Contacts of the helix formed by residues 264 - 276 (chain C) in PDB entry 3KQ4
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 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261C LYS 5.1 0.8 + - - +
262C PHE 3.6 0.2 - - - -
263C HIS* 1.3 80.0 + - + +
265C PRO* 1.3 66.5 - - - +
266C MET* 2.9 22.2 + - - +
267C SER* 2.8 42.6 + - - +
268C ILE* 3.2 4.5 + - - +
366C TRP* 2.9 45.1 + - + +
401C ASP* 3.2 31.0 + - - +
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Residues in contact with PRO 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.8 2.5 - - + +
43C MET* 3.7 18.0 - - + +
46C SER* 3.7 34.8 - - - +
54C ASN* 6.2 0.4 - - - +
57C ILE* 4.0 9.2 - - + +
263C HIS 3.3 8.9 - - - +
264C ASN* 1.3 88.6 - - - +
266C MET* 1.3 61.1 + - - +
268C ILE* 3.4 15.8 + - + +
269C ALA* 3.0 21.3 + - - +
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASN* 3.5 29.6 - - - +
56C SER* 3.2 29.4 - - - +
57C ILE* 4.9 0.4 - - - +
133C TYR* 5.6 0.9 - - - +
264C ASN* 2.9 13.7 + - - +
265C PRO* 1.3 79.3 - - - +
267C SER* 1.3 59.4 + - - +
269C ALA* 3.0 20.8 + - - +
270C GLN* 3.0 45.7 + - + +
365C SER* 3.5 24.2 - - - +
366C TRP* 3.2 38.4 - - + +
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Residues in contact with SER 267 (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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224C TYR* 4.1 13.0 - - - -
261C LYS 4.4 1.9 + - - -
262C PHE* 3.2 32.8 - - - -
264C ASN* 2.8 20.0 + - - +
266C MET* 1.3 77.3 - - - +
268C ILE* 1.3 64.3 + - - +
270C GLN* 3.4 5.9 + - - +
271C ILE* 3.2 23.6 + - - +
366C TRP* 3.2 31.3 - - - -
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Residues in contact with ILE 268 (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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39C ILE* 3.5 53.2 - - + +
40C GLN 4.6 0.7 - - - +
42C LEU* 4.4 7.0 - - + -
43C MET* 3.9 18.4 - - + +
262C PHE* 3.4 31.9 - - + +
263C HIS 3.8 15.3 - - - +
264C ASN 3.6 6.5 - - - +
265C PRO* 3.5 15.5 - - + +
266C MET 3.1 0.4 - - - -
267C SER* 1.3 76.7 - - - +
269C ALA* 1.3 58.3 + - - +
271C ILE* 2.9 9.9 + - - +
272C LEU* 2.7 42.1 + - + +
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C MET* 3.7 18.8 - - - -
56C SER* 3.7 27.1 - - - +
57C ILE* 3.8 10.3 - - + -
60C ALA* 3.7 10.1 - - + +
265C PRO 3.0 13.9 + - - +
266C MET* 3.0 13.8 + - - +
268C ILE* 1.3 77.3 - - - +
270C GLN* 1.3 55.8 + - - +
272C LEU* 4.6 0.4 - - - -
273C PRO* 3.2 22.3 - - - +
280C TYR* 4.0 6.7 + - - -
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Residues in contact with GLN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER* 4.0 3.0 + - - -
133C TYR* 3.6 20.2 + - - -
171C ASP* 5.4 1.7 - - - +
175C MET* 4.5 2.4 - - - +
224C TYR 4.5 12.0 - - - +
227C GLY* 3.5 22.8 - - - +
228C LEU* 3.7 32.4 + - + +
231C GLN* 4.4 6.8 + - - +
266C MET* 3.0 43.9 + - + +
267C SER* 3.4 7.1 + - - +
268C ILE 3.0 0.8 + - - -
269C ALA* 1.3 79.8 - - - +
271C ILE* 1.3 58.3 - - - +
273C PRO* 4.1 4.1 - - - +
