Contacts of the helix formed by residues 261 - 283 (chain F) in PDB entry 4OIO
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 PRO 261 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.4 39.7 - - + +
259F ARG* 4.2 28.0 - - - +
260F ILE* 1.3 92.1 - - + +
262F VAL* 1.3 60.7 + - - +
263F HIS* 3.3 30.7 - - + +
264F MET* 3.1 5.9 + - + +
265F VAL* 2.9 24.8 + - - +
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ARG* 6.1 5.8 - - + -
252F ALA* 4.2 23.6 - - + -
259F ARG* 5.4 0.2 - - - +
260F ILE 3.6 1.4 + - - -
261F PRO* 1.3 71.4 - - - +
263F HIS* 1.3 65.6 + - + +
265F VAL* 3.3 9.7 + - - +
266F GLU* 2.9 41.6 + - - +
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Residues in contact with HIS 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 4.9 2.9 - - - -
261F PRO* 3.3 30.3 - - + +
262F VAL* 1.3 87.8 - - + +
264F MET* 1.3 84.6 + - + +
266F GLU* 3.2 18.0 - - + +
267F THR* 3.0 31.6 + - - -
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Residues in contact with MET 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D TYR* 4.2 19.5 - - + +
35D ARG* 3.9 25.1 - - - +
260F ILE* 3.6 19.1 - - + -
261F PRO* 3.1 12.7 + - + +
263F HIS* 1.3 95.7 + - + +
265F VAL* 1.3 59.8 + - - +
267F THR* 3.3 18.8 + - - -
268F ILE* 2.9 43.0 + - + +
307F THR* 5.2 7.6 - - - -
310F ILE* 4.9 8.1 - - + -
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Residues in contact with VAL 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ALA* 4.2 28.5 - - + +
256F ARG* 4.8 16.8 - - - +
260F ILE* 3.4 30.1 - - + +
261F PRO 2.9 19.6 + - - +
262F VAL* 3.5 10.3 - - - +
264F MET* 1.3 76.1 - - - +
266F GLU* 1.3 57.7 + - + +
268F ILE* 3.1 10.0 + - - +
269F ASN* 2.9 48.3 + - - +
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Residues in contact with GLU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F VAL* 2.9 31.0 + - + +
263F HIS* 3.2 24.5 - - - +
265F VAL* 1.3 73.0 - - - +
267F THR* 1.3 60.6 + - - +
269F ASN* 3.8 12.4 - - - +
270F LYS* 2.9 28.6 + - - +
273F ARG* 4.6 2.8 + - - +
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Residues in contact with THR 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F HIS 3.0 16.5 + - - -
264F MET* 3.4 24.4 - - - +
265F VAL 3.2 0.2 - - - -
266F GLU* 1.3 78.1 - - - +
268F ILE* 1.3 59.0 + - - +
270F LYS* 3.2 10.1 + - + +
271F LEU* 2.9 27.4 + - - +
295F MET* 5.4 0.9 - - - +
299F TRP* 3.8 33.8 - - + -
307F THR* 4.6 5.8 - - + -
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Residues in contact with ILE 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ARG* 4.6 11.4 - - - +
260F ILE* 4.0 24.2 - - + -
264F MET* 2.9 31.5 + - + +
265F VAL* 3.1 10.5 + - - +
267F THR* 1.3 76.4 - - - +
269F ASN* 1.3 62.7 + - - +
271F LEU* 3.2 11.5 - - + +
272F SER* 2.9 27.9 + - - -
307F THR* 4.2 17.9 - - + -
308F LEU* 6.0 2.5 - - + -
310F ILE* 4.7 3.6 - - + -
311F ALA* 3.6 37.2 - - + +
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Residues in contact with ASN 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ARG* 5.3 3.3 + - - -
265F VAL* 2.9 41.3 + - - +
266F GLU* 3.9 9.3 - - - +
267F THR 3.3 0.4 - - - -
268F ILE* 1.3 79.9 - - - +
270F LYS* 1.3 60.2 + - - +
272F SER* 3.3 9.0 + - - -
273F ARG* 2.9 39.6 + - - +
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Residues in contact with LYS 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLU 2.9 18.9 + - - +
267F THR* 3.2 9.8 + - + +
269F ASN* 1.3 73.6 - - - +
271F LEU* 1.3 59.4 + - - +
273F ARG* 3.5 26.8 - - - +
274F THR* 2.9 37.5 + - - +
295F MET* 3.6 35.9 + - + +
299F TRP* 5.3 6.5 - - + +
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Residues in contact with LEU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F THR 2.9 13.6 + - - +
268F ILE* 3.2 11.9 - - + +
270F LYS* 1.3 76.9 - - - +
272F SER* 1.3 56.8 + - - +
274F THR* 3.4 2.4 + - - -
275F ALA* 2.9 28.4 + - - +
291F ILE* 3.7 25.0 - - + +
295F MET* 3.6 30.2 - - + +
299F TRP* 4.3 11.4 - - + -
304F VAL* 4.2 11.0 - - + +
307F THR* 3.6 31.6 - - + -
308F LEU* 3.6 33.0 - - + -
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Residues in contact with SER 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ILE* 2.9 15.7 + - - -
269F ASN* 3.5 13.9 - - - -
270F LYS 3.2 0.2 - - - -
