Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 2GH0
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ASP* 3.7 15.6 - - - +
220A CYS* 4.5 0.9 - - - +
221A ALA* 3.1 35.7 + - + +
222A PRO 3.3 1.0 - - - -
223A ASN* 1.3 73.8 - - - +
225A ARG* 1.3 60.9 + - - +
226A GLY* 3.6 5.0 + - - -
227A CYS* 3.1 29.5 + - + +
228A GLY* 3.1 17.0 + - - -
307A ASN 4.1 3.5 - - - +
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Residues in contact with ARG 225 (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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223A ASN* 3.3 12.0 + - - +
224A ASP* 1.3 74.5 - - - +
226A GLY* 1.3 57.0 + - - +
228A GLY 3.8 0.2 - - - -
229A GLU* 2.9 33.2 + - - +
307A ASN* 3.6 35.5 + - - +
308A VAL* 3.4 35.2 - - + +
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Residues in contact with GLY 226 (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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160A ASP* 4.5 4.0 - - - -
224A ASP* 3.2 5.1 + - - -
225A ARG* 1.3 77.9 - - - +
227A CYS* 1.3 56.1 + - - +
229A GLU* 3.4 9.9 + - - +
230A ARG* 2.9 29.5 + - - +
203C SER* 4.1 2.9 + - - -
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Residues in contact with CYS 227 (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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160A ASP* 3.7 30.5 + - - -
161A LEU 4.6 0.2 - - - -
162A CYS* 3.5 16.9 - - - -
219A PRO 3.6 4.9 - - - -
220A CYS* 2.1 56.1 - - + -
224A ASP* 3.1 31.9 + - - +
226A GLY* 1.3 73.3 - - - +
228A GLY* 1.3 57.6 + - - +
230A ARG* 3.2 5.5 + - - +
231A ARG* 2.9 25.6 + - - +
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Residues in contact with GLY 228 (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 CYS* 3.5 12.2 - - - -
224A ASP 3.1 9.1 + - - -
225A ARG 3.4 0.2 + - - -
227A CYS* 1.3 79.5 - - - +
229A GLU* 1.3 56.7 + - - +
231A ARG* 3.4 11.2 + - - +
232A ARG* 2.9 29.8 + - - +
306A SER 4.1 1.7 - - - +
307A ASN* 3.6 29.1 - - - -
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Residues in contact with GLU 229 (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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225A ARG 2.9 18.2 + - - +
226A GLY* 3.7 7.8 - - - +
228A GLY* 1.3 74.1 - - - +
230A ARG* 1.3 65.6 + - - +
232A ARG* 3.3 12.1 + - - +
233A ASN* 2.9 40.9 + - - +
307A ASN* 3.6 17.2 + - + +
202C ASN* 2.6 29.1 - - - +
203C SER* 3.2 14.2 + - - +
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Residues in contact with ARG 230 (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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160A ASP* 4.3 5.2 - - - +
162A CYS* 3.7 19.1 + - + -
163A LEU* 3.6 40.8 - - - +
166A ALA* 3.4 24.0 - - - +
179A ARG* 3.5 5.9 - - - +
215A LEU* 5.9 0.6 - - - +
226A GLY 2.9 14.8 + - - +
227A CYS* 3.5 8.7 - - - +
229A GLU* 1.3 76.3 - - - +
231A ARG* 1.3 62.3 + - - +
233A ASN 3.1 3.6 + - - -
234A THR* 2.8 33.2 + - - +
142C ASP* 6.0 1.4 - - - +
143C GLU* 2.4 34.5 + - - +
199C MET* 3.6 26.2 + - + +
200C ASP 5.2 3.2 + - - -
203C SER* 3.1 15.7 + - - +
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Residues in contact with ARG 231 (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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162A CYS* 4.0 7.6 - - - -
216A LEU* 3.4 28.8 - - + +
218A CYS* 2.8 34.9 + - - -
220A CYS* 3.8 30.0 + - - +
227A CYS 2.9 13.1 + - - +
228A GLY* 3.6 13.4 + - - +
230A ARG* 1.3 78.8 - - - +
232A ARG* 1.3 62.4 + - - +
233A ASN 3.3 0.3 + - - -
234A THR* 3.4 19.2 + - - -
303A ASN* 4.6 0.9 - - - +
304A PHE* 3.6 33.0 - - + +
306A SER 4.6 3.4 + - - -
307A ASN 5.4 0.6 - - - -
308A VAL 5.5 0.2 - - - -
309A ASN* 3.1 29.1 + - - +
310A THR* 3.8 18.8 - - - +
349A MET* 3.6 12.6 - - - +
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Residues in contact with ARG 232 (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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228A GLY 2.9 17.2 + - - +
229A GLU* 3.8 12.2 + - - +
230A ARG 3.3 0.2 - - - -
231A ARG* 1.3 76.9 - - - +
233A ASN* 1.3 87.0 + - - +
235A ILE 4.9 0.2 + - - -
237A PRO* 3.3 15.2 - - - +
238A ASN* 6.0 0.4 + - - +
303A ASN* 2.8 29.0 + - - +
304A PHE* 3.3 30.3 - - + +
305A VAL 3.9 14.5 + - - -
306A SER* 3.9 25.4 - - - +
307A ASN* 4.6 14.5 - - - +
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Residues in contact with ASN 233 (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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229A GLU* 2.9 38.1 + - - +
230A ARG 3.1 1.1 + - - -
232A ARG* 1.3 105.9 + - - +
234A THR* 1.3 60.0 + - - +
235A ILE 3.3 2.7 - - - -
236A ALA* 2.9 22.3 + - - -
237A PRO* 3.6 19.9 - - + +
238A ASN* 4.1 15.1 + - - -
199C MET* 3.6 5.1 - - + +
203C SER* 3.3 24.6 - - - +
205C TRP* 3.5 11.0 + - + -
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Residues in contact with THR 234 (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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162A CYS* 6.0 0.3 - - - +
179A ARG* 6.0 0.2 - - - +
182A TYR* 2.7 36.2 + - - +
204A PHE* 6.6 0.2 - - + -
215A LEU* 3.8 39.2 + - + +
216A LEU* 4.3 13.0 - - + -
230A ARG* 2.8 30.0 + - - +
231A ARG* 3.4 16.0 + - - -
232A ARG 3.5 0.2 - - - -
233A ASN* 1.3 76.2 - - - +
235A ILE* 1.4 57.9 + - + +
199C MET* 4.1 11.4 - - - -
205C TRP* 3.3 13.6 + - + -
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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