Contacts of the helix formed by residues 304 - 317 (chain B) in PDB entry 1OI4
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 ASP 304 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258B LYS* 3.9 14.6 + - - +
300B TYR 5.0 3.1 - - - +
301B LEU 3.0 13.5 + - - +
302B ARG 3.2 0.8 - - - -
303B GLY* 1.3 79.5 - - - +
305B ASN* 1.3 65.4 + - - +
306B ARG* 2.8 69.7 + - - +
307B PHE* 3.1 25.0 + - + -
308B VAL* 3.3 12.0 + - - +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 4.2 1.0 + - - -
304B ASP* 1.3 72.1 + - - +
306B ARG* 1.3 55.4 + - + +
308B VAL* 3.6 12.0 - - - +
309B THR* 2.7 45.6 + - - +
312B ARG* 5.4 3.6 + - - -
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LYS* 3.8 30.3 + - - +
279B ILE* 3.6 32.9 - - + +
280B ASP* 2.8 46.4 + - - -
304B ASP* 2.8 38.4 + - - +
305B ASN* 1.3 73.5 - - + +
307B PHE* 1.3 56.0 + - + +
309B THR* 3.9 4.7 - - - -
310B PHE* 3.0 27.7 + - - +
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.9 26.7 - - + +
256B ILE* 4.3 5.6 - - + -
257B GLU* 3.6 34.8 - - - -
258B LYS* 3.9 21.3 - - + -
279B ILE* 3.7 30.3 - - + -
301B LEU* 3.7 51.1 - - + +
304B ASP* 3.1 30.4 + - + -
306B ARG* 1.3 73.5 - - - +
308B VAL* 1.3 65.7 + - - +
310B PHE* 3.4 6.1 + - - +
311B THR* 3.0 27.9 + - - -
330B LEU* 4.5 3.4 - - + -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ARG* 3.7 30.1 - - - +
304B ASP 3.3 11.2 + - - +
305B ASN* 3.2 15.3 + - - +
307B PHE* 1.3 78.4 - - - +
309B THR* 1.3 57.6 + - - +
311B THR* 3.1 7.7 + - - -
312B ARG* 2.9 45.9 + - - +
330B LEU* 4.6 4.3 - - + -
333B SER* 3.5 43.3 - - - +
334B ALA* 3.8 2.1 - - - +
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ASN* 2.7 29.7 + - - +
306B ARG* 3.9 5.6 - - - -
308B VAL* 1.3 74.4 - - - +
310B PHE* 1.3 57.0 + - - +
312B ARG* 3.3 27.2 + - - +
313B ASP* 2.8 48.2 + - - +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ALA* 4.2 4.7 - - + -
229B LEU* 4.0 22.9 - - + -
256B ILE* 5.5 1.8 - - + -
279B ILE* 3.7 21.5 - - + -
282B VAL* 4.1 20.6 - - + -
283B THR 3.8 6.3 - - - -
284B PRO* 3.7 37.5 - - + +
287B PHE* 3.9 25.4 - + - -
290B LEU* 4.0 24.9 - - + -
306B ARG 3.0 19.0 + - - +
307B PHE* 3.6 5.6 - - - +
309B THR* 1.3 78.4 - - - +
311B THR* 1.3 58.3 + - - +
313B ASP* 4.6 0.9 - - - -
314B PHE* 2.9 41.5 + + - +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 3.5 17.0 - - - +
290B LEU* 4.5 8.3 - - + +
292B LEU* 4.5 6.4 - - + +
307B PHE 3.0 15.5 + - - -
308B VAL* 3.5 8.5 - - - -
310B PHE* 1.3 74.6 - - - +
312B ARG* 1.3 66.2 + - - +
314B PHE* 3.2 5.0 + - - +
315B VAL* 2.9 25.6 + - + +
330B LEU* 3.6 36.3 - - + +
331B LEU* 3.8 25.4 - - + -
334B ALA* 3.9 4.3 - - + -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ASN* 5.4 3.8 + - - -
308B VAL* 2.9 38.4 + - - +
309B THR* 3.5 39.8 + - - +
311B THR* 1.3 78.3 - - - +
313B ASP* 1.3 69.0 + - - +
315B VAL* 3.3 1.7 + - - +
316B ASN* 2.9 45.1 + - - +
333B SER 4.7 2.4 + - - -
334B ALA* 3.5 33.0 + - + +
336B VAL* 3.9 8.5 - - + +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 3.9 24.0 - - + +
309B THR* 2.8 40.8 + - - +
310B PHE* 5.0 0.5 - - - -
312B ARG* 1.3 83.6 + - - +
314B PHE* 1.3 63.2 + - - +
316B ASN* 3.4 8.1 + - - +
317B SER* 3.1 22.5 + - - -
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ALA* 4.8 0.2 - - + -
284B PRO* 3.6 40.3 - - + +
287B PHE* 3.7 14.8 - + + -
288B ASP 3.9 0.2 - - - -
289B ALA* 3.2 34.3 - - - -
290B LEU* 3.6 17.0 - - + -
310B PHE* 2.9 29.9 + + - +
311B THR 3.7 3.6 - - - +
312B ARG 3.2 0.2 - - - -
313B ASP* 1.3 76.3 - - - +
315B VAL* 1.3 61.1 + - - +
317B SER* 2.5 26.0 + - - -
318B GLY 3.8 1.4 + - - -
319B LYS* 3.4 33.4 + - + +
320B PRO 3.4 16.8 - - - -
321B VAL* 3.7 16.8 - - + -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B THR* 2.9 21.4 + - + +
312B ARG 3.8 1.8 - - - +
314B PHE* 1.3 75.3 - - - +
316B ASN* 1.3 65.3 + - - +
318B GLY* 3.1 2.8 + - - -
321B VAL* 4.0 17.9 - - + -
331B LEU* 3.7 28.9 - - + -
336B VAL* 3.6 29.6 - - + +
340B ARG* 4.1 21.9 + - - +
370B GLN* 2.9 30.7 + - - +
371B LEU* 5.5 5.2 - - + -
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Residues in contact with ASN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 2.9 43.1 + - - +
313B ASP* 4.0 8.0 + - - +
315B VAL* 1.3 78.3 - - - +
317B SER* 1.3 60.1 + - - +
318B GLY* 3.4 1.0 + - - -
336B VAL* 4.2 14.2 - - - +
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 5.7 3.5 - - - +
313B ASP 3.1 12.9 + - - -
314B PHE* 2.5 21.6 + - - -
315B VAL 3.1 0.4 - - - -
316B ASN* 1.3 76.3 - - - +
318B GLY* 1.3 59.0 + - - +
319B LYS* 3.2 35.7 + - - +
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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
------------------------------------------------------------
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