Contacts of the helix formed by residues 337 - 349 (chain W) in PDB entry 1O1F
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 TYR 337 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W LYS* 3.8 20.2 - - + -
26W ALA* 4.5 11.7 - - + -
27W PRO* 3.6 42.4 - - + -
30W VAL* 4.1 18.7 - - + +
334W GLU* 2.8 16.1 + - + +
336W LYS* 1.3 123.2 + - + +
338W SER* 1.4 62.5 + - - -
339W VAL* 3.3 4.0 - - - -
340W TRP* 3.0 8.5 + - + +
341W ILE* 2.9 38.7 + - + +
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Residues in contact with SER 338 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140W LEU 3.8 0.2 - - - +
141W SER* 3.2 27.9 + - - -
144W ALA* 3.5 11.3 - - - +
298W VAL* 5.9 1.1 - - - +
299W MET 4.4 2.4 + - - -
300W SER* 3.7 15.5 - - - -
332W PRO* 5.2 5.9 - - - +
334W GLU* 3.8 7.9 + - - -
335W ARG* 3.3 25.0 + - - +
336W LYS 3.8 0.2 - - - -
337W TYR* 1.4 72.8 - - - +
339W VAL* 1.3 55.3 - - - +
341W ILE* 3.1 7.7 + - - +
342W GLY* 2.8 32.6 + - - -
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Residues in contact with VAL 339 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP* 3.4 34.1 - - - +
106W THR* 4.2 2.7 - - + -
137W GLN* 4.0 25.6 - - + +
140W LEU* 3.3 26.0 - - + +
141W SER* 3.1 24.5 - - - +
154W ASP* 4.2 17.3 - - - +
300W SER* 4.5 4.3 - - - +
335W ARG 6.1 0.2 - - - +
337W TYR* 5.0 1.1 - - - -
338W SER* 1.3 82.2 - - - +
340W TRP* 1.3 61.1 + - - +
343W GLY 3.2 14.4 + - - -
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Residues in contact with TRP 340 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 2.8 44.9 + - + +
11W ASP* 4.0 10.5 - - + +
18W LYS* 3.4 37.7 + - + -
19W ALA* 3.6 5.7 - - - +
20W GLY* 3.6 27.4 - - - -
21W PHE 3.5 23.6 - - - -
24W ASP* 3.8 17.0 - - + -
25W ASP 4.3 0.4 - - - -
26W ALA* 3.5 28.3 - - - -
27W PRO* 3.7 16.6 - - + -
140W LEU* 5.7 0.2 - - - -
337W TYR* 3.0 17.9 + - + +
339W VAL* 1.3 78.8 - - - +
341W ILE* 1.3 67.6 + - + +
343W GLY* 3.0 4.3 + - - -
344W SER* 2.9 33.3 + - - -
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Residues in contact with ILE 341 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W ASP* 3.5 27.8 - - - +
26W ALA* 4.9 0.4 - - + -
144W ALA* 4.5 6.7 - - + +
334W GLU* 3.7 41.5 - - + +
337W TYR* 2.9 35.4 + - + +
338W SER* 3.6 5.6 - - - +
340W TRP* 1.3 84.2 - - + +
342W GLY* 1.3 57.2 - - - +
344W SER* 3.0 6.7 + - - -
345W ILE* 3.0 46.8 + - + +
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Residues in contact with GLY 342 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140W LEU* 3.4 30.7 - - - +
143W TYR* 3.7 7.9 - - - -
144W ALA* 3.5 14.7 - - - +
338W SER 2.8 10.7 + - - -
339W VAL 3.8 0.9 - - - -
340W TRP 3.2 0.2 - - - -
341W ILE* 1.3 75.9 - - - +
343W GLY* 1.3 55.4 + - - +
345W ILE* 3.7 2.8 + - - +
346W LEU* 3.1 29.6 + - - +
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Residues in contact with GLY 343 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W VAL* 3.9 15.9 - - - -
104W LEU* 4.3 6.9 - - - +
140W LEU* 3.8 19.0 - - - +
339W VAL 3.2 8.4 + - - -
340W TRP 3.0 8.2 + - - -
342W GLY* 1.3 75.6 - - - +
344W SER* 1.3 53.8 + - - +
346W LEU* 3.8 1.5 - - - +
347W ALA* 2.8 38.3 + - - +
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Residues in contact with SER 344 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W VAL* 3.9 10.0 - - - +
21W PHE 3.7 1.9 + - - -
22W ALA* 3.4 5.0 - - - +
23W GLY* 2.8 28.5 + - - -
24W ASP 3.0 16.0 + - - -
340W TRP* 2.9 30.0 + - - -
341W ILE* 3.3 10.8 - - - -
343W GLY* 1.3 72.3 - - - +
345W ILE* 1.3 57.8 + - - +
348W SER* 2.7 35.9 + - - -
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Residues in contact with ILE 345 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W TYR* 3.5 29.2 - - + +
144W ALA* 4.4 18.8 - - - +
341W ILE* 3.0 39.4 + - + +
342W GLY* 3.8 3.1 - - - +
344W SER* 1.3 75.4 - - - +
346W LEU* 1.3 66.5 + - - +
348W SER* 2.7 20.6 + - - -
349W LEU* 2.9 21.6 + - + +
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Residues in contact with LEU 346 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W LEU* 4.2 12.1 - - + -
133W TYR* 4.5 8.1 - - + +
135W ALA* 4.7 0.9 - - + -
140W LEU* 3.7 25.1 - - + -
143W TYR* 3.8 23.8 - - + +
342W GLY 3.1 14.3 + - - +
343W GLY 3.8 1.3 - - - +
345W ILE* 1.3 80.8 - - - +
347W ALA* 1.3 61.5 + - - +
349W LEU* 3.1 23.9 - - + +
352W PHE* 3.2 49.4 - - + +
355W MET* 5.5 3.6 - - + -
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Residues in contact with ALA 347 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3W ASP 5.7 0.2 - - - +
7W ALA* 4.3 7.4 - - + +
9W VAL* 4.5 2.0 - - + -
22W ALA* 3.9 15.9 - - + -
104W LEU* 4.2 17.5 - - + -
343W GLY 2.8 22.5 + - - +
346W LEU* 1.3 74.8 - - - +
348W SER* 1.3 61.2 + - - +
349W LEU 3.3 4.2 + - - +
352W PHE* 3.9 12.6 - - - -
356W TRP* 4.1 29.9 + - + -
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Residues in contact with SER 348 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W GLU* 5.0 19.4 - - - +
7W ALA* 5.7 0.2 - - - -
22W ALA* 3.9 6.7 - - - +
23W GLY* 4.0 20.1 + - - -
344W SER 2.7 23.7 + - - -
345W ILE* 2.7 14.6 + - - -
347W ALA* 1.3 75.9 - - - +
349W LEU* 1.3 65.9 + - - +
350W SER* 3.6 1.4 + - - -
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Residues in contact with LEU 349 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143W TYR* 4.2 20.4 - - - +
345W ILE* 2.9 23.8 + - + +
346W LEU* 3.1 20.3 + - + +
347W ALA 4.3 2.3 - - - +
348W SER* 1.3 81.8 - - - +
350W SER* 1.3 80.7 - - - +
351W THR* 3.2 28.9 - - - +
352W PHE* 3.3 18.8 + - + +
353W GLN* 4.2 3.8 + - - +
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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