Contacts of the helix formed by residues 327 - 340 (chain B) in PDB entry 1ITU
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 ALA 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B SER* 4.9 4.7 - - - -
15B PRO 3.3 17.9 - - - +
17B ILE* 3.4 23.7 - - + +
113B PHE* 4.0 13.5 - - + -
323B LYS 3.0 2.5 + - - +
324B GLY 4.0 0.9 - - - -
325B ALA 3.6 1.0 - - - -
326B LEU* 1.3 82.3 - - + +
328B ASP* 1.3 67.2 + - - +
329B ASN 3.4 2.5 - - - -
330B LEU* 3.3 8.9 + - - +
331B LEU* 3.0 30.5 + - + +
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Residues in contact with ASP 328 (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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14B SER* 4.3 8.5 + - - -
110B ARG* 5.4 2.4 + - - -
113B PHE* 6.0 0.2 - - - -
323B LYS* 3.0 36.6 + - - +
324B GLY* 3.7 7.9 - - - -
327B ALA* 1.3 81.3 - - - +
329B ASN* 1.3 59.6 + - - +
331B LEU* 3.9 17.6 - - - +
332B ARG* 3.0 28.6 + - - +
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Residues in contact with ASN 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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246B LEU* 3.7 15.3 - - + -
280B ALA 3.0 23.6 + - - -
281B ARG* 3.0 28.9 + - - +
283B VAL 3.0 19.2 + - - -
324B GLY* 2.9 35.7 + - - +
325B ALA 3.7 0.6 - - - +
328B ASP* 1.3 70.4 - - - +
330B LEU* 1.3 61.4 + - - +
332B ARG* 3.1 17.8 + - - +
333B VAL* 3.0 34.1 + - - +
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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
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17B ILE* 3.9 20.9 - - + +
64B PHE* 3.7 33.7 - - + -
109B ILE* 3.9 18.6 - - + -
193B LEU* 4.8 11.4 - - + -
216B ILE* 4.8 7.2 - - + -
246B LEU* 3.5 24.3 - - + +
248B MET* 3.9 27.1 - - + -
324B GLY 4.5 0.4 + - - -
327B ALA* 3.3 11.3 + - - +
329B ASN* 1.3 79.3 - - - +
331B LEU* 1.3 54.3 + - - +
333B VAL* 3.2 2.3 + - + -
334B PHE* 2.7 40.6 + - + +
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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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17B ILE* 4.2 5.6 - - + -
106B SER* 3.9 29.6 - - - +
109B ILE* 4.1 27.1 - - + -
110B ARG* 3.7 42.4 - - + +
113B PHE* 4.7 9.6 - - + -
327B ALA* 3.0 28.0 + - + +
328B ASP* 3.9 18.6 - - - +
329B ASN 3.3 0.2 - - - -
330B LEU* 1.3 74.8 - - - +
332B ARG* 1.3 59.4 + - - +
334B PHE* 3.7 4.3 - - - +
335B GLU* 2.8 37.3 + - - +
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Residues in contact with ARG 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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110B ARG* 5.3 0.6 - - - +
214B PRO* 6.1 0.8 - - - +
244B ASP* 3.2 44.5 + - - -
245B SER 3.8 2.6 + - - -
246B LEU* 5.0 0.2 - - - +
281B ARG* 2.9 56.4 + - - +
328B ASP 3.0 19.1 + - - +
329B ASN* 3.1 36.5 + - - +
330B LEU 3.3 0.2 - - - -
331B LEU* 1.3 77.0 - - - +
333B VAL* 1.3 75.3 + - - +
335B GLU* 3.4 10.4 + - - +
336B ALA* 3.0 23.9 + - + +
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Residues in contact with VAL 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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193B LEU* 3.8 18.6 - - + -
214B PRO* 3.9 24.0 - - + +
215B VAL 4.3 0.7 - - - +
216B ILE* 3.8 15.9 - - + -
244B ASP 3.8 11.7 - - - +
245B SER 4.4 0.7 - - - -
246B LEU* 3.9 17.7 - - + -
329B ASN 3.0 21.4 + - - +
330B LEU* 3.7 5.8 - - + +
332B ARG* 1.3 98.8 - - - +
