Contacts of the helix formed by residues 333 - 347 (chain X) in PDB entry 3OEF
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 LEU 333 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ILE* 4.6 10.8 - - + -
332X LEU* 1.3 79.3 - - - +
334X ILE* 1.3 67.2 + - - +
335X ASP* 4.2 7.6 - - + +
336X GLU* 3.0 19.1 + - + +
337X TRP* 3.1 12.9 + - - -
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Residues in contact with ILE 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 3.8 30.1 - - + +
60X GLN 4.1 4.0 - - - +
61X SER* 3.4 30.5 - - - +
62X ILE* 3.3 30.7 - - + +
65X ALA* 4.4 9.1 - - + +
333X LEU* 1.3 74.5 - - - +
335X ASP* 1.3 69.6 + - - +
336X GLU 3.1 0.2 + - - -
337X TRP* 3.2 3.8 + - - +
338X LYS* 2.8 30.0 + - + +
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Residues in contact with ASP 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X LEU* 5.8 0.2 - - - +
333X LEU* 3.2 6.2 - - + +
334X ILE* 1.3 90.2 - - - +
336X GLU* 1.3 56.6 + - - +
338X LYS* 3.7 15.6 + - - +
339X SER* 3.0 28.4 + - - -
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Residues in contact with GLU 336 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332X LEU* 4.0 38.6 - - + +
333X LEU* 3.0 16.0 + - + +
335X ASP* 1.3 75.5 - - - +
337X TRP* 1.3 67.0 + - - +
338X LYS 3.1 1.1 - - - -
339X SER* 3.2 6.2 + - - +
340X LEU* 2.9 36.0 + - + +
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Residues in contact with TRP 337 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 5.0 0.9 - - - -
62X ILE* 3.9 23.7 - - + +
65X ALA* 3.6 23.8 - - + +
66X LYS* 3.5 38.2 - - + +
69X TYR* 3.6 38.6 - + + -
327X PHE* 3.5 33.4 - + + -
330X ARG* 3.6 14.8 + - + -
332X LEU* 3.5 45.0 + - + +
333X LEU 3.1 23.0 + - - -
334X ILE* 3.7 1.8 - - - +
336X GLU* 1.3 76.8 - - - +
338X LYS* 1.3 58.1 + - - +
340X LEU* 3.4 12.2 + - + +
341X THR* 2.9 34.0 + - - -
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Residues in contact with LYS 338 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 3.9 39.5 - - + +
96X LEU* 4.1 18.6 + - + -
97X GLU 5.1 4.0 + - - -
99X PHE* 2.8 47.0 + - + +
100X ASN* 4.6 10.1 + - - +
334X ILE* 2.8 19.0 + - + +
335X ASP* 3.7 17.9 + - - +
337X TRP* 1.3 74.3 - - - +
339X SER* 1.3 59.0 + - - +
341X THR* 3.4 2.4 + - - -
342X TYR* 2.9 28.6 + - - +
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Residues in contact with SER 339 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96X LEU* 4.0 29.9 - - - +
335X ASP 3.0 18.8 + - - -
336X GLU* 3.2 6.9 + - - -
338X LYS* 1.3 74.9 - - - +
340X LEU* 1.3 66.1 + - - +
342X TYR* 3.3 3.0 + - - +
343X ASP* 3.0 36.0 + - - +
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Residues in contact with LEU 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X TYR* 3.5 26.2 - - + +
327X PHE* 6.1 0.7 - - + -
332X LEU* 4.0 26.0 - - + -
336X GLU* 2.9 31.3 + - + +
337X TRP* 3.7 18.2 - - + +
339X SER* 1.3 75.6 - - - +
341X THR* 1.3 63.5 + - - +
343X ASP* 3.3 18.5 - - + +
344X GLU* 3.2 24.3 + - - +
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Residues in contact with THR 341 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X PHE* 3.9 27.1 - - + -
65X ALA 4.3 0.3 + - - -
68X THR* 4.0 13.7 - - + -
69X TYR* 3.4 30.7 + - - +
72X LEU* 4.0 16.4 - - + -
99X PHE* 4.0 8.1 - - + -
102X VAL* 4.4 4.7 - - + -
337X TRP 2.9 21.1 + - - -
338X LYS 3.6 4.9 - - - -
340X LEU* 1.3 76.3 - - - +
342X TYR* 1.3 63.4 + - - +
344X GLU* 3.0 6.9 + - - +
345X VAL* 2.9 21.6 + - + +
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Residues in contact with TYR 342 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X THR* 4.5 10.8 - - + -
93X ALA 4.7 3.0 + - - -
94X ARG 3.8 5.0 + - - -
95X SER* 3.3 33.8 + - - -
96X LEU* 3.6 35.0 - - + -
99X PHE* 3.5 39.9 - + + -
338X LYS 2.9 20.5 + - - +
339X SER* 3.6 5.2 - - - +
341X THR* 1.3 72.5 - - - +
343X ASP* 1.3 67.5 + - - +
345X VAL* 3.1 4.8 + - + +
346X ILE* 3.0 58.8 + - + +
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Residues in contact with ASP 343 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339X SER* 3.0 26.6 + - - +
340X LEU* 3.3 24.1 - - - +
342X TYR* 1.3 81.4 - - - +
344X GLU* 1.3 62.3 + - + +
346X ILE* 3.4 5.8 + - - +
347X SER* 3.0 31.1 + - - -
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Residues in contact with GLU 344 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X TYR* 3.9 12.6 + - + -
72X LEU* 3.6 18.8 - - + +
73X ARG* 3.6 34.2 + - + -
76X LYS* 2.8 59.0 + - + +
89X VAL* 4.8 0.2 - - - +
340X LEU 3.5 12.1 - - - +
341X THR 3.0 8.5 + - - +
343X ASP* 1.3 79.6 - - + +
345X VAL* 1.3 67.6 + - - +
347X SER* 3.7 4.9 - - - -
348X PHE* 3.4 6.6 + - - +
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Residues in contact with VAL 345 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72X LEU* 3.8 14.6 - - + -
89X VAL* 4.1 33.8 - - + +
90X PHE* 4.4 7.6 - - - -
91X THR* 4.1 24.0 - - + +
99X PHE* 4.2 20.9 - - + -
102X VAL* 4.9 4.3 - - + -
341X THR* 2.9 19.7 + - + +
342X TYR* 3.5 8.7 - - + +
344X GLU* 1.3 77.8 - - - +
346X ILE* 1.3 68.7 + - + +
348X PHE* 3.4 18.4 + - - +
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Residues in contact with ILE 346 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X THR* 5.7 2.5 - - + -
342X TYR* 3.0 59.0 + - + +
343X ASP* 3.8 6.1 - - - +
345X VAL* 1.3 82.8 - - + +
347X SER* 1.3 61.1 + - - +
348X PHE 3.5 3.3 + - - +
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Residues in contact with SER 347 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X LYS* 2.9 27.1 + - - -
343X ASP 3.0 17.2 + - - -
344X GLU* 3.7 4.7 + - - -
345X VAL 3.3 0.2 - - - -
346X ILE* 1.3 77.3 - - - +
348X PHE* 1.3 66.7 + - - +
349X VAL* 3.3 11.8 + - - +
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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