Contacts of the helix formed by residues 211 - 231 (chain A) in PDB entry 2G5W
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 SER 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY 3.6 2.8 + - - -
210A GLY* 1.3 74.9 - - - +
212A ILE* 1.3 60.0 + - - +
213A ALA* 4.1 7.8 + - - +
214A ASN* 2.9 45.4 + - - +
215A ARG* 3.0 12.0 + - - +
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Residues in contact with ILE 212 (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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210A GLY 3.8 0.4 + - - -
211A SER* 1.3 72.3 - - - +
213A ALA* 1.3 62.9 + - - +
215A ARG* 3.3 27.6 + - - +
216A CYS* 3.2 22.6 + - - -
250A ASP* 6.0 0.2 - - - +
252A ASP* 5.7 3.1 - - + +
255A SER* 4.0 28.9 - - - +
256A LEU* 4.3 18.6 - - + +
259A ALA* 3.3 30.7 - - + -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 3.2 8.1 - - - +
212A ILE* 1.3 77.4 - - - +
214A ASN* 1.3 64.4 + - - +
216A CYS* 3.4 9.0 + - - +
217A ARG* 3.3 23.0 + - - +
259A ALA* 5.6 1.1 - - - +
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Residues in contact with ASN 214 (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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196A PHE* 5.8 0.2 - - - -
206A ASP 3.8 1.4 + - - -
207A GLN* 3.1 25.7 + - - +
208A TYR* 3.3 21.2 - - - -
209A GLY 3.1 29.1 + - - +
211A SER* 2.9 25.1 + - - +
213A ALA* 1.3 78.2 - - - +
215A ARG* 1.3 63.0 + - - +
217A ARG* 3.1 37.7 + - - +
218A PHE 4.7 0.5 + - - -
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Residues in contact with ARG 215 (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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196A PHE* 3.2 39.4 - - - +
197A LEU* 2.8 34.6 + - - +
199A ASP* 3.5 37.4 + - - +
202A ASN* 3.8 20.6 - - - +
208A TYR 4.2 0.4 - - - -
210A GLY 2.8 37.7 + - - +
211A SER 3.0 7.0 + - - +
212A ILE* 3.3 38.4 + - - +
214A ASN* 1.3 76.5 - - - +
216A CYS* 1.3 59.5 + - - +
217A ARG 3.4 0.4 + - - -
218A PHE* 4.4 2.4 + - - +
219A LEU 5.1 0.3 + - - -
250A ASP* 3.3 25.3 + - - -
251A SER* 5.2 0.4 + - - -
256A LEU* 4.3 8.6 - - + +
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.9 12.1 - - + -
212A ILE* 3.2 19.2 + - - +
213A ALA* 3.7 10.5 - - - +
214A ASN 3.2 0.4 - - - -
215A ARG* 1.3 75.8 - - - +
217A ARG* 1.3 64.2 + - - +
218A PHE 3.0 4.3 + - - -
219A LEU* 3.1 5.5 + - - +
220A LYS* 2.9 23.2 + - + +
256A LEU* 4.8 2.7 - - - -
259A ALA* 4.1 26.0 - - - -
260A VAL* 4.0 27.6 - - - -
263A MET* 4.4 16.7 - - + +
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Residues in contact with ARG 217 (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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207A GLN* 3.0 44.1 + - - +
208A TYR* 4.0 10.5 - - + -
213A ALA* 3.3 13.6 + - - +
214A ASN* 3.1 35.6 + - - +
216A CYS* 1.3 76.5 - - - +
218A PHE* 1.3 61.6 + - - +
220A LYS* 3.5 18.8 - - + +
221A GLN* 3.1 42.7 + - + +
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Residues in contact with PHE 218 (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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156A LEU* 5.7 1.8 - - + -
161A ILE* 3.9 30.3 - - + -
164A VAL* 4.4 13.0 - - + -
165A VAL* 4.6 4.9 - - + -
168A TYR* 4.7 1.3 - + - -
192A LEU* 3.6 30.5 - - + -
193A ILE* 3.5 40.2 - - + -
196A PHE* 3.5 50.3 - + + -
208A TYR* 4.0 11.6 - + + -
214A ASN 4.7 0.4 + - - -
215A ARG 4.4 1.2 + - - +
216A CYS 3.0 0.8 + - - -
217A ARG* 1.3 75.6 - - - +
219A LEU* 1.3 66.4 + - - +
221A GLN* 3.3 4.8 + - - +
222A VAL* 3.0 44.4 + - + +
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Residues in contact with LEU 219 (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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185A ILE* 4.0 19.3 - - + -
187A GLY* 5.1 1.8 - - - -
193A ILE* 3.8 28.0 - - + +
196A PHE* 5.8 0.2 - - - +
197A LEU* 4.3 20.0 - - + -
215A ARG 5.1 0.6 + - - -
216A CYS 3.1 7.9 + - - +
218A PHE* 1.3 78.6 - - - +
220A LYS* 1.3 54.6 + - - +
222A VAL* 3.0 7.4 + - + +
223A VAL* 2.7 53.6 + - + +
237A VAL* 4.2 10.1 - - + -
239A VAL* 4.2 13.0 - - + -
260A VAL* 3.9 22.0 - - + -
263A MET* 3.8 20.2 - - + -
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Residues in contact with LYS 220 (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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216A CYS* 2.9 13.1 + - + +
217A ARG* 3.5 24.0 - - + +
219A LEU* 1.3 76.6 - - - +
221A GLN* 1.3 53.1 + - + +
223A VAL* 3.4 2.3 + - - +
224A GLU* 2.8 72.8 + - + +
263A MET* 3.7 39.4 - - + +
267A LEU* 4.5 7.3 - - + +
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Residues in contact with GLN 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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161A ILE* 3.5 18.6 - - - +
