Contacts of the strand formed by residues 237 - 246 (chain A) in PDB entry 1G24
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 ILE 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.3 24.0 - - + -
143A LEU* 4.3 15.3 - - + -
150A ILE* 3.3 23.3 - - + -
155A PHE* 3.6 38.6 - - + -
158A ALA* 5.0 2.0 - - + -
187A PRO* 3.0 15.4 + - + +
188A ILE* 3.5 10.4 - - + +
189A ILE 2.8 28.8 + - - +
228A MET* 4.4 5.6 - - + -
229A ARG 3.6 3.6 - - - +
236A GLN* 1.3 70.5 - - - +
238A ILE* 1.3 66.3 + - - +
239A ILE* 3.8 26.0 - - + -
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Residues in contact with ILE 238 (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 ILE* 3.4 28.5 - - + +
191A LYS* 3.7 36.1 - - + +
227A ASP* 3.9 2.1 - - - +
228A MET* 3.5 3.1 + - - -
229A ARG* 2.7 49.4 + - + +
230A LEU 4.7 1.1 - - - +
231A SER* 4.3 20.9 - - - -
236A GLN* 3.8 19.3 - - + +
237A ILE* 1.3 74.0 - - - +
239A ILE* 1.3 63.7 + - - +
240A THR* 4.1 5.0 + - - +
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Residues in contact with ILE 239 (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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134A TYR* 4.0 21.1 - - + +
135A LEU* 4.5 4.9 - - + -
188A ILE* 3.7 23.6 - - + -
189A ILE 2.7 11.5 + - - +
190A THR* 3.3 19.3 - - + +
191A LYS* 2.6 35.9 + - - +
223A TYR* 6.2 0.4 - - + -
225A ILE* 3.8 37.2 - - + -
227A ASP 3.5 3.1 - - - +
228A MET* 4.1 22.2 - - + -
237A ILE* 3.8 15.9 - - + -
238A ILE* 1.3 75.9 - - - +
240A THR* 1.3 62.4 + - - +
241A ALA* 4.9 0.9 - - + -
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Residues in contact with THR 240 (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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125A MET* 4.9 2.9 - - + -
191A LYS* 3.4 23.6 - - + +
193A LYS* 3.8 30.3 - - + +
225A ILE* 3.8 1.9 - - - +
226A ASP* 2.9 24.5 + - + +
227A ASP* 2.9 33.4 + - + +
238A ILE* 4.7 5.9 + - - +
239A ILE* 1.3 74.1 + - - +
241A ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 241 (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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190A THR* 4.9 4.5 - - + -
191A LYS 2.9 7.7 + - - +
192A PHE* 3.4 15.4 - - + -
193A LYS* 2.7 36.9 + - - +
223A TYR* 3.9 22.2 - - + -
224A HIS 3.2 19.7 - - - +
225A ILE* 4.0 7.0 - - + -
226A ASP* 3.8 4.9 - - - -
239A ILE* 4.2 0.8 - - + -
240A THR* 1.3 76.5 - - - +
242A THR* 1.3 55.3 + - - +
243A MET 4.0 0.2 - - - -
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Residues in contact with THR 242 (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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46A TYR* 4.8 12.1 - - + +
193A LYS* 3.1 21.7 + - - +
223A TYR* 3.3 2.9 - - - -
224A HIS* 2.9 37.1 + - - -
226A ASP* 2.6 24.3 + - - -
241A ALA* 1.3 71.9 - - - +
243A MET* 1.3 73.7 + - - +
244A MET* 3.4 7.4 + - + +
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Residues in contact with MET 243 (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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173A ILE* 4.2 5.4 - - + -
192A PHE* 3.5 36.5 - - + -
193A LYS 3.0 20.7 + - - +
194A VAL* 4.0 22.9 - - + -
195A ALA* 5.3 5.5 + - - +
198A SER* 5.7 4.5 - - - +
217A LEU* 3.8 27.8 - - + -
221A SER* 4.1 20.9 - - - -
222A THR 3.7 15.9 - - - +
223A TYR* 3.9 11.7 - - + -
241A ALA 3.9 2.0 + - - -
242A THR* 1.3 78.1 - - - +
244A MET* 1.3 61.2 + - - +
245A GLY* 4.2 8.5 - - - +
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Residues in contact with MET 244 (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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166A ASP* 3.4 35.4 - - - +
222A THR* 2.9 34.1 + - + +
224A HIS* 3.9 20.9 - - + -
242A THR* 3.4 12.5 + - + +
243A MET* 1.3 76.6 - - - +
245A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 245 (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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220A HIS 4.2 0.3 - - - +
221A SER* 3.1 6.0 - - - -
222A THR* 2.9 29.9 + - - -
243A MET* 3.7 9.7 - - - +
244A MET* 1.3 80.8 - - - +
246A THR* 1.3 60.2 + - - -
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Residues in contact with THR 246 (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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199A LYS* 3.9 11.2 - - + -
218A PRO* 3.6 23.4 - - + +
219A ARG 2.7 20.9 + - - -
220A HIS 3.6 4.0 - - - -
221A SER* 3.4 16.6 - - - -
245A GLY* 1.3 74.9 - - - -
247A ALA* 1.3 60.1 + - - +
248A ILE* 2.9 27.5 + - - +
249A ASN* 3.0 27.2 + - - +
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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