Contacts of the helix formed by residues 218 - 235 (chain A) in PDB entry 5OO2
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A ARG* 3.4 5.7 + - - +
216A ARG 3.9 0.4 + - - -
217A PRO* 1.3 76.9 - - - +
219A ASP* 1.3 65.3 + - - +
220A GLY* 3.5 5.7 + - - -
221A GLU* 3.0 41.2 + - - +
222A TYR* 3.2 10.6 + - - -
374A GLU* 5.6 0.6 + - - -
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Residues in contact with ASP 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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202A TYR* 4.0 0.8 + - - +
204A ARG* 2.7 37.6 + - - +
207A ASN* 4.4 5.7 + - - -
218A SER* 1.3 73.7 - - - +
220A GLY* 1.3 64.6 + - - +
222A TYR* 2.9 16.3 + - - +
223A ASP* 3.0 20.0 + - - +
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Residues in contact with GLY 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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218A SER* 3.3 7.2 + - - -
219A ASP* 1.3 79.0 - - - +
221A GLU* 1.3 63.0 + - - +
223A ASP* 3.5 17.8 + - - +
224A ARG* 3.5 19.2 + - - +
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Residues in contact with GLU 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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183A ASN* 3.5 15.4 - - - +
188A ASP* 5.0 0.2 - - - +
191A TYR* 6.0 3.7 - - + -
217A PRO* 3.3 14.3 - - + +
218A SER* 3.0 39.8 + - - +
220A GLY* 1.3 75.5 - - - +
222A TYR* 1.3 63.3 + - - +
224A ARG* 3.2 10.7 + - - +
225A TYR* 3.0 46.6 + - + +
374A GLU* 4.7 7.1 - - - +
377A ARG* 3.1 28.2 + - - -
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Residues in contact with TYR 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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88A TYR* 5.7 1.9 + - - -
89A PHE* 4.7 16.2 + + - -
90A PRO* 5.6 0.2 - - + -
177A TRP* 4.6 15.9 + + - -
182A ASP* 5.8 0.3 + - - -
202A TYR* 3.3 15.7 - + - +
204A ARG* 3.5 40.6 - - + -
206A ASP* 3.0 35.1 + - - +
216A ARG* 3.0 16.1 + - - -
217A PRO* 4.2 13.9 - - + +
218A SER 3.2 10.5 + - - +
219A ASP 2.9 7.6 + - - +
221A GLU* 1.3 75.0 - - - +
223A ASP* 1.3 60.4 + - - +
225A TYR* 3.1 26.6 + + - +
226A LEU* 2.8 53.4 + - + +
507A 9YW 5.5 2.1 + - - -
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Residues in contact with ASP 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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196A PRO* 4.0 12.7 - - + +
199A LEU* 3.8 20.6 - - + +
202A TYR* 2.5 36.4 + - - -
219A ASP* 3.0 15.6 + - - +
220A GLY* 3.7 12.7 - - - +
221A GLU 3.3 0.2 - - - -
222A TYR* 1.3 75.9 - - - +
224A ARG* 1.3 58.4 + - + +
226A LEU 3.6 0.2 + - - -
227A TRP* 3.0 28.6 + - - +
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Residues in contact with ARG 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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191A TYR* 3.3 48.0 + - + +
192A ALA* 3.7 28.7 + - - +
194A VAL* 3.2 29.0 + - + +
196A PRO* 4.3 15.0 - - + +
220A GLY 3.5 14.6 + - - +
221A GLU* 3.2 10.2 + - - +
222A TYR 3.2 0.4 - - - -
223A ASP* 1.3 75.5 - - + +
225A TYR* 1.3 65.9 + - - +
227A TRP* 3.2 2.1 + - - +
228A LEU* 3.2 28.1 + - - +
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Residues in contact with TYR 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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175A HIS* 2.8 28.1 + + + -
177A TRP* 3.6 42.0 - + + -
182A ASP* 3.4 27.0 + - + -
183A ASN* 3.7 5.2 - - - +
191A TYR* 3.4 43.6 - + - -
217A PRO* 3.9 9.4 - - + +
221A GLU* 3.0 46.1 + - + -
222A TYR* 3.1 34.7 + + - +
224A ARG* 1.3 76.6 - - - +
226A LEU* 1.3 64.0 + - + +
228A LEU* 3.5 5.7 + - - -
229A LEU* 3.6 7.3 - - - +
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Residues in contact with LEU 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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89A PHE* 3.8 26.9 - - + -
90A PRO* 4.0 18.4 - - + -
94A ARG* 4.1 16.2 + - - +
177A TRP* 4.7 6.3 - - + -
199A LEU* 3.9 21.5 - - + +
202A TYR* 3.8 16.8 - - + -
222A TYR* 2.8 54.6 + - + +
