Contacts of the helix formed by residues 180 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A TYR* 4.5 6.2 - - + -
175A ALA* 3.3 26.0 + - + +
178A ARG* 3.0 10.7 - - + +
179A ASN* 1.3 73.8 - - - +
181A ILE* 1.3 58.4 + - - +
182A PRO* 3.4 12.6 - - - +
183A GLY* 3.0 15.0 + - - -
184A LEU* 3.0 27.1 + - - +
446A LYS* 3.9 10.9 - - - -
447A TYR* 2.6 34.7 + - - -
450A GLU* 5.0 0.3 - - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.1 17.5 + - + +
180A ASP* 1.3 67.4 - - - +
182A PRO* 1.4 75.2 - - + +
184A LEU* 3.0 28.4 + - + +
185A LEU* 2.9 20.1 + - - +
242A ILE* 3.8 24.0 - - + -
245A ILE* 4.6 11.9 - - + -
249A ILE* 4.9 0.4 - - + +
425A ALA* 3.6 31.4 - - + +
428A ALA* 4.6 6.7 - - + -
429A LEU* 3.8 37.5 - - + -
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.4 10.8 - - - +
181A ILE* 1.4 93.9 - - + +
183A GLY* 1.3 55.2 + - - +
185A LEU* 3.1 10.8 + - + +
186A TYR* 2.9 29.7 + - - +
428A ALA* 4.5 17.5 - - + +
429A LEU* 6.1 0.2 - - - -
432A LEU* 4.3 32.8 - - + -
439A PHE* 3.6 9.7 - - + -
443A CYS* 5.5 2.7 - - - -
446A LYS* 6.2 1.8 - - + -
447A TYR* 4.2 4.3 - - - +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.4 2.5 - - - +
175A ALA* 3.9 11.0 - - - -
180A ASP* 3.0 19.1 + - - -
182A PRO* 1.3 71.8 - - - +
184A LEU* 1.3 54.1 + - - +
186A TYR* 3.8 0.8 - - - +
187A SER* 2.7 41.8 + - - -
447A TYR* 3.1 29.3 + - - -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 3.9 26.7 - - + -
175A ALA* 3.9 18.6 - - + -
176A VAL* 3.9 17.3 - - + +
179A ASN* 5.8 0.7 - - - -
180A ASP 3.0 12.8 + - - +
181A ILE* 3.0 41.4 + - + +
183A GLY* 1.3 74.3 - - - +
185A LEU* 1.3 54.8 + - - +
187A SER* 3.1 4.1 + - - -
188A ILE* 3.0 40.1 + - + +
242A ILE* 4.0 20.9 - - + +
245A ILE* 5.5 2.5 - - + -
246A ALA* 4.6 16.4 - - + +
249A ILE* 4.3 10.8 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE 2.9 11.7 + - - +
182A PRO* 3.3 10.8 - - + +
184A LEU* 1.3 75.3 - - - +
186A TYR* 1.3 58.3 + - - +
189A GLY* 3.0 24.4 + - - -
190A CYS* 3.3 3.7 + - - -
249A ILE* 3.8 19.8 - - + +
390A TYR* 3.6 36.3 - - + +
393A ALA* 3.7 29.4 - - + -
394A LYS* 3.9 21.5 - - + +
429A LEU* 4.4 8.7 - - + -
432A LEU* 3.6 24.0 - - + -
439A PHE* 4.0 3.6 - - + -
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.4 5.2 - - + -
182A PRO 2.9 15.9 + - - +
183A GLY* 3.2 4.7 + - - +
185A LEU* 1.3 76.3 - - - +
187A SER* 1.3 60.4 + - - +
190A CYS* 2.9 18.4 + - + +
191A LEU* 2.8 62.7 + - + +
439A PHE* 3.8 15.5 - + + -
440A MET* 3.8 28.7 + - + -
443A CYS* 3.4 38.6 - - + -
444A LEU* 3.8 14.2 - - - +
447A TYR* 3.6 21.3 - + - -
454A PHE* 3.6 20.0 - + - -
461A PHE* 4.2 8.0 - - - -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY* 3.3 25.6 - - - -
171A VAL* 4.0 7.0 - - - -
172A PHE* 3.4 28.7 - - - +
183A GLY 2.7 28.2 + - - -
184A LEU* 3.1 9.5 + - - -
186A TYR* 1.3 74.1 - - - +
188A ILE* 1.3 62.5 + - - +
191A LEU* 3.6 10.5 - - - +
192A GLY 2.9 24.1 + - - -
222A GLN* 3.2 10.1 + - - -
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 4.1 18.4 - - + -
184A LEU* 3.0 22.4 + - + +
187A SER* 1.3 81.6 - - - +
189A GLY* 1.3 67.0 + - - +
192A GLY* 3.3 18.9 - - - -
219A ASP* 3.5 18.6 - - - +
222A GLN* 3.6 30.5 - - + +
223A ALA 4.7 0.9 - - - +
246A ALA* 3.9 31.4 - - + +
249A ILE* 3.8 11.4 - - + +
250A SER* 3.7 21.8 - - - -
253A ARG* 3.4 17.4 - - + +
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU 3.0 14.4 + - - -
188A ILE* 1.3 80.4 - - - +
190A CYS* 1.3 61.6 + - - +
193A SER* 2.7 29.2 + - - -
249A ILE* 3.5 18.8 - - - +
253A ARG* 4.8 1.6 - - - -
389A ILE* 4.0 10.0 - - - +
393A ALA* 4.0 13.5 - - - -
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Residues in contact with CYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.8 11.2 - - - -
186A TYR* 2.9 16.2 + - + +
189A GLY* 1.3 77.7 - - - +
191A LEU* 1.3 68.4 + - - +
192A GLY 3.3 0.7 - - - -
193A SER* 3.2 3.4 + - - -
194A ILE* 3.0 29.2 + - + +
389A ILE* 4.3 5.3 - - + +
390A TYR* 4.0 26.5 - - - -
436A MET* 5.7 0.7 - - - -
439A PHE* 3.9 19.3 - - - -
440A MET* 3.5 36.8 - - + -
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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