162A PRO* 5.1 6.1 - - - +
165A VAL* 3.9 19.3 - - + +
208A TYR* 2.8 36.5 + - - -
217A ARG* 3.1 27.3 + - + +
218A PHE 3.7 5.5 + - - +
219A LEU 3.3 0.2 - - - -
220A LYS* 1.3 76.8 - - + +
222A VAL* 1.3 59.6 + - - +
224A GLU* 3.2 14.3 + - - +
225A GLY* 2.8 29.3 + - - -
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Residues in contact with VAL 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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165A VAL* 4.0 18.5 - - + +
168A TYR* 3.7 44.0 - - + -
185A ILE* 4.1 20.2 - - + -
193A ILE* 4.6 2.7 - - + -
218A PHE* 3.0 47.4 + - + +
219A LEU* 3.0 10.6 + - + +
221A GLN* 1.3 75.3 - - - +
223A VAL* 1.3 62.8 + - - +
225A GLY* 4.0 0.5 - - - -
226A VAL* 3.1 25.1 + - - +
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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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185A ILE* 4.7 8.1 - - + -
219A LEU* 2.7 47.6 + - + +
220A LYS* 3.8 5.4 - - - +
222A VAL* 1.3 72.5 - - - +
224A GLU* 1.3 56.1 + - - +
226A VAL* 3.6 3.8 + - - +
227A VAL* 3.0 47.1 + - + +
235A VAL* 5.0 2.2 - - + -
237A VAL* 3.7 20.9 - - + -
263A MET* 4.9 0.4 - - + -
264A LEU* 4.1 17.7 - - + -
267A LEU* 3.7 20.9 - - + -
275A LEU* 4.3 10.5 - - + -
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Residues in contact with GLU 224 (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 LYS* 2.8 55.3 + - - +
221A GLN* 3.2 18.0 + - - +
223A VAL* 1.3 74.3 - - - +
225A GLY* 1.3 56.7 + - - +
227A VAL* 3.7 4.8 - - - +
228A SER* 2.9 35.6 + - - +
267A LEU* 3.4 33.6 - - + +
270A VAL* 5.5 2.5 - - + +
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Residues in contact with GLY 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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165A VAL* 4.7 5.8 - - - -
169A CYS* 3.5 27.0 - - - -
221A GLN 2.8 19.4 + - - -
222A VAL 4.0 0.7 - - - -
224A GLU* 1.3 72.8 - - - +
226A VAL* 1.3 56.4 + - - +
228A SER* 3.4 9.0 - - - -
229A ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 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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107A LEU* 4.6 0.2 - - + -
168A TYR* 3.9 39.0 - - + +
169A CYS* 4.1 0.9 - - - +
172A ALA* 4.1 8.7 - - + -
183A ILE* 3.4 32.8 - - + -
185A ILE* 4.0 14.1 - - + -
222A VAL 3.1 17.6 + - - +
223A VAL* 4.0 3.4 - - - +
225A GLY* 1.3 73.9 - - - +
227A VAL* 1.3 60.6 + - - +
229A ALA* 3.1 7.7 + - - +
230A ILE* 3.0 29.0 + - + +
235A VAL* 3.6 15.9 - - + -
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Residues in contact with VAL 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 VAL* 3.0 27.8 + - + +
224A GLU* 3.7 5.6 - - - +
226A VAL* 1.3 74.5 - - - +
228A SER* 1.3 59.3 + - - +
231A GLY* 2.8 31.7 + - - -
232A ALA* 3.7 25.6 - - + +
235A VAL* 4.0 9.2 - - + -
267A LEU* 5.5 5.2 - - + -
271A ASN* 3.4 37.0 - - + +
275A LEU* 3.8 22.0 - - + -
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Residues in contact with SER 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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224A GLU* 2.9 24.6 + - - +
225A GLY* 3.4 8.9 - - - -
227A VAL* 1.3 78.8 - - - +
229A ALA* 1.3 62.5 + - - +
231A GLY 4.7 0.5 + - - -
271A ASN* 5.7 1.3 - - - -
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Residues in contact with ALA 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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169A CYS* 4.5 13.9 - - + +
172A ALA* 5.1 0.7 - - + -
173A LEU* 4.0 35.3 - - + +
225A GLY 3.0 13.9 + - - +
226A VAL* 3.1 11.1 + - - +
228A SER* 1.3 79.9 - - - +
230A ILE* 1.3 65.7 + - + +
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Residues in contact with ILE 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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172A ALA* 3.8 21.8 - - + +
173A LEU* 4.2 9.2 - - + +
176A ILE* 3.7 34.1 - - + -
183A ILE* 3.8 22.9 - - + +
226A VAL* 3.0 18.6 + - + +
229A ALA* 1.3 87.7 - - + +
231A GLY* 1.3 67.0 + - - +
234A LYS* 3.5 57.3 + - + +
235A VAL* 3.9 4.0 - - + -
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Residues in contact with GLY 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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227A VAL* 2.8 19.8 + - - -
228A SER 4.7 0.6 + - - -
229A ALA 3.8 0.8 - - - -
230A ILE* 1.3 81.5 - - - +
232A ALA* 1.3 66.3 + - - -
233A SER* 3.2 6.7 - - - -
234A LYS 3.2 11.0 + - - -
235A VAL* 3.4 11.6 - - - +
271A ASN* 5.8 0.9 - - - -
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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