Contacts of the helix formed by residues 328 - 335 (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 PRO 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ALA* 3.9 18.8 - - + +
324B ILE* 4.0 6.1 - - - +
325B CYS 3.2 20.6 - - - +
326B HIS 3.2 1.3 - - - -
327B GLY* 1.3 87.8 - - - +
329B GLN* 1.3 61.0 + - - +
330B LEU 3.1 0.9 - - - -
331B LEU* 2.9 31.4 + - + +
332B ILE* 2.9 16.7 + - - +
337B ILE* 5.2 0.4 - - + +
342B LEU* 5.0 5.2 - - + -
343B THR 3.9 20.0 - - - +
344B ALA* 4.0 11.4 - - + -
348B ILE* 4.4 3.4 - - + -
352B VAL* 4.6 9.0 - - + -
373B THR* 4.3 3.6 - - + -
374B SER 5.2 0.2 - - - +
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Residues in contact with GLN 329 (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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99A ASP* 5.6 0.2 + - - -
129A GLN* 4.8 12.5 - - - +
295B GLY 4.9 0.9 - - - +
298B PRO* 3.7 13.0 - - + +
299B ASP* 3.9 16.0 + - - +
302B ARG* 3.3 38.2 + - - +
326B HIS* 2.8 42.7 + - - +
328B PRO* 1.3 77.8 - - - +
330B LEU* 1.3 58.2 + - - +
332B ILE* 3.3 11.3 + - + -
333B SER* 3.0 30.5 + - - -
348B ILE* 3.7 33.8 - - + +
351B ASP* 5.1 2.4 + - + -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 4.2 8.5 - - + +
292B LEU* 3.9 30.3 - - + -
298B PRO* 4.3 19.1 - - + +
301B LEU* 4.0 29.2 - - + +
302B ARG* 3.6 33.9 - - + +
307B PHE* 4.5 10.5 - - + +
308B VAL* 4.6 6.7 - - + +
311B THR* 3.6 20.5 - - - +
327B GLY 3.1 9.7 + - - +
329B GLN* 1.3 77.3 - - - +
331B LEU* 1.3 57.7 + - - +
333B SER* 3.5 3.5 + - - -
334B ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 331 (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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292B LEU* 4.3 7.4 - - + -
311B THR* 3.8 13.9 - - + -
315B VAL* 3.7 30.1 - - + -
321B VAL* 4.3 12.3 - - + -
323B ALA* 4.0 17.3 - - + -
328B PRO* 2.9 21.4 + - + +
330B LEU* 1.3 76.4 - - - +
332B ILE* 1.3 64.7 + - - +
334B ALA* 3.3 1.8 + - - +
335B ASP 3.0 15.8 + - - -
336B VAL* 3.5 14.4 + - + +
337B ILE* 3.7 18.8 - - + +
342B LEU* 4.5 4.3 - - + -
371B LEU* 3.5 35.4 - - + -
373B THR* 4.6 0.9 - - + -
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Residues in contact with ILE 332 (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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150A ILE* 4.0 9.1 - - + +
151A ASP* 3.4 21.3 - - - +
154A ASN* 4.0 17.6 - - - +
302B ARG* 3.8 5.6 - - - +
328B PRO 2.9 18.5 + - - +
329B GLN* 3.3 19.7 + - + +
331B LEU* 1.3 76.7 - - - +
333B SER* 1.3 58.1 + - - +
335B ASP* 2.8 23.9 + - - +
337B ILE* 3.9 22.9 - - + -
348B ILE* 4.9 2.2 - - + +
351B ASP* 3.8 35.7 - - + +
352B VAL* 3.8 13.7 - - + -
355B ALA* 4.0 9.0 - - + +
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Residues in contact with SER 333 (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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147A PRO 4.4 0.3 + - - -
150A ILE* 3.7 20.9 - - - +
302B ARG* 2.8 44.5 + - - +
308B VAL* 3.5 33.1 - - - +
312B ARG* 4.7 2.6 + - - -
329B GLN 3.0 8.9 + - - -
330B LEU 3.7 4.7 - - - -
331B LEU 3.3 0.2 - - - -
332B ILE* 1.3 77.9 - - - +
334B ALA* 1.3 60.2 + - - +
335B ASP* 3.2 4.5 + - - +
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Residues in contact with ALA 334 (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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308B VAL* 3.8 12.5 - - - +
311B THR* 3.9 7.9 - - + -
312B ARG* 3.5 51.8 + - + +
330B LEU 2.9 18.5 + - - +
331B LEU 3.7 5.8 - - - +
332B ILE 3.2 0.2 - - - -
333B SER* 1.3 73.6 - - - +
335B ASP* 1.3 71.7 + - - +
336B VAL* 3.4 13.9 - - + +
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Residues in contact with ASP 335 (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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150A ILE* 5.1 12.8 - - + +
154A ASN* 5.2 8.1 + - - +
331B LEU 3.0 1.8 + - - -
332B ILE* 2.8 19.5 + - - +
333B SER 4.1 4.0 - - - +
334B ALA* 1.3 82.7 - - - +
336B VAL* 1.3 61.6 + - - +
337B ILE* 3.7 3.7 + - - +
338B ARG* 5.0 12.9 + - - +
355B ALA* 4.5 14.0 - - - +
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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