Contacts of the strand formed by residues 236 - 244 (chain C) in PDB entry 4K81
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 GLU 236 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C MET 3.3 4.7 - - - +
209C VAL* 3.6 2.1 - - - -
210C SER* 3.0 47.4 + - - -
234C TYR 3.7 0.2 + - - -
235C PRO* 1.3 73.9 - - - +
237C ILE* 1.3 66.8 + - - +
238C HIS* 3.7 20.7 - - + -
257C PHE* 3.7 23.2 - - + -
258C LEU 3.6 8.1 - - - +
259C ARG* 2.8 39.1 + - + +
272C ALA* 5.4 1.6 - - - +
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Residues in contact with ILE 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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204C PHE* 3.9 23.3 - - + -
208C MET* 3.3 27.1 - - + +
209C VAL* 3.9 21.1 - - + -
228C PHE* 4.3 15.3 - - + -
234C TYR* 4.8 4.0 - - + -
235C PRO 3.8 1.1 + - - +
236C GLU* 1.3 76.3 - - - +
238C HIS* 1.3 62.4 + - - +
256C PHE 3.7 0.3 - - - +
257C PHE* 3.4 3.5 - - - -
258C LEU* 2.7 51.0 + - + +
333C TRP* 3.7 30.8 - - + -
336C ALA* 4.0 18.8 - - + -
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Residues in contact with HIS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLU 5.0 0.7 - - - -
207C HIS* 3.2 39.2 + - - +
208C MET* 3.2 23.0 + - - +
209C VAL 4.0 2.8 - - - -
210C SER* 3.3 21.0 + - - -
236C GLU* 3.7 33.4 - - + -
237C ILE* 1.3 74.4 - - - +
239C GLY* 1.3 57.2 + - - +
255C TYR* 2.8 30.1 + + + +
256C PHE 3.1 12.1 - - - +
257C PHE* 4.2 11.2 - + + -
333C TRP* 3.9 5.6 - - - -
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Residues in contact with GLY 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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207C HIS* 5.3 5.6 - - - -
208C MET* 5.4 5.2 - - - -
238C HIS* 1.3 75.7 - - - +
240C PHE* 1.3 65.7 + - - -
255C TYR* 3.3 18.8 - - - -
256C PHE* 2.9 31.5 + - - +
333C TRP* 3.6 12.3 - - - -
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Residues in contact with PHE 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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239C GLY* 1.3 75.9 - - - -
241C LEU* 1.3 71.8 + - - +
253C LYS* 3.8 37.2 - - + -
254C ILE* 3.3 19.3 - - - -
255C TYR* 3.5 33.1 - + + -
269C GLY* 5.5 10.1 - - - -
270C THR* 5.8 2.9 - - - -
325C GLU* 5.2 14.6 + - + +
329C SER* 4.8 4.2 + - - -
333C TRP* 4.3 2.8 + - - -
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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
----------------------------------------------------------
240C PHE* 1.3 84.3 - - - +
242C HIS* 1.3 66.4 + - - +
253C LYS* 3.5 2.8 - - - -
254C ILE* 2.8 34.9 + - - +
256C PHE* 3.5 33.3 - - + -
263C LEU* 5.3 1.1 - - + -
306C PHE* 4.0 26.9 - - + -
322C LEU* 4.0 14.4 - - + -
323C CYS 3.7 12.8 - - - +
324C ALA* 4.2 11.4 - - + +
325C GLU* 5.8 2.0 - - - +
329C SER* 4.7 1.1 - - - +
333C TRP* 3.5 46.0 - - + +
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Residues in contact with HIS 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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241C LEU* 1.3 78.4 - - - +
243C ALA* 1.3 61.4 + - - +
251C TRP* 3.9 12.5 - - + +
252C LYS* 3.2 8.4 + - - +
253C LYS* 4.0 37.4 + - + +
301C PRO* 3.5 30.1 - - + +
302C THR* 5.2 4.4 - - + +
322C LEU* 3.4 7.3 - - - +
323C CYS* 2.9 52.6 + - + -
324C ALA 4.9 6.3 - - - -
325C GLU* 3.8 24.4 + - + -
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Residues in contact with ALA 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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242C HIS* 1.3 78.6 - - - +
244C LYS* 1.3 62.5 - - - +
245C GLU 4.1 0.5 + - - -
250C SER 3.8 1.4 - - - +
251C TRP* 3.6 9.2 - - - -
252C LYS* 2.9 36.5 + - - +
254C ILE* 4.4 11.6 - - + +
256C PHE* 4.1 15.9 - - + -
280C PHE* 4.4 9.4 - - + -
321C MET 3.8 5.4 - - - +
322C LEU* 3.8 17.3 - - + -
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Residues in contact with LYS 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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243C ALA* 1.3 75.2 - - - +
245C GLU* 1.3 69.0 + - - +
246C GLN 4.0 0.2 + - - -
247C GLY* 4.0 11.5 - - - +
248C LYS 3.2 31.3 + - - +
249C LYS* 3.5 27.6 - - + +
250C SER 3.8 5.4 - - - +
251C TRP* 3.7 41.0 - - + +
280C PHE* 5.3 7.0 - - - -
298C HIS 5.7 0.7 - - - +
319C LEU 5.7 0.7 - - - +
320C LYS* 5.7 1.0 - - - -
321C MET* 3.5 42.7 + - + +
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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