Contacts of the helix formed by residues 188 - 197 (chain A) in PDB entry 2CXO
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ASN* 3.1 26.0 + - + +
187A ILE* 1.3 80.3 - - - +
189A GLY* 1.3 66.8 + - - +
190A THR* 2.9 24.4 + - - -
191A HIS* 2.9 20.4 + - - +
192A ILE 4.3 0.9 + - - -
221A ASN* 5.3 0.2 - - - +
342B ASP* 3.4 10.7 - - - +
343B GLN* 2.8 30.7 + - + +
412B THR* 4.3 8.5 + - - -
421B HIS* 4.8 0.8 + - - -
422B HIS* 4.9 1.9 + - - -
425B LEU* 3.8 30.3 - - + +
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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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187A ILE 2.9 7.8 + - - -
188A ASP* 1.3 73.9 + - - +
190A THR* 1.3 61.7 + - - +
191A HIS 3.2 0.6 + - - -
192A ILE* 3.6 3.9 + - - +
193A ALA* 2.9 29.2 + - - +
412B THR* 5.4 1.0 + - - -
414B HIS* 4.3 9.6 - - - -
416B ILE* 3.7 15.9 - - - +
421B HIS* 3.6 22.7 - - - +
422B HIS* 5.1 2.0 + - - +
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Residues in contact with THR 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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188A ASP* 3.0 23.4 + - - -
189A GLY* 1.3 77.2 - - - +
191A HIS* 1.3 62.8 + - - +
194A LYS* 3.0 26.9 + - + +
342B ASP* 5.4 1.7 + - - -
343B GLN* 3.9 15.7 - - + -
344B TYR* 3.5 47.7 - - + +
412B THR* 4.4 5.3 + - - -
413B GLN* 5.0 1.4 + - - +
414B HIS* 3.3 24.8 - - - +
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Residues in contact with HIS 191 (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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165A LEU* 6.4 1.8 - - + -
183A PHE* 3.2 22.0 + - + -
184A VAL* 4.4 4.7 - - + -
185A SER* 3.2 40.7 + - - -
186A ASN* 3.2 21.0 + - - +
188A ASP 2.9 14.6 + - - +
190A THR* 1.3 82.2 - - - +
192A ILE* 1.3 60.4 + - - +
194A LYS* 4.2 1.4 - - - +
195A THR* 2.9 29.3 + - - -
343B GLN* 3.7 34.7 + - + +
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Residues in contact with ILE 192 (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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153A ILE* 5.3 0.2 - - + -
155A ILE* 4.3 17.7 - - + -
184A VAL* 3.7 30.9 - - + +
188A ASP 4.3 0.4 + - - -
189A GLY* 3.6 3.5 + - - +
191A HIS* 1.3 75.8 - - - +
193A ALA* 1.3 63.7 + - - +
195A THR* 3.3 1.7 + - - -
196A LEU* 2.9 65.3 + - + +
206A PHE* 5.0 1.8 - - + -
221A ASN* 3.7 28.7 + - - +
224A THR* 4.1 11.0 - - + -
225A ALA* 4.5 3.1 - - + +
416B ILE* 3.4 28.7 - - + -
421B HIS* 3.9 7.6 - - + +
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Residues in contact with ALA 193 (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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189A GLY 2.9 20.4 + - - +
190A THR 4.1 1.1 - - - +
192A ILE* 1.3 80.7 - - - +
194A LYS* 1.3 59.9 + - - +
196A LEU* 3.5 6.0 + - - +
197A ALA* 3.1 28.8 + - - +
414B HIS* 4.0 28.0 - - + +
416B ILE* 4.1 18.2 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A TRP* 5.0 2.0 - - - -
190A THR* 3.0 22.4 + - + +
191A HIS* 4.4 1.6 - - - +
193A ALA* 1.3 75.0 - - - +
195A THR* 1.3 66.6 + - - +
197A ALA* 3.7 31.5 + - - +
198A SER* 3.7 15.5 + - - -
172B LYS* 5.2 10.1 - - + -
344B TYR* 3.4 29.4 - - + +
414B HIS* 3.8 23.6 - - - +
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Residues in contact with THR 195 (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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153A ILE* 4.2 4.3 - - + -
182A TRP* 3.7 39.2 - - + -
183A PHE 4.7 2.6 + - - -
184A VAL* 3.6 25.1 - - + +
191A HIS* 2.9 22.8 + - - -
192A ILE* 3.3 4.9 + - - -
194A LYS* 1.3 78.0 - - - +
196A LEU* 1.3 65.0 + - + +
198A SER* 3.1 15.4 + - - -
199A LEU* 3.3 30.2 - - + +
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Residues in contact with LEU 196 (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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192A ILE* 2.9 47.4 + - + +
193A ALA* 4.1 5.4 - - - +
195A THR* 1.3 73.2 - - + +
197A ALA* 1.3 62.2 + - - +
199A LEU* 3.1 27.2 + - + +
206A PHE* 3.7 35.0 - - + -
224A THR* 4.7 8.1 - - + +
225A ALA* 4.6 6.3 - - - -
228A TRP* 3.7 59.3 + - + +
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Residues in contact with ALA 197 (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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193A ALA 3.1 18.8 + - - +
194A LYS* 3.7 29.4 - - - +
195A THR 3.2 0.4 - - - -
196A LEU* 1.3 76.6 - - - +
198A SER* 1.3 59.5 + - - +
199A LEU 3.4 2.4 + - - +
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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