Contacts of the helix formed by residues 235 - 244 (chain C) in PDB entry 4L28
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 THR 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C THR* 4.6 10.3 - - - +
69C ALA 5.5 0.2 - - - -
70C PRO* 4.2 22.9 - - + -
121C ARG* 2.9 23.0 + - - +
125C ARG* 5.3 2.2 - - - +
231C ALA* 2.7 26.0 + - + +
234C ASP* 1.3 88.3 - - + +
236C THR* 1.3 70.2 + - - +
237C ALA 3.3 1.8 - - - -
238C ASP* 3.2 3.5 + - - +
239C GLU* 3.0 30.6 + - - +
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Residues in contact with THR 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LYS* 4.5 8.7 - - + -
110C GLU* 4.6 7.4 - - - +
118C VAL* 6.1 0.2 - - + -
121C ARG* 3.1 36.2 + - - +
231C ALA 3.7 0.2 + - - -
232C HIS* 2.8 39.7 + - + +
235C THR* 1.3 76.5 + - - +
237C ALA* 1.3 58.5 + - - +
239C GLU* 3.2 4.2 + - - +
240C ILE* 3.0 38.0 + - + +
260C THR* 5.4 1.1 - - + -
264C ILE* 4.0 20.2 - - + -
373C ILE* 5.7 2.2 - - + -
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Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C HIS 2.9 17.7 + - - +
233C TYR 4.0 2.0 - - - +
236C THR* 1.3 74.6 - - - +
238C ASP* 1.3 62.2 + - - +
240C ILE* 3.3 10.8 + - - +
241C LEU* 2.9 34.0 + - - +
264C ILE* 4.0 20.4 - - + +
267C LYS* 3.8 31.0 - - + -
268C LEU* 4.6 4.2 - - + +
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Residues in contact with ASP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PRO* 4.2 17.4 - - + +
234C ASP 3.0 26.8 + - - +
235C THR* 3.2 5.0 + - - +
237C ALA* 1.3 74.3 - - - +
239C GLU* 1.3 60.7 + - + +
241C LEU* 3.4 8.2 + - - +
242C GLN* 2.9 33.2 + - - +
267C LYS* 3.1 32.9 + - - +
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PRO* 5.8 6.4 - - + +
85C GLY* 3.8 1.6 - - - -
86C ASP* 3.0 41.3 + - - +
87C THR 3.4 1.4 + - - +
108C LYS* 2.8 27.3 + - - +
121C ARG* 2.9 30.5 + - - -
235C THR* 3.0 20.4 + - - +
236C THR 3.5 6.5 - - - +
238C ASP* 1.3 75.2 - - + +
240C ILE* 1.3 60.3 + - - +
242C GLN* 3.8 7.1 - - - +
243C GLN* 2.9 40.2 + - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C MET* 4.1 22.2 - - + -
108C LYS* 4.1 16.2 - - + -
236C THR* 3.0 24.3 + - + +
237C ALA* 3.7 5.6 - - - +
239C GLU* 1.3 77.8 - - - +
241C LEU* 1.3 61.3 + - - +
243C GLN 4.0 0.3 - - - -
244C CYS* 3.1 27.0 + - - +
248C LEU* 3.9 26.5 - - + -
251C LEU* 4.1 14.8 - - + -
264C ILE* 3.8 32.5 - - + -
268C LEU* 5.2 3.8 - - + -
371C VAL* 4.5 7.6 - - + -
373C ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C ALA 2.9 21.2 + - - +
238C ASP* 3.8 7.4 - - - +
240C ILE* 1.3 76.5 - - - +
242C GLN* 1.3 62.2 + - - +
244C CYS* 3.5 1.3 + - - -
245C ASP* 3.2 2.8 + - - -
246C GLY* 2.9 46.3 + - - +
248C LEU* 5.1 6.3 - - + -
267C LYS* 4.2 17.9 - - + -
268C LEU* 3.9 21.5 - - + -
271C LYS* 3.8 30.5 - - + +
272C CYS* 4.2 20.4 - - + -
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.4 26.8 - - + +
238C ASP* 2.9 19.7 + - - +
239C GLU* 3.8 6.9 - - - +
241C LEU* 1.3 76.3 - - - +
243C GLN* 1.3 67.4 + - + +
245C ASP* 3.4 10.1 + - - +
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Residues in contact with GLN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.6 36.5 + - + +
76A ILE* 3.5 19.3 - - - +
77A LEU* 6.4 0.2 - - - +
86C ASP 5.6 1.0 - - - -
87C THR 3.2 21.1 + - - -
88C PRO* 4.0 2.2 - - - +
89C MET* 3.5 44.2 - - + +
108C LYS* 3.3 20.2 + - - -
239C GLU* 2.9 22.5 + - + +
240C ILE 4.0 2.7 - - - +
242C GLN* 1.3 79.8 - - + +
244C CYS* 1.3 59.1 + - - +
245C ASP* 3.3 2.9 + - - +
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Residues in contact with CYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 4.8 1.6 - - - -
89C MET* 4.0 21.3 - - - -
106C LEU* 4.3 6.3 - - - -
240C ILE* 3.1 23.3 + - - +
241C LEU* 4.3 3.4 - - - +
243C GLN* 1.3 77.3 - - - +
245C ASP* 1.3 70.6 + - - +
246C GLY 3.1 1.6 - - - +
247C LYS* 3.1 24.5 + - - +
248C LEU* 4.5 6.3 - - + -
369C ARG* 3.0 35.1 + - - +
371C VAL* 4.0 18.6 - - - -
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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