271F LEU* 1.3 74.5 - - - +
273F ARG* 1.3 60.0 + - - +
275F ALA* 3.1 7.9 + - - +
276F ARG* 2.9 40.2 + - - +
308F LEU* 6.2 0.2 - - - +
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Residues in contact with ARG 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F GLU* 4.6 2.6 + - - +
269F ASN* 2.9 19.9 + - - +
270F LYS* 3.5 42.4 + - - +
272F SER* 1.3 75.0 - - - +
274F THR* 1.3 59.3 + - - +
276F ARG* 3.3 34.5 + - - +
277F GLN* 2.9 39.3 + - + +
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Residues in contact with THR 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F LYS* 2.9 25.3 + - - +
271F LEU 3.6 4.7 - - - -
273F ARG* 1.3 77.8 + - - +
275F ALA* 1.3 55.7 + - - +
277F GLN* 3.2 10.3 + - + +
278F LEU* 2.9 33.6 + - + +
291F ILE* 4.5 4.0 - - + +
294F ALA* 3.8 34.8 + - + +
295F MET* 3.1 26.7 - - + +
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Residues in contact with ALA 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ARG* 4.6 5.6 - - - +
271F LEU* 2.9 15.1 + - + +
272F SER* 3.1 11.9 + - - +
274F THR* 1.3 77.3 - - - +
276F ARG* 1.3 56.1 + - - +
278F LEU* 4.6 1.1 - - - -
279F GLN* 2.9 26.7 + - - +
286F PRO* 3.4 19.1 - - + +
291F ILE* 4.3 23.5 - - + +
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Residues in contact with ARG 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C ARG* 3.4 27.1 - - - +
373C VAL 5.0 2.8 + - - -
374C ASN* 2.9 33.6 + - - +
376C ARG* 3.4 40.4 - - - +
272F SER* 2.9 22.1 + - - +
273F ARG* 3.3 40.1 - - - +
274F THR 3.3 0.2 - - - -
275F ALA* 1.3 72.1 - - - +
277F GLN* 1.3 60.9 + - - +
279F GLN* 3.2 5.5 + - - +
280F GLN* 2.9 30.9 + - - +
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Residues in contact with GLN 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C LYS* 4.6 21.2 - - - +
273F ARG* 2.9 25.8 + - + +
274F THR* 3.2 11.9 + - + +
276F ARG* 1.3 76.3 - - + +
278F LEU* 1.3 60.0 + - + +
280F GLN* 3.1 19.0 + - - +
281F GLU* 2.9 29.6 + - - +
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Residues in contact with LEU 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F THR* 2.9 20.1 + - + +
277F GLN* 1.3 78.9 - - + +
279F GLN* 1.3 57.7 + - - +
281F GLU* 3.7 22.3 - - - +
282F LEU* 2.9 42.5 + - + +
286F PRO* 3.6 15.7 - - + -
290F GLU* 3.4 40.8 - - + +
291F ILE* 3.6 17.7 - - + +
294F ALA* 3.7 22.4 - - + -
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Residues in contact with GLN 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 3.6 24.1 - - + -
116C GLY* 4.7 1.8 - - - -
117C HIS* 5.9 1.4 - - - -
375C SER* 4.1 12.8 + - - -
376C ARG* 3.5 16.4 + - - +
379C GLU* 3.4 27.4 + - - +
275F ALA 2.9 17.9 + - - +
276F ARG* 3.4 8.5 - - - +
277F GLN 3.1 0.2 - - - -
278F LEU* 1.3 78.3 - - - +
280F GLN* 1.3 58.7 + - - +
283F GLY* 2.9 30.8 + - - -
284F ARG 3.1 27.3 - - - +
285F GLU* 3.2 26.8 + - - +
286F PRO* 3.7 5.8 - - + +
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Residues in contact with GLN 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.6 19.2 - - + +
114C PHE* 4.1 35.5 + - - +
370C ALA* 3.1 37.2 + - + +
373C VAL 3.6 18.4 + - - +
375C SER* 4.1 10.5 + - - +
276F ARG 2.9 17.0 + - - +
277F GLN* 3.6 18.1 + - - +
279F GLN* 1.3 79.3 + - - +
281F GLU* 1.3 59.9 + - - +
283F GLY 4.5 1.0 + - - -
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F GLN 2.9 14.9 + - - +
278F LEU* 3.7 24.6 - - - +
280F GLN* 1.3 80.0 - - - +
282F LEU* 1.3 74.4 + - + +
283F GLY 3.5 0.6 + - - -
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Residues in contact with LEU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F LEU* 2.9 36.9 + - + +
279F GLN 3.2 0.2 + - - -
281F GLU* 1.3 93.5 - - + +
283F GLY* 1.3 63.4 + - - +
284F ARG* 3.3 31.4 + - + +
286F PRO* 4.6 4.7 - - + -
290F GLU* 3.3 39.5 - - + +
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Residues in contact with GLY 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C PRO* 4.7 1.4 - - - +
95C TYR* 4.0 21.4 + - - -
114C PHE* 3.6 33.2 - - - -
117C HIS* 3.7 9.0 + - - -
279F GLN 2.9 9.8 + - - -
280F GLN 4.5 1.2 + - - -
281F GLU 3.5 3.0 + - - -
282F LEU* 1.3 77.8 - - - +
284F ARG* 1.3 60.1 + - - +
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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