Contacts of the helix formed by residues 222 - 238 (chain A) in PDB entry 3GNI
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 ASN 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL 5.6 0.2 + - - -
174A GLU* 4.0 15.2 + - - +
175A MET 4.9 6.5 + - - -
176A SER* 5.8 2.4 - - - +
178A PHE* 5.6 3.2 - - - -
220A SER* 2.9 16.4 + - - +
221A GLU* 1.3 76.7 - - - +
223A TYR* 1.3 65.0 + - - +
224A VAL* 3.0 22.0 + - - +
225A THR* 3.3 21.7 + - - +
226A LYS* 3.1 22.3 + - - +
138B ILE* 4.1 23.8 - - - +
140B ASP* 3.4 5.4 - - - -
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU 3.7 0.4 + - - -
222A ASN* 1.3 72.0 + - - +
224A VAL* 1.3 70.9 + - + +
226A LYS* 3.8 6.4 - - + +
227A ARG* 3.0 64.2 + - - +
267A SER* 3.6 20.0 + - - -
269A ASN* 3.2 3.8 + - - -
270A ILE* 4.4 9.1 - - + +
104B LEU* 3.8 23.6 - - + -
105B GLU* 2.7 36.6 + - + -
138B ILE* 4.6 0.7 - - + -
140B ASP* 2.6 26.9 + - + +
141B ASN* 3.7 30.3 - - + +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 3.8 23.1 - - + -
222A ASN* 3.0 6.7 + - - +
223A TYR* 1.3 82.9 - - + +
225A THR* 1.3 59.4 - - - +
227A ARG* 3.8 5.1 - - + +
228A GLN* 2.7 60.2 + - + +
104B LEU* 3.7 31.4 - - + -
112B VAL* 5.3 7.2 - - + -
116B GLN* 4.6 2.2 - - - +
138B ILE* 3.8 19.1 - - + -
140B ASP* 4.5 0.2 + - - -
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 3.5 21.3 + - + +
174A GLU* 3.7 30.6 + - + +
185A PHE* 6.1 1.3 - - + -
217A LEU* 4.0 13.0 - - + +
220A SER* 3.6 19.1 - - - +
222A ASN* 3.3 21.7 + - - +
224A VAL* 1.3 76.9 - - - +
226A LYS* 1.3 56.0 + - - +
228A GLN* 4.0 8.0 - - - +
229A SER* 2.5 45.9 + - - +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU 3.9 11.9 + - - +
218A LEU* 3.6 27.7 + - + +
219A HIS* 4.5 3.8 + - - +
220A SER* 3.6 20.3 + - - +
222A ASN 3.1 14.2 + - - +
223A TYR* 3.8 5.6 - - + +
225A THR* 1.3 80.0 - - - +
227A ARG* 1.3 62.7 + - - +
229A SER* 4.1 1.0 - - - -
230A LEU* 3.0 30.2 + - + +
262A LEU* 4.0 21.3 - - + +
265A ASP* 3.5 19.4 + - - +
270A ILE* 3.9 21.5 - - + -
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Residues in contact with ARG 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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223A TYR* 3.0 50.2 + - + +
224A VAL* 3.8 6.1 - - + +
226A LYS* 1.3 76.2 - - - +
228A GLN* 1.3 64.5 + - + +
231A LYS* 3.2 9.8 + - + +
269A ASN* 3.1 25.4 + - + +
270A ILE* 3.3 19.6 - - + +
273A GLU* 2.5 36.4 + - - +
104B LEU* 2.8 29.5 + - - +
107B CYS 3.0 19.4 + - - -
108B SER* 3.8 9.3 + - - +
109B ASN* 3.3 26.1 + - - -
112B VAL* 4.2 13.0 - - - +
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL 5.5 2.4 - - - +
178A PHE* 5.5 0.8 - - - -
182A SER* 5.0 4.5 + - - +
185A PHE* 3.6 50.3 - - + +
224A VAL* 2.7 40.1 + - + +
225A THR* 4.0 5.6 - - - +
227A ARG* 1.3 75.7 - - + +
229A SER* 1.3 57.9 + - - +
231A LYS* 3.2 10.5 + - - +
232A LEU* 2.9 29.6 + - - +
112B VAL* 5.7 2.4 - - + +
116B GLN* 3.4 28.1 + - - +
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 5.8 0.2 - - - +
185A PHE* 3.9 14.4 - - - -
214A TYR* 2.5 39.6 + - - -
217A LEU* 3.7 34.1 - - - +
218A LEU* 4.0 6.7 - - - -
225A THR* 2.5 27.7 + - - +
226A LYS 4.1 2.5 - - - -
228A GLN* 1.3 75.8 - - - +
230A LEU* 1.3 57.1 + - - +
233A LEU* 3.0 13.5 + - - +
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Residues in contact with LEU 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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218A LEU* 3.9 13.0 - - + +
226A LYS* 3.0 21.2 + - + +
229A SER* 1.3 76.7 - - - +
231A LYS* 1.3 62.4 + - - +
233A LEU* 3.5 7.7 - - + +
234A GLY* 3.2 17.7 + - - -
259A MET* 3.9 24.9 - - + -
262A LEU* 3.8 25.4 - - + -
270A ILE* 3.4 42.4 - - + +
273A GLU* 3.8 22.4 - - + +
274A ALA* 3.6 13.5 - - + +
277A VAL* 4.3 4.6 - - + +
