Contacts of the helix formed by residues 253 - 270 (chain A) in PDB entry 4OGB
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 THR 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASN 3.8 2.2 + - - +
252A LEU* 1.3 75.0 - - - +
254A LYS* 1.3 67.2 + - - +
255A LYS* 3.4 11.7 + - - +
256A GLN* 2.9 42.6 + - + +
257A ARG* 2.8 21.3 + - - +
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Residues in contact with LYS 254 (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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253A THR* 1.3 71.6 - - - +
255A LYS* 1.3 56.6 + - - +
257A ARG* 3.3 24.3 + - + +
258A GLN* 2.9 60.4 + - + +
213B ILE 4.5 0.4 + - - -
214B ASN 2.8 30.6 + - - -
216B ASN* 3.0 15.6 + - - -
506B EDO 4.0 22.4 - - - +
244D GLU* 2.9 36.8 + - + +
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Residues in contact with LYS 255 (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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253A THR* 3.1 11.0 + - - +
254A LYS* 1.3 74.5 - - - +
256A GLN* 1.3 66.3 + - - +
258A GLN* 3.4 6.5 + - - +
259A SER* 3.2 18.5 + - - -
505A EDO 3.5 23.9 - - - +
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Residues in contact with GLN 256 (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 THR 5.4 2.0 + - - -
135A PHE* 3.7 26.3 - - - -
188A LEU* 3.7 11.2 - - + +
251A ASN 4.6 0.7 - - - +
252A LEU* 3.3 22.3 - - + +
253A THR* 2.9 44.0 + - + +
255A LYS* 1.3 77.3 - - - +
257A ARG* 1.3 57.7 - - - +
260A LEU* 2.9 32.5 + - - +
505A EDO 3.4 23.3 - - - +
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Residues in contact with ARG 257 (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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247A ASP* 6.1 0.9 - - - -
249A PHE 3.6 17.2 + - - +
250A GLN 5.4 1.4 + - - -
252A LEU* 3.1 31.3 + - + -
253A THR 2.8 12.6 + - - +
254A LYS* 3.4 35.4 - - + +
256A GLN* 1.3 77.9 - - - +
258A GLN* 1.3 56.6 + - + +
260A LEU* 4.3 2.5 - - - -
261A ARG* 2.9 32.1 + - - +
506A EDO 3.4 36.3 + - - +
216B ASN* 4.4 5.1 + - - +
244D GLU* 2.9 42.8 + - - -
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Residues in contact with GLN 258 (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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254A LYS* 2.9 49.2 + - + +
255A LYS* 4.0 6.0 - - - +
256A GLN 3.4 0.2 - - - -
257A ARG* 1.3 76.7 - - - +
259A SER* 1.3 57.7 + - - +
261A ARG* 3.9 5.6 - - - +
262A LYS* 3.1 28.1 + - - +
210B GLN* 4.6 2.2 + - - +
213B ILE* 4.5 8.1 - - - +
214B ASN* 2.8 30.5 + - - +
506B EDO 3.6 22.2 - - - -
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Residues in contact with SER 259 (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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188A LEU* 3.5 20.6 - - - +
255A LYS 3.2 15.2 + - - -
258A GLN* 1.3 77.3 - - - +
260A LEU* 1.3 65.5 + - - +
262A LYS* 3.2 6.8 + - - +
263A MET* 3.0 37.1 + - - +
303A TYR* 6.0 0.5 - - - -
505A EDO 3.7 16.4 - - - -
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Residues in contact with LEU 260 (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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188A LEU* 3.9 12.7 - - + +
191A LEU* 3.9 12.8 - - + +
192A ALA* 3.6 36.8 - - + +
195A PHE* 5.3 0.4 - - + -
238A PHE* 6.1 0.7 - - + -
249A PHE* 3.6 47.1 - - + -
252A LEU* 3.8 15.0 - - + -
256A GLN 2.9 18.5 + - - +
257A ARG 3.8 2.7 - - - +
259A SER* 1.3 75.5 + - - +
261A ARG* 1.3 59.8 + - - +
263A MET* 3.4 9.3 + - - +
264A VAL* 2.9 42.2 + - + +
506A EDO 4.3 6.3 - - - -
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Residues in contact with ARG 261 (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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238A PHE* 3.4 49.1 - - + -
257A ARG 2.9 18.8 + - - +
258A GLN* 3.9 6.3 - - - +
259A SER 3.2 0.2 - - - -
260A LEU* 1.3 78.4 - - - +
262A LYS* 1.3 62.3 + - - +
264A VAL* 3.4 1.2 + - - +
265A ILE* 3.0 33.2 + - + +
506A EDO 3.8 18.8 + - - -
213B ILE* 5.7 0.2 - - - +
216B ASN* 5.9 2.7 - - - -
220B ALA 3.3 16.6 + - - -
221B LEU* 3.8 25.3 + - - +
224B ASN* 3.8 11.9 + - - +
225B ASP* 2.8 40.8 + - - +
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Residues in contact with LYS 262 (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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258A GLN 3.1 19.0 + - - +