223A ASP 4.1 3.1 - - - +
225A TYR* 1.3 75.8 - - + +
227A TRP* 1.3 66.3 + - - +
229A LEU* 3.2 32.3 + - + +
230A GLU* 3.4 6.6 + - - +
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Residues in contact with TRP 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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194A VAL* 4.1 13.9 - - + -
195A VAL 3.7 10.7 + - - -
196A PRO* 3.6 20.2 - - + -
197A GLY* 3.5 34.3 - - - -
198A LYS 3.5 24.7 - - - -
199A LEU* 3.8 19.0 - - + +
223A ASP 3.0 19.5 + - - +
224A ARG* 3.2 4.7 + - - +
226A LEU* 1.3 76.6 - - - +
228A LEU* 1.3 63.6 + - - +
230A GLU* 2.8 33.6 + - + +
231A GLU* 3.0 48.4 + - + -
247A SER* 5.0 0.2 - - - -
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Residues in contact with LEU 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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174A TYR 3.7 6.1 - - - +
175A HIS* 3.5 35.4 - - + +
191A TYR* 3.8 23.6 - - + -
194A VAL* 4.0 17.7 - - + -
224A ARG 3.2 12.2 + - - +
225A TYR 3.7 1.3 - - - +
226A LEU 3.3 0.4 - - - -
227A TRP* 1.3 75.5 - - - +
229A LEU* 1.3 62.8 + - - +
231A GLU* 3.1 35.0 + - - +
232A MET* 3.1 18.5 + - - +
246A MET* 3.6 11.8 - - + +
247A SER* 4.4 0.4 - - - -
248A PHE* 3.7 36.3 - - + +
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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
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90A PRO* 4.0 19.5 - - + -
94A ARG* 4.3 10.8 - - + +
95A TRP* 3.4 61.2 - - + -
175A HIS* 3.8 15.5 - - + +
177A TRP* 3.9 5.8 - - + -
225A TYR 3.6 14.6 - - - +
226A LEU* 3.2 21.7 + - + +
227A TRP 3.1 0.6 - - - -
228A LEU* 1.3 77.6 - - - +
230A GLU* 1.3 60.9 + - - +
232A MET* 3.2 9.7 + - + +
233A LYS* 2.8 39.0 + - + +
237A TYR* 4.9 1.1 - - - +
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Residues in contact with GLU 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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94A ARG* 4.4 10.4 + - - +
198A LYS 5.3 0.4 - - - +
199A LEU* 4.1 8.7 - - + -
200A PRO* 4.0 25.5 - - + +
226A LEU 3.4 9.3 + - - +
227A TRP* 2.8 41.5 + - + +
229A LEU* 1.3 79.2 - - - +
231A GLU* 1.3 58.6 + - - +
233A LYS* 3.2 34.6 + - - +
234A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TRP* 3.0 43.1 + - + +
228A LEU* 3.1 18.7 + - - +
230A GLU* 1.3 78.0 - - - +
232A MET* 1.3 62.0 + - - +
234A ALA* 3.4 13.1 + - - +
235A VAL* 3.6 13.2 + - - +
245A VAL* 3.8 20.3 - - + +
246A MET* 3.7 12.6 - - - +
247A SER* 2.4 51.4 + - - -
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A TRP* 4.8 4.7 - - - -
112A GLY 4.3 1.6 - - - +
113A ILE* 3.5 34.5 - - + -
174A TYR* 3.7 20.6 - - + +
175A HIS* 4.1 14.6 - - + -
228A LEU 3.1 11.8 + - - +
229A LEU* 3.6 7.4 - - - +
231A GLU* 1.3 74.1 - - - +
233A LYS* 1.3 65.2 + - - +
235A VAL* 3.1 8.7 + - - +
237A TYR* 3.0 52.0 + - + -
242A LEU* 4.0 21.5 - - + -
246A MET* 3.7 28.7 - - + -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ALA 4.9 1.2 + - - -
94A ARG* 2.8 27.4 + - - +
95A TRP* 3.2 20.6 - - - +
96A ALA* 4.2 5.8 - - + +
100A LEU* 3.7 24.2 - - + +
229A LEU* 2.8 25.7 + - + +
230A GLU* 3.2 39.0 + - - +
232A MET* 1.3 73.2 - - - +
234A ALA* 1.3 62.0 + - - +
236A ARG* 3.1 15.9 + - - +
237A TYR* 3.2 27.1 - - + +
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Residues in contact with ALA 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 GLU 3.0 18.1 + - - +
231A GLU* 3.8 7.9 - - - +
232A MET 3.1 0.8 - - - -
233A LYS* 1.3 77.2 - - - +
235A VAL* 1.3 64.8 + - + +
236A ARG* 3.4 4.7 + - - +
241A ARG* 4.3 5.4 + - - -
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Residues in contact with VAL 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 GLU 3.7 6.7 - - - +
232A MET 3.4 10.8 - - - +
234A ALA* 1.3 80.6 - - + +
236A ARG* 1.3 71.5 + - - +
237A TYR 3.1 2.9 + - - +
238A ASP* 3.1 19.9 + - - +
241A ARG* 3.5 49.1 + - + +
242A LEU* 3.6 26.9 - - + -
245A VAL* 3.6 32.8 - - + -
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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