Contacts of the helix formed by residues 260 - 280 (chain A) in PDB entry 1O1L
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 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ALA 3.8 15.3 - - - +
258A GLU* 3.0 12.6 + - - +
259A PHE* 1.3 75.5 - - - +
261A PRO* 1.3 72.3 - - - +
262A ALA* 3.4 8.6 + - - +
263A VAL* 3.0 25.6 + - + +
264A HIS* 2.8 27.2 + - - +
30D ARG* 3.7 1.8 - - - +
116D HIS* 5.6 0.4 - - - -
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Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A THR* 1.3 88.4 - - - +
262A ALA* 1.3 61.7 + - - +
264A HIS* 3.4 2.8 + - + +
265A ALA* 3.0 23.4 + - - +
26D GLU* 4.7 0.7 - - - +
30D ARG* 3.7 32.3 - - + +
33D VAL* 3.9 17.5 - - + +
34D VAL* 4.6 1.8 - - + +
51D PRO* 4.6 4.7 - - + -
55D MET* 3.9 44.9 - - + -
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.8 12.1 + - - +
260A THR* 3.2 7.6 + - - +
261A PRO* 1.3 78.8 - - - +
263A VAL* 1.3 63.8 + - + +
265A ALA* 3.4 7.3 + - - +
266A SER* 3.1 25.6 + - - -
51D PRO* 4.4 23.6 - - + +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 3.8 35.4 - - + +
154A ALA* 6.2 1.6 - - + -
155A ALA* 4.1 16.2 - - + -
258A GLU 3.5 28.9 - - - +
259A PHE* 4.6 4.0 - - + -
260A THR* 3.0 16.2 + - + +
262A ALA* 1.3 74.8 - - + +
264A HIS* 1.3 62.4 + - - +
266A SER* 3.2 1.7 + - - -
267A LEU* 2.9 48.5 + - + +
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Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.1 21.6 - - + +
259A PHE* 3.6 26.5 - + + -
260A THR 2.8 16.9 + - - +
261A PRO 3.5 5.2 - - - +
263A VAL* 1.3 77.9 - - - +
265A ALA* 1.3 61.4 + - - +
267A LEU* 3.3 2.7 + - - +
268A ASP* 3.0 20.6 + - - +
30D ARG* 3.1 38.8 + - + +
34D VAL* 3.9 28.2 - - + +
35D TYR* 5.6 1.4 + - - -
109D VAL* 4.8 12.4 - - + +
112D CYS* 4.0 27.9 - - + -
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.6 1.0 + - - -
148A ASP* 4.9 0.9 - - - +
261A PRO 3.0 16.5 + - - +
262A ALA* 3.7 6.3 - - - +
263A VAL 3.3 0.2 - - - -
264A HIS* 1.3 75.7 - - - +
266A SER* 1.3 61.6 + - - +
268A ASP* 3.4 2.4 + - - +
269A LYS* 3.1 31.8 + - + +
33D VAL* 4.1 27.4 - - + +
34D VAL* 4.1 18.6 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.4 2.3 - - - +
148A ASP* 2.6 38.9 + - - -
151A ASN* 3.1 38.1 + - - -
152A VAL* 3.8 5.8 - - - +
262A ALA 3.1 12.0 + - - -
263A VAL 3.2 4.0 + - - -
265A ALA* 1.3 74.2 - - - +
267A LEU* 1.3 61.7 + - - +
269A LYS* 3.4 3.7 + - - +
270A PHE* 2.9 28.6 + - - +
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Residues in contact with LEU 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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152A VAL* 4.0 32.3 - - + +
155A ALA* 4.3 13.0 - - + -
156A TRP* 5.6 7.0 - - + -
248A LEU* 3.7 16.2 - - + -
251A LEU* 3.7 30.3 - - + -
255A LEU* 6.1 0.9 - - + -
259A PHE* 4.3 17.9 - - + -
263A VAL* 2.9 36.3 + - + +
264A HIS 3.8 1.3 - - - +
266A SER* 1.3 76.8 - - - +
268A ASP* 1.3 65.5 + - - +
270A PHE* 3.2 10.1 + - + +
271A LEU* 2.9 30.1 + - + +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.7 35.0 + - - +
244A SER* 5.6 5.4 - - - -
245A HIS* 6.0 0.2 - - - -
248A LEU* 3.4 27.4 - - + +
264A HIS 3.0 17.9 + - - +
265A ALA 3.8 4.3 - - - +
267A LEU* 1.3 78.4 - - - +
269A LYS* 1.3 61.4 + - - +
271A LEU* 3.4 4.7 + - - +
272A ALA* 3.2 22.7 + - - +
34D VAL* 4.2 8.3 - - + -
35D TYR* 3.6 24.2 + - - -
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Residues in contact with LYS 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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141A ARG* 3.2 55.2 + - + +
142A GLY 3.6 10.5 - - - +
143A VAL 2.6 28.5 + - - -
144A LEU* 3.9 8.7 - - + -
145A SER* 4.3 2.6 - - - +
148A ASP* 2.5 33.8 + - - +
265A ALA* 3.1 19.9 + - + +
266A SER 3.6 7.4 - - - +
267A LEU 3.3 0.2 - - - -
268A ASP* 1.3 73.7 - - - +
270A PHE* 1.3 65.0 + - - +
272A ALA* 3.3 4.0 + - - +
273A SER* 3.0 25.6 + - - -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.7 24.8 - - + +
152A VAL* 3.8 25.4 - - + -
156A TRP* 5.8 4.9 - + - -
