Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 3I0W
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 GLY 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS* 4.0 8.3 - - - -
219A VAL* 1.3 75.2 - - - +
221A PRO* 1.3 66.8 - - - +
224A ALA* 2.9 30.7 + - - +
21B T 2.8 37.5 + - - -
22B C 4.3 3.1 - - - -
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Residues in contact with PRO 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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210A HIS* 3.2 25.7 - - + +
214A LYS* 4.1 17.0 - - + +
220A GLY* 1.3 84.0 - - - +
222A GLN* 1.3 56.1 + - - +
225A ASP* 3.2 27.3 + - - +
263A ARG* 4.7 13.9 - - - -
21B T 3.5 13.5 - - + +
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Residues in contact with GLN 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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125A SER* 5.0 3.1 + - - -
221A PRO* 1.3 78.0 - - - +
223A VAL* 1.3 71.1 + - + +
225A ASP* 3.3 3.5 + - - +
226A CYS* 3.0 26.3 + - - -
239A PRO* 3.1 45.9 + - - +
240A VAL 3.3 19.6 - - - +
241A ASP* 3.5 13.8 - - - +
19B 8OG 3.3 31.0 + - - +
20B G 3.3 32.9 - - - +
21B T 3.3 6.4 + - - +
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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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122A PHE* 3.4 37.7 - - + +
123A ILE 4.1 0.7 - - - +
125A SER* 4.4 6.5 - - - +
126A ALA* 4.5 5.6 - - + -
218A GLY 4.1 3.8 - - - +
219A VAL* 3.9 15.3 - - + -
220A GLY 4.0 5.6 - - - +
222A GLN* 1.3 76.6 - - + +
224A ALA* 1.3 58.3 + - - +
226A CYS* 3.2 7.5 + - - +
227A ILE* 2.9 52.9 + - + +
20B G 3.5 10.8 - - - +
21B T 2.8 31.2 + - - +
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Residues in contact with ALA 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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210A HIS* 3.6 24.0 - - + +
213A LEU* 3.5 19.8 - - + +
214A LYS* 3.8 10.8 - - + -
219A VAL* 3.6 17.2 - - + +
220A GLY 2.9 20.6 + - - +
223A VAL* 1.3 76.9 - - - +
225A ASP* 1.3 61.7 + - - +
227A ILE* 3.3 2.2 + - - -
228A MET* 3.0 25.3 + - - +
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Residues in contact with ASP 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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210A HIS* 2.9 19.2 + - - -
221A PRO 3.2 13.5 + - - +
222A GLN 3.3 4.0 + - - +
224A ALA* 1.3 78.4 - - - +
226A CYS* 1.3 63.1 + - - +
228A MET* 3.5 14.7 + - - +
229A LEU* 2.9 27.8 + - - +
237A ALA* 3.6 2.3 - - + +
238A PHE 3.0 28.9 + - - +
239A PRO* 3.6 20.8 - - + +
263A ARG* 2.7 35.0 + - - -
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Residues in contact with CYS 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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118A ILE* 4.8 0.9 - - - -
122A PHE* 3.5 39.3 - - + -
222A GLN* 3.0 32.9 + - - -
223A VAL* 3.2 7.4 + - - +
225A ASP* 1.3 76.0 - - - +
227A ILE* 1.3 58.2 + - - +
229A LEU* 4.6 1.8 - - - -
230A PHE* 2.9 51.3 + - + +
239A PRO* 3.6 17.9 - - - -
19B 8OG 4.0 8.5 - - - -
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Residues in contact with ILE 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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115A PRO 4.8 1.1 - - - +
118A ILE* 3.7 17.7 - - + +
119A LEU* 3.6 47.8 - - + +
122A PHE* 4.3 2.5 - - + -
198A LEU* 6.0 0.4 - - + -
213A LEU* 3.8 24.0 - - + -
