Contacts of the strand formed by residues 242 - 250 (chain C) in PDB entry 3H90
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 242 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C GLY* 5.3 3.5 - - - -
76C GLY* 5.9 0.2 - - - -
238C GLN* 3.4 1.3 - - - +
239C SER* 3.1 33.5 + - - -
241C PRO* 1.3 83.3 - - + +
243C ARG* 1.3 62.2 + - - +
244C PHE* 3.8 19.7 - - - -
277C GLY* 3.3 32.1 - - - +
278C SER* 5.0 0.4 - - - -
279C ASP* 5.7 1.8 - - - -
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Residues in contact with ARG 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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210C LEU* 4.2 16.6 - - + -
214C GLU* 2.9 39.7 + - - -
237C ARG 3.4 9.4 - - - +
238C GLN* 3.4 31.3 + - + +
241C PRO 3.8 9.3 + - - +
242C THR* 1.3 76.3 - - - +
244C PHE* 1.3 63.2 + - - +
245C ILE* 4.0 2.0 + - + -
275C PHE* 3.7 25.6 - - - +
276C PRO* 4.8 10.5 + - - +
278C SER* 3.1 23.1 + - - +
279C ASP* 2.9 27.2 + - - +
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Residues in contact with PHE 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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73A PHE* 5.4 0.8 - - + -
235A ARG* 4.3 2.5 - - - -
73C PHE* 3.7 26.0 - + + -
74C GLY* 3.9 21.5 - - - -
235C ARG 3.6 0.7 - - - +
236C THR* 3.3 8.0 - - - -
237C ARG* 2.6 73.4 + - + +
239C SER* 3.7 28.3 - - - -
242C THR* 3.8 24.2 - - - -
243C ARG* 1.3 71.3 - - - +
245C ILE* 1.3 63.9 + - - +
246C GLN* 4.3 5.2 - - - +
279C ASP* 3.3 38.4 - - + -
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Residues in contact with ILE 245 (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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210C LEU* 4.5 9.2 - - + -
218C ILE* 3.8 30.3 - - + -
234C LEU* 4.1 20.0 - - + -
235C ARG 3.5 2.9 - - - -
236C THR* 4.2 5.4 - - + -
243C ARG* 4.8 0.2 - - + -
244C PHE* 1.3 79.6 - - - +
246C GLN* 1.3 68.6 + - - +
247C ILE* 5.3 4.9 - - + -
271C ILE* 3.6 30.1 - - + -
275C PHE* 4.5 5.6 - - + -
278C SER* 3.7 23.1 - - - +
279C ASP 3.0 6.9 + - - -
280C VAL* 3.1 21.2 - - + +
281C ILE* 2.9 26.6 + - - +
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Residues in contact with GLN 246 (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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73A PHE* 3.5 29.5 - - - -
237A ARG* 5.8 0.2 - - - +
246A GLN* 4.1 17.8 + - - +
279A ASP* 4.7 1.7 - - - +
281A ILE* 3.9 30.0 - - + +
233C ASP* 4.0 1.3 - - - -
234C LEU* 3.2 10.7 - - - +
235C ARG* 2.9 70.1 + - + +
237C ARG* 5.2 4.6 - - - +
244C PHE* 5.7 3.0 - - - +
245C ILE* 1.3 76.1 - - - +
247C ILE* 1.3 62.4 + - - +
281C ILE* 3.3 24.5 - - + +
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Residues in contact with ILE 247 (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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281A ILE* 4.6 0.7 - - - +
218C ILE* 4.9 2.9 - - + -
219C ILE* 5.9 3.8 - - + -
222C VAL* 4.1 22.2 - - + -
231C ALA* 3.8 22.4 - - + -
232C HIS 4.6 0.7 - - - +
233C ASP 2.8 17.3 - - - +
234C LEU* 3.9 26.0 - - + -
245C ILE* 5.3 4.9 - - + -
246C GLN* 1.3 76.9 - - - +
248C HIS* 1.3 84.1 + - - +
249C LEU* 3.9 10.1 - - + -
271C ILE* 5.6 1.8 - - + -
281C ILE 3.3 2.2 + - - +
282C ILE* 3.4 31.3 - - + -
283C HIS* 3.0 24.9 + - - +
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Residues in contact with HIS 248 (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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281A ILE* 4.3 13.8 - - + +
1C ZN 4.6 1.6 - - - -
3C ZN 2.1 33.7 - - - -
231C ALA* 3.1 8.3 - - - +
232C HIS* 2.9 48.6 + + + +
233C ASP* 3.1 35.2 + - + +
247C ILE* 1.3 81.0 - - - +
249C LEU* 1.3 61.4 + - - +
283C HIS* 3.1 33.5 - + + +
285C ASP* 3.1 4.1 + - - +
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Residues in contact with LEU 249 (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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222C VAL* 3.7 27.1 - - + -
228C VAL* 3.8 17.0 - - + -
230C GLY 3.8 1.6 - - - -
231C ALA* 4.2 1.8 - - + -
247C ILE* 3.9 23.1 - - + -
248C HIS* 1.3 76.2 - - - +
250C GLU* 1.3 60.8 + - - +
251C MET* 3.2 26.0 + - + +
264C ALA* 3.8 17.0 - - - -
267C VAL* 3.9 24.5 - - + -
282C ILE* 3.7 21.1 - - + +
283C HIS 2.8 8.4 + - - +
284C GLN* 3.5 1.7 - - - -
285C ASP* 2.8 27.7 + - - +
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Residues in contact with GLU 250 (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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228C VAL* 4.9 0.6 - - - +
229C SER* 3.0 33.8 + - - +
230C GLY* 2.7 37.6 + - - +
231C ALA* 3.6 10.3 + - - +
232C HIS* 3.1 40.7 + - + +
249C LEU* 1.3 72.4 - - - +
251C MET* 1.3 62.2 + - - +
285C ASP* 3.4 7.2 - - + -
286C PRO 3.9 11.4 - - - +
289C VAL* 3.9 23.1 - - + +
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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