Contacts of the strand formed by residues 235 - 242 (chain C) in PDB entry 4KYI
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 ASN 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR 2.8 18.3 + - - +
68C HIS* 3.4 35.9 + - + +
69C VAL 2.8 27.5 + - - +
222C ARG* 4.3 5.7 + - - +
233C ILE 4.3 0.4 + - - -
234C LYS* 1.3 67.8 - - - +
236C LEU* 1.3 69.3 + - - +
237C SER* 3.9 7.8 + - - -
252C SER* 4.9 0.4 - - - -
253C GLU* 3.0 31.8 + - - +
254C ASP* 3.0 30.4 + - - +
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Residues in contact with LEU 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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69C VAL 3.3 10.8 - - - +
79C ALA* 3.8 33.7 - - + +
80C SER* 3.7 26.7 - - - +
83C ALA* 3.7 13.7 - - + -
215C LEU* 3.7 29.2 - - + +
218C LEU* 4.4 8.0 - - + +
234C LYS 3.1 3.8 + - - +
235C ASN* 1.3 72.4 + - - +
237C SER* 1.3 81.9 + - - +
238C VAL* 4.6 13.0 - - + -
252C SER* 3.5 3.5 - - - -
253C GLU* 3.4 28.0 + - - +
261C ILE* 4.0 11.9 - - + -
265C VAL* 5.2 0.9 - - + -
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C HIS* 5.3 0.2 - - - -
69C VAL 2.9 8.4 + - - +
70C SER* 3.2 22.7 - - - -
71C GLY 3.0 26.3 + - - +
235C ASN* 3.9 11.6 + - - -
236C LEU* 1.3 80.3 + - - +
238C VAL* 1.3 63.7 + - - +
239C VAL* 6.1 0.2 - - - -
250C ARG* 4.9 10.0 + - - -
251C TYR 3.4 6.3 - - - -
252C SER* 3.4 14.3 + - - -
297C GLU 5.8 2.5 - - - -
298C ILE* 5.2 9.5 - - - +
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Residues in contact with VAL 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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71C GLY* 3.4 10.1 - - - +
76C ALA* 4.1 23.3 - - + +
215C LEU* 5.1 9.2 - - + -
236C LEU* 4.6 15.3 - - + -
237C SER* 1.3 78.8 - - - +
239C VAL* 1.3 65.1 + - - +
249C GLU 4.0 0.2 - - - +
250C ARG* 3.5 4.3 - - - +
251C TYR* 2.9 45.9 + - + +
264C VAL* 3.6 36.3 - - + +
265C VAL* 4.5 15.5 - - + -
268C SER* 5.1 0.9 - - - -
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Residues in contact with VAL 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 SER* 4.5 4.9 - - - +
71C GLY 3.4 9.0 + - - +
72C ALA* 3.7 10.5 - - + +
238C VAL* 1.3 78.1 - - - +
240C VAL* 1.3 66.9 + - - +
248C LEU* 3.8 34.5 - - + -
249C GLU 3.5 11.0 - - - +
250C ARG* 4.6 13.5 - - + -
268C SER* 2.8 26.5 + - - -
289C GLY* 3.6 9.1 - - - +
294C ASN* 4.6 4.3 - - - +
296C PRO* 3.8 32.1 - - + -
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Residues in contact with VAL 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 VAL* 1.3 80.0 - - - +
241C THR* 1.3 67.1 + - - +
242C ASN* 5.4 0.2 - - - -
248C LEU* 3.5 13.0 - - - +
249C GLU* 2.9 49.9 + - + +
251C TYR* 3.9 13.9 - - + -
264C VAL* 3.9 25.1 - - + -
267C TRP* 4.0 7.0 - - + -
268C SER* 3.7 23.8 - - - +
286C ILE* 3.9 21.5 - - + -
287C ALA 3.9 2.0 - - - +
289C GLY* 3.6 9.2 - - - +
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Residues in contact with THR 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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291A ILE* 4.2 19.3 - - + +
292A LEU* 3.7 27.1 - - + +
240C VAL* 1.3 77.3 - - - +
242C ASN* 1.3 66.6 + - - +
243C GLN* 3.3 11.5 + - + +
247C GLU 4.3 2.0 - - - -
248C LEU* 4.2 8.1 - - - +
286C ILE* 3.6 2.8 - - - -
287C ALA 3.1 29.9 + - - -
288C ASP 2.5 26.6 + - - -
289C GLY* 3.4 9.4 - - - -
291C ILE* 4.6 10.4 + - + +
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Residues in contact with ASN 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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240C VAL* 4.1 2.4 - - - +
241C THR* 1.3 70.9 - - - +
243C GLN* 1.3 52.9 + - - +
244C THR* 3.0 9.7 + - - -
245C LYS* 2.8 43.7 + - + +
246C HIS* 2.6 37.2 + - - -
247C GLU* 3.2 19.9 + - + +
249C GLU* 4.0 25.0 + - + +
280C ASN* 4.6 0.2 - - - +
284C GLU* 3.6 22.4 + - - +
285C TYR 3.6 5.5 + - - -
286C ILE* 3.6 26.4 - - + +
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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