1 + - - +
193O SER* 2.6 25.9 + - - -
249O ILE* 3.5 16.4 - - - +
252O PRO* 5.8 0.6 - - - +
253O ARG* 4.9 1.6 - - - -
389O ILE 3.6 15.0 - - - +
393O ALA* 4.0 11.7 - - - -
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Residues in contact with CYS 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185O LEU* 3.5 5.1 + - - -
186O TYR* 3.0 16.4 + - + +
189O GLY* 1.3 79.8 - - - +
191O LEU* 1.3 68.1 + - - +
192O GLY 3.2 0.9 - - - -
193O SER* 3.2 2.3 + - - -
194O ILE* 2.9 30.7 + - + +
389O ILE* 4.5 7.6 - - + -
390O TYR* 4.0 35.7 - - - -
436O MET* 5.4 1.1 - - - -
439O PHE* 4.1 11.2 - - - -
440O MET* 3.7 35.9 - - + -
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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