259A SER* 3.2 5.6 + - - +
261A ARG* 1.3 78.7 - - - +
263A MET* 1.3 58.3 + - + +
265A ILE* 3.4 2.6 + - - +
266A ASP* 3.0 43.5 + - - +
303A TYR* 4.0 21.1 - - + +
512A EDO 3.1 47.1 + - - +
225B ASP* 5.8 0.9 - - - -
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Residues in contact with MET 263 (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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188A LEU* 3.7 35.2 - - + +
189A GLU* 3.5 34.5 - - + +
192A ALA* 3.8 14.6 - - + -
259A SER* 3.0 37.9 + - - +
260A LEU* 3.8 1.3 - - - +
262A LYS* 1.3 77.2 - - + +
264A VAL* 1.3 57.4 + - - +
266A ASP* 3.3 1.7 + - - +
267A ILE* 2.9 36.6 + - + +
303A TYR* 3.6 35.2 - - + +
307A ILE* 4.0 7.0 - - + -
310A LEU* 4.7 8.1 - - - -
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Residues in contact with VAL 264 (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 ALA* 3.8 24.5 - - - +
195A PHE* 3.8 22.9 - - + -
196A ALA* 4.2 12.1 - - + -
199A ILE* 3.8 23.6 - - + -
234A LEU* 3.9 2.9 - - + -
238A PHE* 3.5 24.9 - - + -
260A LEU* 2.9 29.8 + - + +
261A ARG 3.8 3.8 - - - +
263A MET* 1.3 75.2 - - - +
265A ILE* 1.3 61.8 + - - +
267A ILE* 3.3 1.4 + - - +
268A VAL* 3.0 24.8 + - - +
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Residues in contact with ILE 265 (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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234A LEU* 3.8 14.7 - - + +
238A PHE* 3.9 15.9 - - + -
261A ARG* 3.0 49.0 + - + +
262A LYS* 3.8 3.4 - - - +
264A VAL* 1.3 75.3 - - - +
266A ASP* 1.3 64.4 + - - +
268A VAL 3.5 0.2 + - - -
269A LEU* 3.0 44.1 + - + +
512A EDO 3.5 21.5 - - - -
224B ASN* 3.3 37.5 - - + +
225B ASP* 3.9 7.0 - - + +
226B SER* 4.6 0.2 - - - +
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Residues in contact with ASP 266 (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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262A LYS* 3.0 20.7 + - - +
263A MET 3.7 3.1 - - - +
265A ILE* 1.3 76.0 - - - +
267A ILE* 1.3 62.6 + - - +
269A LEU* 4.2 5.6 - - - +
270A ALA* 3.3 13.2 + - - +
303A TYR* 2.7 32.2 + - - -
307A ILE* 3.8 17.5 - - + +
311A GLN* 3.0 25.2 + - - +
507A EDO 4.8 0.7 + - - -
512A EDO 2.5 30.8 + - - -
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Residues in contact with ILE 267 (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 ALA* 4.1 9.6 - - + +
193A ALA* 4.0 26.5 - - + +
196A ALA* 3.6 13.7 - - + -
263A MET 2.9 24.4 + - - +
264A VAL 3.8 3.4 - - - +
265A ILE 3.2 0.2 - - - -
266A ASP* 1.3 74.8 - - - +
268A VAL* 1.3 66.0 + - - +
270A ALA* 3.2 16.8 + - - +
271A THR* 3.5 8.7 + - - +
307A ILE* 4.0 15.0 - - + -
310A LEU* 3.9 22.4 - - + +
311A GLN* 4.0 18.3 - - + +
314A VAL* 3.6 35.2 - - + -
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Residues in contact with VAL 268 (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 ALA* 3.7 33.2 - - + +
199A ILE* 4.3 4.5 - - + -
200A HIS* 4.0 28.0 - - + +
230A GLU* 3.8 17.6 - - + +
233A HIS* 4.5 3.1 - - + -
234A LEU* 3.6 35.4 - - + +
264A VAL 3.0 15.4 + - - +
267A ILE* 1.3 73.2 - - + +
269A LEU* 1.3 61.5 + - - +
271A THR* 2.5 36.0 + - - +
314A VAL* 6.5 0.2 - - + -
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Residues in contact with LEU 269 (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 SER* 4.5 9.5 + - - +
230A GLU* 4.2 7.6 - - + -
231A ASN* 3.8 40.2 - - - +
234A LEU* 3.7 14.6 - - + -
265A ILE* 3.0 40.3 + - + +
266A ASP* 4.3 6.7 - - - +
268A VAL* 1.3 75.6 - - - +
270A ALA* 1.3 59.1 + - - +
271A THR 3.1 1.3 + - - -
272A ASP* 3.4 21.3 + - - +
275A LYS* 3.9 9.6 - - - +
507A EDO 4.4 6.7 - - - +
512A EDO 5.7 0.9 - - - -
224B ASN* 5.4 0.4 - - + -
226B SER* 4.6 11.2 - - - +
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Residues in contact with ALA 270 (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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266A ASP 3.3 15.8 + - - +
267A ILE 3.2 12.7 + - - +
268A VAL 3.1 0.4 - - - -
269A LEU* 1.3 76.9 - - - +
271A THR* 1.3 59.8 + - - +
272A ASP 3.3 7.2 - - - +
275A LYS* 4.5 4.2 - - - +
279A LEU* 3.5 26.5 - - + +
311A GLN* 3.8 32.1 - - + +
315A HIS* 4.2 8.3 + - - +
507A EDO 4.0 10.7 + - - +
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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