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Residues in contact with LYS 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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189A LYS* 5.5 7.0 - - - +
227A ARG* 3.2 13.4 + - + +
228A GLN* 3.2 13.0 + - - +
230A LEU* 1.3 75.7 - - - +
232A LEU* 1.3 64.7 + - - +
234A GLY* 3.3 3.0 + - - -
235A GLU* 2.7 52.2 + - + +
273A GLU* 3.7 27.5 + - + +
276A HIS* 6.0 0.2 - - - -
109B ASN* 3.5 35.9 - - - +
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PHE* 3.8 22.9 - - + -
188A PHE* 3.9 22.0 - - + -
189A LYS* 3.8 30.1 - - + -
192A LEU* 4.1 12.1 - - + -
193A THR* 3.8 20.6 - - + -
214A TYR* 3.4 17.5 - - + +
228A GLN 2.9 14.7 + - - +
231A LYS* 1.3 76.0 - - - +
233A LEU* 1.3 57.8 + - - +
235A GLU* 3.2 16.5 + - + +
236A LEU* 2.9 45.8 + - + +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.9 28.0 - - + -
214A TYR* 3.5 17.8 + - + -
218A LEU* 3.8 15.9 - - + -
229A SER 3.0 14.9 + - - +
230A LEU* 3.5 11.0 - - + +
231A LYS 3.2 0.2 - - - -
232A LEU* 1.3 76.0 - - - +
234A GLY* 1.3 62.3 + - - +
236A LEU* 3.3 10.3 + - + +
237A LEU* 3.0 46.7 + - + +
249A TYR* 3.4 30.7 - - + +
259A MET* 3.8 19.3 - - + -
277A VAL* 4.4 7.2 - - + -
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Residues in contact with GLY 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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230A LEU 3.2 9.0 + - - -
231A LYS* 3.3 4.2 + - - -
233A LEU* 1.3 78.9 - - - +
235A GLU* 1.3 60.7 + - - +
237A LEU* 3.5 1.3 + - - -
238A LEU* 3.1 33.0 + - - +
273A GLU 5.7 0.2 - - - -
276A HIS* 3.3 27.6 + - - -
277A VAL* 3.7 14.7 - - - +
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Residues in contact with GLU 235 (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 LYS* 4.2 21.8 + - - -
193A THR* 5.9 3.8 - - + +
231A LYS* 2.7 54.4 + - + +
232A LEU* 3.2 18.7 + - + +
234A GLY* 1.3 75.9 - - - +
236A LEU* 1.3 62.2 + - - +
238A LEU* 3.9 3.0 + - - +
239A ASP* 3.6 20.4 + - - +
276A HIS* 4.7 9.6 - - + +
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Residues in contact with LEU 236 (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 LEU* 3.7 40.2 - - + +
193A THR* 4.1 17.3 - - + -
203A LEU* 4.9 12.1 - - + -
210A PHE* 4.8 15.9 - - + -
211A PHE* 5.7 3.6 - - + -
214A TYR* 4.9 4.5 - - + -
232A LEU* 2.9 38.0 + - + +
233A LEU* 3.6 13.9 - - + +
235A GLU* 1.3 78.6 - - - +
237A LEU* 1.3 65.4 + - + +
239A ASP* 3.4 7.5 + - + +
242A ASN* 2.8 41.6 + - - +
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Residues in contact with LEU 237 (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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211A PHE* 5.0 8.7 - - + -
233A LEU* 3.0 34.5 + - + +
234A GLY* 4.2 2.7 - - - +
235A GLU 3.5 0.2 - - - -
236A LEU* 1.3 78.2 - - + +
238A LEU* 1.3 67.1 + - + +
239A ASP 3.2 6.6 + - - +
242A ASN* 5.0 1.2 - - + +
243A PHE* 5.5 0.5 - - - -
245A ILE* 5.0 3.6 - - + -
246A MET* 3.6 55.5 - - + +
249A TYR* 3.8 31.9 - - + -
250A ILE* 4.9 7.0 - - + -
277A VAL* 3.6 34.1 - - + +
280A VAL* 5.5 3.6 - - + -
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Residues in contact with LEU 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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234A GLY* 3.1 28.5 + - - +
235A GLU* 4.3 3.6 - - - +
236A LEU 3.4 0.4 - - - -
237A LEU* 1.3 80.4 - - + +
239A ASP* 1.3 61.1 + - - +
240A ARG* 3.6 4.7 + - - -
246A MET* 6.1 1.1 - - - -
276A HIS* 3.4 30.3 - - + +
277A VAL* 5.6 0.4 - - - -
279A LYS* 4.8 10.1 - - - +
280A VAL* 3.7 33.7 - - + -
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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
------------------------------------------------------------
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