208A LEU* 4.4 14.6 - - + -
211A ALA* 4.1 6.3 - - + -
212A VAL* 3.6 38.6 - - + -
215A VAL* 4.2 14.1 - - + -
218A MET* 3.8 22.0 - - - -
266A SER 2.9 18.2 + - - +
267A LEU* 3.5 10.3 - - + +
269A LYS* 1.3 76.3 - - - +
271A LEU* 1.3 69.2 + - + +
273A SER* 3.1 5.8 + - - -
274A VAL* 3.0 42.7 + - + +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 6.3 2.0 - - + -
208A LEU* 4.1 23.8 - - + -
244A SER* 3.6 41.7 + - - +
247A LEU* 4.1 30.1 - - + -
248A LEU* 4.2 16.8 - - + -
251A LEU* 5.7 3.8 - - + -
267A LEU* 2.9 23.9 + - + +
268A ASP* 4.1 4.7 - - - +
270A PHE* 1.3 87.8 - - + +
272A ALA* 1.3 58.2 + - - +
274A VAL* 3.3 6.5 + - + +
275A SER* 2.9 33.1 + - - -
285A HEM 5.4 3.2 - - + +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.1 14.8 - - - +
244A SER* 5.4 1.1 - - - -
268A ASP 3.2 17.1 + - - +
269A LYS* 3.6 4.9 - - - +
270A PHE 3.2 0.2 - - - -
271A LEU* 1.3 74.1 - - - +
273A SER* 1.3 59.3 + - - +
275A SER* 3.4 7.6 + - - -
276A THR* 3.0 32.4 + - - -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL 5.9 0.5 - - - -
144A LEU* 4.1 20.1 + - - +
218A MET* 3.8 16.4 - - - -
269A LYS 3.0 16.7 + - - -
270A PHE* 3.1 8.7 + - - -
272A ALA* 1.3 72.8 - - - +
274A VAL* 1.3 66.9 + - - +
276A THR* 3.2 7.6 + - - -
277A VAL* 3.0 26.7 + - - +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.2 13.9 - - + -
211A ALA* 4.4 6.3 - - + -
218A MET* 3.8 18.4 - - + -
222A LEU* 4.3 9.6 - - + +
270A PHE* 3.0 45.4 + - + +
271A LEU* 3.5 9.6 - - - +
273A SER* 1.3 77.0 - - - +
275A SER* 1.3 57.3 + - - +
277A VAL* 3.2 3.1 + - - +
278A LEU* 2.9 38.4 + - + +
285A HEM 4.0 28.3 - - + -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.4 34.0 + - - +
241A LYS* 5.4 3.3 - - - -
244A SER* 3.6 13.2 + - - -
271A LEU 2.9 19.1 + - - -
272A ALA* 3.7 9.1 - - - -
274A VAL* 1.3 77.3 - - - +
276A THR* 1.3 62.9 + - - +
278A LEU* 3.3 5.7 + - - +
279A THR* 3.0 30.3 + - - +
285A HEM 5.0 5.1 - - - +
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Residues in contact with THR 276 (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* 6.5 0.9 - - + -
272A ALA 3.0 20.3 + - - -
273A SER* 3.2 8.0 + - - -
275A SER* 1.3 73.4 - - - +
277A VAL* 1.3 68.8 + - + +
279A THR* 3.3 8.6 + - - -
280A SER* 3.0 24.5 + - - -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A MET* 3.9 17.0 - - + -
219A PRO* 3.9 35.7 - - + +
222A LEU* 3.7 33.9 - - + -
226A SER* 2.7 30.4 + - - +
273A SER* 3.0 18.2 + - - +
274A VAL 3.6 6.7 - - - +
276A THR* 1.3 78.9 - - + +
278A LEU* 1.3 54.8 + - + +
280A SER* 2.9 18.5 + - - +
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Residues in contact with LEU 278 (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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222A LEU* 4.1 23.6 - - + -
225A LEU* 4.1 26.7 - - + +
226A SER* 3.7 25.8 + - - +
229A HIS* 4.1 8.9 - - + +
240A PHE* 3.8 18.4 - - + -
274A VAL* 2.9 23.4 + - + +
275A SER 3.9 4.0 - - - +
276A THR 3.2 0.2 - - - -
277A VAL* 1.3 76.9 - - - +
279A THR* 1.3 60.1 + - - +
281A LYS 5.0 0.2 + - - -
282A TYR* 3.6 14.2 - - - -
285A HEM 3.4 55.4 - - + -
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Residues in contact with THR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 4.0 22.0 - - + +
240A PHE* 3.5 36.8 - - + -
275A SER 3.0 17.3 + - - +
276A THR* 3.6 8.1 + - - +
277A VAL 3.2 0.2 - - - -
278A LEU* 1.3 78.4 - - - +
280A SER* 1.3 64.3 + - - +
281A LYS 3.1 5.0 + - - -
282A TYR* 3.3 31.6 + - + +
283A ARG 5.1 0.2 + - - -
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Residues in contact with SER 280 (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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1A MET* 3.0 26.1 + - - +
226A SER* 3.4 6.1 + - - -
276A THR* 3.0 15.2 + - - -
277A VAL* 2.9 25.2 + - - +
278A LEU 3.4 0.2 - - - -
279A THR* 1.3 78.4 - - - +
281A LYS* 1.3 68.8 + - - +
282A TYR 3.4 0.7 + - - -
283A ARG* 3.8 4.2 + - - +
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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