Contacts of the helix formed by residues 213 - 229 (chain A) in PDB entry 4OBP
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 ARG 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASP* 2.7 39.0 + - - +
212A TYR* 1.3 105.3 + - + +
214A SER* 1.3 62.0 + - - +
215A ASP 3.2 0.4 - - - -
216A LEU* 3.1 20.3 + - + +
217A TRP 3.3 4.5 + - - -
274A TYR* 3.1 34.6 + - + +
275A MET* 3.3 28.7 + - - +
277A ARG* 2.9 52.8 + - - +
278A PRO 3.7 15.3 - - - +
279A SER 4.7 0.2 - - - +
402A MES 4.4 8.7 - - - -
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.9 8.5 - - - +
152A ARG* 4.1 7.0 + - - -
196A ALA* 3.9 7.1 - - - +
198A GLU* 3.4 23.1 + - - -
199A VAL* 3.9 21.5 - - - -
210A TYR* 3.5 13.1 - - - -
211A ASP* 2.7 22.6 + - - +
213A ARG* 1.3 76.6 - - - +
215A ASP* 1.3 62.4 + - - +
217A TRP* 3.4 5.7 + - - +
218A SER* 3.1 24.6 + - - -
277A ARG* 3.7 1.6 - - - +
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Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.7 18.7 - - + +
145A HIS* 2.8 27.6 + - + +
150A ILE* 3.5 10.1 - - - +
151A HIS* 2.9 31.0 + - - +
152A ARG* 2.9 28.6 + - - -
154A ILE* 4.2 6.4 + - + +
212A TYR 3.2 7.3 + - - +
214A SER* 1.3 76.1 + - - +
216A LEU* 1.4 59.5 + - - +
218A SER* 3.3 9.0 + - - -
219A CYS* 2.9 28.1 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.6 29.6 - - + -
141A LEU* 4.3 8.1 - - + -
145A HIS* 4.3 2.2 - - + -
212A TYR* 4.2 4.3 - - + +
213A ARG* 3.1 25.4 + - + +
215A ASP* 1.4 73.4 - - - +
217A TRP* 1.3 64.3 + - - +
219A CYS* 3.2 5.7 + - - +
220A GLY 3.0 17.5 + - - -
269A CYS* 3.3 13.6 - - - +
277A ARG* 4.3 6.5 - - - -
278A PRO 3.0 26.5 - - - +
279A SER* 3.6 3.8 - - - +
280A THR* 3.5 40.4 - - + +
283A LEU* 4.0 14.4 - - + -
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Residues in contact with TRP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR 5.1 0.6 + - - -
194A TRP 3.6 11.0 - - - -
195A MET 3.3 11.5 + - - -
196A ALA* 3.4 24.0 - - + -
197A PRO* 3.7 34.3 - - + -
213A ARG 3.3 4.2 + - - -
214A SER 3.5 9.0 - - - +
215A ASP 3.4 0.2 - - - -
216A LEU* 1.3 76.3 - - - +
218A SER* 1.4 58.1 + - - +
220A GLY 3.0 16.3 + - - -
221A ILE* 3.0 26.0 + - + +
245A ILE* 4.4 12.5 - - + +
249A PRO 5.4 0.2 - - - -
250A PRO* 4.5 0.2 - - + -
251A PRO* 3.7 34.8 - - + -
269A CYS 3.2 13.0 + - - -
270A LEU* 3.3 48.4 - - + +
271A VAL 3.8 5.4 - - - -
272A LYS* 4.0 15.5 - - + -
277A ARG* 3.8 19.7 - - - +
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG 5.6 2.8 + - - -
154A ILE* 3.4 32.3 + - - -
194A TRP* 2.7 27.8 + - - -
195A MET* 4.7 0.9 - - - -
196A ALA 4.7 2.1 + - - -
214A SER 3.1 13.4 + - - -
215A ASP* 3.5 11.3 + - - -
216A LEU 3.3 0.2 - - - -
217A TRP* 1.4 76.5 - - - +
219A CYS* 1.3 52.7 + - - +
221A ILE* 3.3 5.7 + - - +
222A THR* 2.7 37.0 + - - -
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Residues in contact with CYS 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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134A SER* 4.2 11.3 + - - -
137A ILE* 4.0 24.6 - - + +
138A LEU* 3.9 31.4 - - + -
141A LEU* 4.5 1.3 - - + -
154A ILE* 3.8 8.0 - - - +
215A ASP 2.9 14.5 + - - +
216A LEU* 3.2 13.9 + - - +
218A SER* 1.3 74.9 - - - +
220A GLY* 1.3 57.0 + - - +
222A THR* 3.2 7.1 + - - -
223A ALA* 3.0 26.0 + - - +
226A MET* 5.7 0.2 - - - +
265A PHE* 4.4 14.4 - - - -
269A CYS* 4.4 1.1 - - - -
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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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216A LEU 3.0 6.9 + - - -
217A TRP 3.0 7.0 + - - -
219A CYS* 1.3 73.3 - - - +
221A ILE* 1.3 61.6 + - - +
223A ALA* 3.2 8.7 + - - +
224A ILE* 3.1 25.5 + - - +
266A ILE* 3.6 5.1 - - - +
269A CYS* 3.3 29.1 - - - +
270A LEU* 4.0 10.8 - - - -
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Residues in contact with ILE 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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193A TYR 3.5 21.8 - - - +
194A TRP* 3.3 22.9 - - + -