219A VAL* 4.1 9.9 - - + -
223A VAL* 2.9 40.7 + - + +
224A ALA* 3.6 4.9 - - - +
226A CYS* 1.3 76.8 - - - +
228A MET* 1.3 58.9 + - - +
231A SER* 2.7 45.3 + - - +
232A MET* 4.3 7.4 - - + -
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Residues in contact with MET 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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206A ASP* 3.4 32.8 - - + +
209A CYS* 3.8 12.3 - - - -
210A HIS* 3.7 25.8 - - + -
213A LEU* 3.8 2.9 - - + -
224A ALA 3.0 18.0 + - - +
225A ASP* 3.5 24.5 - - - +
227A ILE* 1.3 78.2 - - - +
229A LEU* 1.3 59.7 + - - +
232A MET* 3.1 12.6 + - - -
233A GLN 3.0 24.8 + - - -
234A LYS* 3.0 34.0 + - + -
236A SER* 4.6 1.1 - - - +
237A ALA* 3.6 22.2 - - + +
263A ARG* 4.4 5.2 - - - +
267A ARG* 5.1 1.1 - - - +
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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
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110A ILE* 4.1 15.5 - - + +
111A LEU 4.8 0.5 - - - +
225A ASP 2.9 19.1 + - - +
226A CYS 3.8 2.2 - - - +
228A MET* 1.3 81.0 - - - +
230A PHE* 1.3 89.0 + - + +
231A SER 3.5 0.3 + - - -
233A GLN* 3.6 14.6 + - - +
234A LYS 4.0 11.2 - - - +
235A TYR* 3.6 30.3 - - + -
237A ALA* 4.0 5.8 - - + -
239A PRO* 4.4 9.6 - - + -
275A GLY* 3.7 28.3 - - - +
278A GLN* 3.7 22.2 - - - +
279A GLN* 4.2 0.9 - - - +
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Residues in contact with PHE 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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31A GLN* 3.6 26.0 - - + -
110A ILE* 4.0 11.2 - - + -
111A LEU 3.2 12.0 - - - +
112A ARG* 4.0 0.5 - - - -
113A GLN* 3.0 38.9 + - - +
118A ILE* 4.4 9.6 - - + -
122A PHE* 3.4 39.0 - + - -
226A CYS* 2.9 36.5 + - + +
229A LEU* 1.3 93.5 - - + +
231A SER* 1.3 55.6 + - - +
233A GLN* 4.7 0.9 - - - -
239A PRO* 5.3 0.2 - - + -
278A GLN* 4.7 1.1 - - - -
279A GLN* 3.1 28.3 - - - -
19B 8OG 3.4 21.5 - + - -
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Residues in contact with SER 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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113A GLN 3.2 19.9 - - - +
114A ASP 3.8 4.0 - - - -
115A PRO* 3.4 31.4 - - - +
118A ILE* 3.9 8.9 - - - +
202A LYS* 3.0 23.9 + - - -
227A ILE* 2.7 29.5 + - - +
230A PHE* 1.3 77.2 - - - +
232A MET* 1.3 68.6 + - - +
233A GLN* 3.6 6.5 + - - +
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Residues in contact with MET 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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115A PRO* 4.1 19.3 - - + -
198A LEU* 4.1 23.8 - - + +
201A ILE* 4.1 15.9 - - + -
202A LYS* 3.7 27.4 - - + +
209A CYS* 3.4 26.7 - - - -
213A LEU* 4.1 15.7 - - + -
227A ILE* 4.3 3.8 - - + -
228A MET* 3.1 21.8 + - - +
231A SER* 1.3 90.7 - - - +
233A GLN* 1.3 79.3 + - - +
234A LYS* 3.2 23.4 + - + -
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Residues in contact with GLN 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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111A LEU 4.9 0.2 + - - -
112A ARG* 3.6 58.6 + - + +
202A LYS* 3.3 28.8 + - - +
228A MET 3.0 3.4 + - - -
229A LEU 3.6 11.3 + - - +
230A PHE 4.4 2.2 + - - -
231A SER* 3.6 18.2 + - - +
232A MET* 1.3 79.0 - - - +
234A LYS* 1.3 61.8 + - - +
235A TYR* 3.3 46.0 + - + +
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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