Contacts of the helix formed by residues 245 - 259 (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 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ILE* 5.9 2.6 - - + +
243C GLU 3.5 4.8 + - - +
244C TRP* 1.3 75.0 - - + +
246C CYS* 1.3 65.1 + - - +
247C LYS* 3.8 7.1 + - - +
248C LYS* 3.0 51.1 + - + +
249C THR* 3.4 6.1 + - - -
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Residues in contact with CYS 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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25C SER 5.3 2.0 - - - +
26C CYS* 2.0 55.4 - - + -
230C MET* 5.7 2.0 - - - -
244C TRP* 2.9 50.5 + - + +
245C ASN* 1.3 70.9 + - - +
247C LYS* 1.3 65.8 + - - +
249C THR* 2.9 15.2 + - - -
250C THR* 3.0 13.8 + - - -
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Residues in contact with LYS 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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25C SER 4.8 9.4 + - - +
26C CYS* 3.9 9.5 - - + +
29C PRO* 5.7 4.8 - - - +
245C ASN* 3.2 7.0 + - - +
246C CYS* 1.3 78.3 - - - +
248C LYS* 1.3 62.5 + - - +
250C THR* 3.0 14.3 - - + +
251C ASP* 3.0 42.5 + - - +
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Residues in contact with LYS 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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214C ILE* 6.5 0.2 - - + -
215C LYS 3.7 2.2 + - - -
216C ASP* 2.9 14.7 + - - +
217C ASN* 2.8 44.8 - - - +
218C GLY* 3.5 11.7 - - - +
245C ASN* 3.0 40.5 + - + +
246C CYS 3.0 0.2 + - - -
247C LYS* 1.3 79.9 - - - +
249C THR* 1.3 58.2 + - - +
251C ASP* 3.1 6.9 + - - +
252C MET* 2.9 29.3 + - + +
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Residues in contact with THR 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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214C ILE* 5.1 1.4 - - - +
218C GLY* 2.7 33.5 + - - +
220C ILE* 4.4 4.4 - - + +
226C THR* 4.0 24.7 - - + -
230C MET* 4.2 18.4 - - + -
244C TRP* 3.1 31.4 + - + -
245C ASN 3.4 2.8 + - - -
246C CYS* 2.9 10.6 + - - -
248C LYS* 1.3 73.0 - - - +
250C THR* 1.3 58.5 + - - +
252C MET* 3.1 3.0 + - - +
253C ILE* 2.9 29.2 + - + +
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Residues in contact with THR 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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26C CYS* 3.5 32.4 + - + +
27C SER 5.4 1.3 - - - +
28C VAL* 4.1 15.8 - - - +
29C PRO* 5.6 4.3 - - + -
230C MET* 4.3 19.3 - - - +
246C CYS* 3.0 8.5 + - - -
247C LYS* 3.0 32.1 - - + +
249C THR* 1.3 78.0 - - - +
251C ASP* 1.3 65.9 + - - +
253C ILE* 4.0 5.8 - - - +
254C LEU* 3.3 27.4 + - + +
275C LEU* 4.2 8.1 - - - +
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Residues in contact with ASP 251 (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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29C PRO* 4.8 10.2 - - - +
32C GLN* 3.9 20.1 + - - -
247C LYS* 3.0 49.0 + - - +
248C LYS* 3.5 4.9 - - - +
250C THR* 1.3 79.0 - - - +
252C MET* 1.3 68.0 + - - +
254C LEU* 3.1 9.7 + - - +
255C ASN* 3.1 24.7 + - - +
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Residues in contact with MET 252 (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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217C ASN* 3.3 27.4 - - - +
218C GLY 4.3 1.6 - - - +
219C ILE* 3.0 42.0 - - + -
223C ILE* 5.5 0.7 - - + -
226C THR* 4.8 1.1 - - + -
248C LYS* 2.9 13.7 + - + +