217A TRP* 3.0 39.7 + - + +
218A SER 3.7 6.5 - - - +
220A GLY* 1.3 72.9 - - - +
222A THR* 1.4 58.2 + - - +
224A ILE* 3.3 6.3 + - - +
225A GLU* 2.9 26.5 + - - +
231A PRO* 3.7 18.7 - - + +
232A PRO* 3.8 12.3 - - + -
251A PRO* 4.0 22.7 - - + -
270A LEU* 3.8 15.9 - - + -
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.5 6.3 - - + -
137A ILE* 4.0 24.7 - - + -
154A ILE* 3.9 4.1 - - + +
155A LYS* 3.7 11.0 - - - +
156A GLY* 4.0 21.5 - - - +
159A VAL* 4.7 2.2 - - + -
194A TRP* 3.5 11.9 - - - +
218A SER 2.7 20.3 + - - -
219A CYS* 3.2 12.8 + - - -
221A ILE* 1.4 75.2 - - - +
223A ALA* 1.3 57.3 + - - +
225A GLU* 3.3 12.0 - - - +
226A MET* 3.0 33.5 + - + +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.0 16.3 - - + +
134A SER* 4.0 9.9 - - - +
219A CYS 3.0 13.2 + - - +
220A GLY 3.2 3.1 + - - +
222A THR* 1.3 72.6 - - - +
224A ILE* 1.3 64.7 + - - +
226A MET* 3.4 13.7 + - - +
227A ALA* 3.1 22.7 + - - +
262A PHE* 3.8 7.2 - - + -
265A PHE* 4.1 8.1 - - + -
266A ILE* 3.5 25.1 - - + -
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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
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220A GLY 3.1 10.4 + - - +
221A ILE* 3.3 8.7 + - + +
223A ALA* 1.3 73.5 - - - +
225A GLU* 1.3 55.3 + - - +
227A ALA* 3.0 2.8 + - - +
228A GLU* 2.8 58.0 + - - +
230A ALA 4.1 5.2 - - - +
232A PRO* 3.8 36.1 - - + -
251A PRO* 4.0 11.4 - - + -
252A ARG 4.4 8.1 - - - +
253A LEU* 4.1 14.6 - - + -
266A ILE* 3.9 20.2 - - + -
270A LEU* 3.7 28.5 - - + -
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Residues in contact with GLU 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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113A ILE* 5.4 2.2 - - - -
114A THR* 2.7 38.8 + - - +
117A VAL* 3.8 8.1 - - + +
156A GLY* 3.1 18.3 + - - -
194A TRP* 3.0 36.1 + - + +
221A ILE 2.9 13.0 + - - +
222A THR* 3.3 12.4 - - - +
224A ILE* 1.3 77.1 - - - +
226A MET* 1.3 55.2 + - + +
229A GLY* 2.7 34.9 + - - +
230A ALA* 3.7 29.8 - - - +
231A PRO* 4.2 3.4 - - - +
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Residues in contact with MET 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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113A ILE* 3.6 21.5 - - + -
117A VAL* 3.4 16.0 - - + +
125A LEU* 2.9 36.2 + - + +
130A ILE* 3.8 21.8 - - + -
133A ILE* 3.6 47.1 - - + -
134A SER* 3.5 25.4 - - - +
137A ILE* 4.5 2.5 - - + -
222A THR* 3.0 31.1 + - + +
223A ALA* 3.7 13.5 - - - +
224A ILE 3.3 0.2 - - - -
225A GLU* 1.3 74.9 - - - +
227A ALA* 1.3 59.7 - - - +
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Residues in contact with ALA 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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124A THR* 2.9 23.9 + - - -
130A ILE* 3.8 12.5 - - + +
223A ALA 3.1 13.2 + - - +
224A ILE 3.0 7.9 + - - +
226A MET* 1.3 78.8 - - - +
228A GLU* 1.3 60.0 + - + +
253A LEU* 3.7 21.3 - - + -
258A TRP* 3.5 31.3 - - + -
262A PHE* 3.9 2.5 - - + -
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Residues in contact with GLU 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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122A GLY 5.3 0.3 - - - +
123A ASN* 3.1 13.5 - - - +
124A THR* 5.2 0.2 - - - -
224A ILE* 2.8 36.3 + - - +
227A ALA* 1.3 80.6 - - + +
229A GLY* 1.3 58.4 + - - +
230A ALA* 3.3 13.8 + - + +
232A PRO* 5.7 1.6 - - - +
252A ARG 4.8 2.1 - - - +
253A LEU* 3.3 14.0 - - + +
254A LYS* 2.8 64.9 + - + +
255A SER* 4.4 2.6 + - - +
258A TRP* 5.0 3.5 + - + +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 5.8 2.8 - - - +
117A VAL* 3.7 18.2 - - - +
118A LYS* 5.7 3.8 + - - +
123A ASN* 3.1 22.0 + - - +
225A GLU* 2.7 27.7 + - - +
227A ALA 3.8 0.2 - - - -
228A GLU* 1.3 71.5 - - - +
230A ALA* 1.3 60.4 + - - +
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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
------------------------------------------------------------
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