Contacts of the helix formed by residues 220 - 237 (chain A) in PDB entry 3GZN
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 PRO 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A TYR* 4.1 2.7 - - - +
218A HIS 3.5 7.7 - - - +
219A THR* 1.4 89.1 - - + +
221A TRP* 1.3 65.4 + - - +
222A ILE 3.1 1.4 + - - -
223A VAL* 3.2 30.1 + - + +
224A ILE* 3.3 8.3 + - - +
339A MET* 3.9 13.0 - - + -
340A ILE 3.8 11.4 - - - +
341A ALA* 3.8 13.2 - - + -
345A LYS* 3.9 24.2 - - + +
346A TYR* 5.2 1.8 - - + -
349A LEU* 3.8 25.1 - - + -
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Residues in contact with TRP 221 (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 LEU* 3.7 22.0 - - + -
192A LEU* 4.8 1.3 - - + -
219A THR 3.5 1.4 + - - -
220A PRO* 1.3 68.2 - - - +
222A ILE* 1.3 69.9 + - + +
223A VAL 3.3 0.2 - - - -
224A ILE* 3.5 11.9 - - - +
225A ILE* 2.9 53.9 + - + +
271A ASN* 3.5 21.3 + - - +
274A GLU* 3.1 30.1 + - + +
275A ALA* 3.7 11.7 - - + +
278A ASN* 3.5 38.4 - - + +
281A THR* 5.3 0.9 - - - -
282A ALA* 3.7 14.1 - - + -
337A PRO* 4.5 10.3 - - + -
338A ASP 4.6 3.0 + - - -
339A MET* 3.2 44.7 - - + +
340A ILE 4.5 2.0 + - - -
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Residues in contact with ILE 222 (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 LEU* 4.0 24.9 - - + -
192A LEU* 3.7 31.2 - - + +
203A PHE* 4.3 7.6 - - + -
220A PRO 3.1 0.6 + - - -
221A TRP* 1.3 90.7 - - + +
223A VAL* 1.3 66.7 + - - +
225A ILE* 3.3 2.4 + - - +
226A ALA* 3.0 22.4 + - - +
336A ILE* 4.2 9.6 - - + -
339A MET* 3.3 36.6 - - + -
349A LEU* 3.9 20.0 - - + -
353A TYR* 3.8 17.9 - - + +
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Residues in contact with VAL 223 (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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202A HIS* 4.4 7.6 - - + +
203A PHE* 4.0 26.2 - - + +
206A TYR* 3.6 45.5 - - + -
208A LEU* 5.6 1.1 - - + -
219A THR* 3.6 20.2 - - + -
220A PRO* 3.2 23.4 + - + +
222A ILE* 1.3 75.9 - - - +
224A ILE* 1.3 63.3 + - - +
226A ALA* 3.0 4.0 + - - +
227A LYS* 2.9 35.2 + - + +
349A LEU* 4.5 4.7 - - + -
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 5.1 5.2 - - + -
219A THR* 3.2 34.1 - - + +
220A PRO 3.3 8.2 + - - +
221A TRP* 3.5 9.0 - - - +
222A ILE 3.3 0.2 - - - -
223A VAL* 1.3 79.5 - - - +
225A ILE* 1.3 64.0 + - - +
227A LYS* 3.3 5.1 + - - +
228A TYR* 3.2 34.8 + - + -
254A ILE* 4.6 2.7 - - + -
271A ASN* 3.4 35.9 - - - +
272A PHE* 3.6 42.8 - - + -
275A ALA* 3.9 13.0 - - + -
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Residues in contact with ILE 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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192A LEU* 4.4 11.9 - - + -
221A TRP* 2.9 49.6 + - + +
222A ILE 4.0 3.6 - - - +
224A ILE* 1.3 72.7 - - - +
226A ALA* 1.3 57.8 + - - +
228A TYR* 3.5 2.0 + - - -
229A LEU* 2.9 27.8 + - + +
250A PHE* 3.7 22.5 - - + -
254A ILE* 4.5 7.2 - - + -
275A ALA* 3.4 34.1 - - + +
278A ASN 4.2 2.0 - - - +
279A VAL* 4.1 14.8 - - + +
282A ALA* 4.5 4.3 - - + +
283A LEU* 4.1 20.4 - - + -
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Residues in contact with ALA 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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192A LEU* 3.7 9.6 - - + +
203A PHE* 3.5 40.8 - - + -
222A ILE 3.0 12.9 + - - +
223A VAL 3.0 9.7 + - - +
225A ILE* 1.3 74.7 - - - +
227A LYS* 1.3 66.6 + - - +
229A LEU* 2.9 19.2 + - - +
230A ALA* 3.0 12.8 + - - +
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Residues in contact with LYS 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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203A PHE* 2.8 30.8 + - - +
204A GLN* 3.9 8.7 - - - +
206A TYR* 2.7 35.2 + - + +
208A LEU* 3.7 46.0 - - + +
223A VAL* 2.9 26.5 + - + +
224A ILE 3.5 6.5 - - - +
226A ALA* 1.3 75.0 - - - +
228A TYR* 1.3 62.5 + - - +
230A ALA* 3.0 26.4 + - - +