249C THR* 3.4 9.6 - - - +
251C ASP* 1.3 78.7 - - - +
253C ILE* 1.3 95.7 + - + +
254C LEU 3.2 0.2 + - - -
255C ASN* 3.4 5.5 + - - +
256C GLU* 3.1 40.7 + - + +
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Residues in contact with ILE 253 (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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223C ILE* 4.7 5.6 - - + +
226C THR* 3.7 29.6 - - + -
230C MET* 4.5 9.4 - - - -
249C THR 2.9 16.7 + - - +
250C THR* 4.1 6.1 - - - +
252C MET* 1.3 97.6 - - + +
254C LEU* 1.3 61.4 + - - +
256C GLU* 3.3 10.5 + - + +
257C ILE* 3.3 29.2 + - + +
262C PHE* 4.1 22.8 - - + -
271C ILE* 4.3 22.2 - - + -
275C LEU* 4.4 16.4 - - + -
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Residues in contact with LEU 254 (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* 3.8 34.1 - - + -
29C PRO* 4.4 9.0 - - + -
32C GLN* 4.0 35.4 - - + +
35C LEU* 3.5 34.6 - - + +
36C VAL* 4.4 11.7 - - + -
250C THR* 3.3 19.6 + - - +
251C ASP* 3.1 11.6 + - - +
252C MET 3.1 0.4 - - - -
253C ILE* 1.3 74.8 - - - +
255C ASN* 1.3 67.0 + - - +
256C GLU 3.0 1.3 - - - -
257C ILE* 3.0 26.9 + - + +
258C LYS* 3.4 4.0 + - - -
275C LEU* 4.9 5.2 - - + -
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Residues in contact with ASN 255 (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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32C GLN* 6.0 0.6 + - - -
251C ASP 3.1 13.8 + - - +
252C MET* 4.0 6.3 - - - +
254C LEU* 1.3 74.8 - - - +
256C GLU* 1.3 56.5 + - - +
257C ILE 3.0 0.2 - - - -
258C LYS* 3.1 47.3 + - - +
259C GLN* 3.1 24.7 + - + +
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Residues in contact with GLU 256 (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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219C ILE* 5.4 1.9 - - - +
223C ILE* 4.3 20.2 - - + -
252C MET* 3.1 34.8 + - - +
253C ILE* 3.3 12.6 - - - +
254C LEU 3.0 0.2 - - - -
255C ASN* 1.3 77.0 - - - +
257C ILE* 1.3 58.0 + - - +
259C GLN* 3.8 14.1 + - - +
261C LYS* 2.8 69.1 + - + +
262C PHE* 4.2 5.5 - - + -
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Residues in contact with ILE 257 (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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35C LEU* 4.0 29.2 - - + +
36C VAL* 5.5 0.7 - - + -
39C ILE* 3.9 35.0 - - + -
253C ILE* 3.3 20.6 - - + +
254C LEU* 3.0 22.9 + - + +
256C GLU* 1.3 76.6 - - - +
258C LYS* 1.3 66.5 + - - +
259C GLN 3.0 1.3 - - - -
260C GLY* 3.0 15.1 + - - +
261C LYS 5.1 0.4 - - - +
262C PHE* 3.6 25.7 + - + -
271C ILE* 4.7 0.2 - - + -
275C LEU* 4.1 19.5 - - + -
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Residues in contact with LYS 258 (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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32C GLN* 3.4 27.5 + - - +
35C LEU* 3.9 34.3 - - + +
254C LEU 3.4 2.0 + - - -
255C ASN* 3.1 33.2 + - - +
257C ILE* 1.3 78.6 - - - +
259C GLN* 1.3 67.1 + - - +
260C GLY 3.3 3.3 + - - -
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Residues in contact with GLN 259 (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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255C ASN* 3.1 31.7 + - + +
256C GLU* 4.0 22.9 - - - +
257C ILE 3.0 1.2 - - - -
258C LYS* 1.3 91.7 + - - +
260C GLY* 1.3 60.3 + - - +
261C LYS* 3.2 14.0 + - + +
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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