274C SER* 4.4 0.2 + - - -
280C TYR* 4.0 16.8 + - - +
366C TRP* 4.1 17.4 + - + -
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Residues in contact with ILE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ILE* 5.0 4.0 - - + -
227C GLY* 3.3 31.0 - - - +
230C MET* 4.8 6.7 - - - -
253C ILE* 4.3 25.8 - - + -
257C ILE* 4.7 3.1 - - + -
262C PHE* 3.5 48.7 - - + -
267C SER 3.2 13.8 + - - +
268C ILE* 3.5 5.6 - - + +
270C GLN* 1.3 73.2 - - - +
272C LEU* 1.3 71.4 + - - +
273C PRO* 3.1 3.8 - - - -
274C SER* 3.0 16.0 + - - +
275C LEU* 3.1 25.2 + - + +
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Residues in contact with LEU 272 (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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36C VAL* 4.8 7.6 - - + -
39C ILE* 5.3 4.7 - - + -
40C GLN* 3.3 38.4 - - + +
43C MET* 3.6 28.9 - - + -
60C ALA* 3.8 5.2 - - + +
64C ALA* 3.4 17.3 - - + -
268C ILE* 2.7 29.4 + - + +
269C ALA* 4.6 2.7 - - - +
271C ILE* 1.3 73.6 - - - +
273C PRO* 1.4 68.8 - - + +
275C LEU* 3.3 8.1 + - + +
276C LYS* 2.9 44.1 + - + +
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Residues in contact with PRO 273 (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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60C ALA* 4.6 11.2 - - + +
63C LEU* 3.9 27.1 - - + -
64C ALA* 5.8 0.4 - - + -
231C GLN* 3.8 18.6 - - - +
269C ALA 3.2 22.2 - - - +
270C GLN 4.1 2.0 - - - +
271C ILE* 3.3 6.1 - - - +
272C LEU* 1.4 90.5 - - + +
274C SER* 1.3 56.7 + - - +
276C LYS* 3.0 6.6 + - + -
277C GLY 2.9 5.9 + - - -
278C LYS* 2.7 43.4 + - + +
280C TYR* 4.3 9.6 - - + -
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLY* 3.2 24.6 + - - -
230C MET* 3.8 36.5 - - - +
231C GLN* 3.6 13.6 + - - +
271C ILE* 3.0 10.1 + - - -
273C PRO* 1.3 74.2 - - - +
275C LEU* 1.3 57.3 + - - +
277C GLY* 2.6 26.7 + - - -
278C LYS 3.8 8.7 - - - +
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Residues in contact with LEU 275 (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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28C VAL* 3.7 38.9 + - + +
36C VAL* 4.2 27.2 - - + +
39C ILE* 4.5 7.6 - - + -
230C MET* 4.9 7.2 - - + -
250C THR* 4.2 12.1 - - - +
253C ILE* 4.4 14.4 - - + -
254C LEU* 4.9 6.5 - - + -
257C ILE* 4.1 25.6 - - + -
271C ILE* 3.1 30.1 + - + +
272C LEU* 3.6 10.3 - - + +
274C SER* 1.3 79.7 - - - +
276C LYS* 1.3 62.2 + - - +
277C GLY 3.1 0.7 + - - -
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Residues in contact with LYS 276 (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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36C VAL* 3.5 20.3 - - + +
37C ASN* 3.2 26.0 + - - -
40C GLN* 3.6 23.2 - - - +
63C LEU 5.0 0.4 - - - +
64C ALA* 3.5 34.3 - - + +
67C TYR* 4.0 1.0 + - - -
272C LEU* 2.9 31.9 + - + +
273C PRO* 3.0 5.1 + - + +
275C LEU* 1.3 78.8 - - - +
277C GLY* 1.3 61.5 + - - +
278C LYS* 3.5 17.3 - - + +
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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