231A GLN* 3.3 6.9 + - - +
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Residues in contact with TYR 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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208A LEU* 4.1 24.2 - - + +
216A HIS* 5.4 0.9 + - - -
224A ILE* 3.2 31.9 + - + +
225A ILE 4.1 0.4 - - - +
227A LYS* 1.3 80.4 - - + +
229A LEU* 1.3 57.1 + - - +
231A GLN* 3.4 29.3 + - - +
232A TRP* 2.9 23.6 + - - +
250A PHE* 3.4 18.3 - - + -
253A LEU* 3.4 37.5 - - + +
254A ILE* 4.0 24.2 - - + -
256A GLN* 5.7 0.4 - - + -
257A GLY* 2.9 29.6 - - - -
272A PHE* 3.6 27.3 - + - -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.9 25.8 - - + +
193A ASP* 5.0 0.9 - - - -
225A ILE* 2.9 18.4 + - + +
226A ALA* 2.9 11.4 + - - +
228A TYR* 1.3 74.4 - - - +
230A ALA* 1.3 58.5 + - - +
232A TRP* 4.0 0.8 - - + +
233A TYR* 3.0 28.9 + - - +
240A ILE* 4.0 26.6 - - + +
241A PRO* 3.7 31.4 - - + -
250A PHE* 3.7 18.2 - - + -
283A LEU* 3.7 19.7 - - + -
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Residues in contact with ALA 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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226A ALA 3.0 9.2 + - - +
227A LYS* 3.2 15.0 - - - +
229A LEU* 1.3 73.2 - - - +
231A GLN* 1.3 56.3 + - - +
233A TYR* 3.0 10.2 + - - +
234A SER* 2.7 37.2 + - - -
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Residues in contact with GLN 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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208A LEU* 5.2 7.9 - - - +
227A LYS 3.3 7.5 + - - +
228A TYR* 3.7 30.2 - - - +
230A ALA* 1.3 77.4 - - - +
232A TRP* 1.3 53.0 + - - +
234A SER* 3.4 8.3 - - - +
235A GLU* 2.7 61.4 + - - +
253A LEU* 3.5 29.2 - - + +
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Residues in contact with TRP 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 TYR 2.9 17.0 + - - +
229A LEU* 4.0 3.8 - - + +
231A GLN* 1.3 74.1 - - - +
233A TYR* 1.3 56.5 + - - +
235A GLU* 3.5 4.2 - - + -
236A THR* 2.5 68.6 + - + +
239A ARG 4.1 12.0 + - - -
240A ILE* 4.4 2.4 - - + -
241A PRO* 4.2 23.1 - - + +
246A GLU* 3.9 25.7 - - + -
249A ASP* 3.7 28.7 - - + -
250A PHE* 3.7 43.5 - + + -
253A LEU* 3.9 20.3 - - + +
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Residues in contact with TYR 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 LEU 3.0 19.2 + - - +
230A ALA* 3.0 8.0 + - - +
232A TRP* 1.3 78.3 - - - +
234A SER* 1.3 58.7 + - - +
236A THR* 3.6 5.0 + - - -
237A ASN* 2.9 27.7 + - - -
238A GLY* 3.0 36.4 + - - -
239A ARG* 5.4 0.7 - - - -
240A ILE* 4.3 18.4 - - + +
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Residues in contact with SER 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 ALA 2.7 20.2 + - - -
231A GLN* 3.4 10.7 + - - +
233A TYR* 1.3 74.5 - - - +
235A GLU* 1.3 63.8 + - - +
236A THR 2.9 7.4 + - - -
237A ASN* 3.0 16.3 + - - +
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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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231A GLN* 2.7 53.4 + - - +
232A TRP* 3.5 5.3 - - + +
234A SER* 1.3 76.5 + - - +
236A THR* 1.3 61.0 + - + +
253A LEU* 4.1 15.9 - - - +
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Residues in contact with THR 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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232A TRP* 2.5 63.5 + - + +
233A TYR* 3.6 4.7 + - - -
235A GLU* 1.3 82.6 - - + +
237A ASN* 1.3 73.7 + - - +
238A GLY* 3.2 4.2 + - - -
239A ARG 3.5 14.3 + - - +
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Residues in contact with ASN 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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233A TYR 2.9 14.0 + - - -
234A SER 3.0 9.0 + - - +
236A THR* 1.3 79.0 - - - +
238A GLY* 1.3 57.3 + - - +
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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