334B PHE* 1.3 57.2 + - - +
336B ALA* 3.2 7.6 + - - +
337B VAL* 3.0 32.9 + - - +
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Residues in contact with PHE 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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64B PHE* 4.3 5.6 - + - -
104B THR 3.8 8.3 - - - -
105B SER* 3.6 25.1 - - - -
106B SER* 3.8 15.7 - - - -
109B ILE* 3.9 16.2 - - + -
121B LEU* 3.6 24.5 - - + -
146B ARG* 4.0 20.2 - - + -
191B GLY 4.5 12.3 - - - -
193B LEU* 4.0 26.9 - - + +
330B LEU* 2.7 26.9 + - + +
331B LEU* 3.7 6.1 - - - +
333B VAL* 1.3 72.3 - - - +
335B GLU* 1.3 62.4 + - - +
337B VAL* 3.3 3.4 + - + +
338B GLU* 3.1 36.2 + - + +
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Residues in contact with GLU 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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106B SER* 3.2 21.0 + - - +
110B ARG* 3.1 38.5 + - - -
331B LEU 2.8 18.7 + - - +
332B ARG* 3.8 10.2 - - - +
334B PHE* 1.3 76.7 - - - +
336B ALA* 1.3 56.7 + - - +
338B GLU* 3.2 10.5 + - - +
339B GLN* 2.8 45.9 + - + +
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Residues in contact with ALA 336 (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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213B ALA* 4.3 0.3 - - - +
214B PRO* 3.6 28.5 - - + -
332B ARG* 3.0 15.6 + - + +
333B VAL* 3.2 8.0 + - - +
335B GLU* 1.3 76.0 - - - +
337B VAL* 1.3 58.6 + - - +
339B GLN* 3.3 8.6 + - - +
340B ALA* 3.0 31.4 + - - +
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Residues in contact with VAL 337 (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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187B LEU 5.4 0.2 - - - +
188B ASN* 4.6 2.3 - - - +
191B GLY* 3.3 40.9 - - - +
192B VAL 3.7 13.5 - - - +
193B LEU* 3.5 26.5 - - + +
213B ALA* 4.1 14.5 - - + +
214B PRO* 3.6 21.1 - - + +
333B VAL 3.0 17.6 + - - +
334B PHE* 3.5 11.0 - - + +
336B ALA* 1.3 76.2 - - - +
338B GLU* 1.3 61.6 + - - +
340B ALA* 3.6 2.4 + - - +
341B SER 3.3 15.2 + - - -
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Residues in contact with GLU 338 (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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104B THR 4.7 0.3 - - - +
105B SER* 3.4 15.9 - - - -
106B SER* 2.7 48.6 + - - -
107B ALA 5.3 0.2 - - - -
191B GLY* 4.9 6.3 - - - +
334B PHE* 3.1 25.1 + - + +
335B GLU* 3.5 12.3 - - - +
336B ALA 3.2 0.2 - - - -
337B VAL* 1.3 76.7 - - + +
339B GLN* 1.3 66.3 + - + +
341B SER* 2.7 26.4 + - - +
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Residues in contact with GLN 339 (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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335B GLU* 2.8 38.6 + - + +
336B ALA* 3.3 8.5 + - - +
338B GLU* 1.3 80.9 + - - +
340B ALA* 1.3 59.9 + - - +
341B SER 3.2 6.8 + - - +
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Residues in contact with ALA 340 (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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188B ASN* 3.4 3.5 - - + +
212B ARG* 2.6 57.8 + - - +
213B ALA* 3.9 22.0 - - + -
336B ALA 3.0 17.1 + - - +
337B VAL 3.9 2.2 - - - +
338B GLU 3.3 0.4 - - - -
339B GLN* 1.3 73.3 - - - +
341B SER* 1.3 59.4 + - - +
342B ASN* 4.9 0.3 - - - +
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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