Contacts of the helix formed by residues 245 - 259 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A ILE* 5.9 2.0 - - + +
243A GLU 3.5 5.2 + - - +
244A TRP* 1.3 75.6 - - + +
246A CYS* 1.3 65.7 + - - +
247A LYS* 3.8 6.6 + - - +
248A LYS* 3.0 50.1 + - + +
249A THR* 3.4 6.1 + - - -
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Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 5.3 1.8 - - - +
26A CYS* 2.0 56.3 - - + -
230A MET* 5.7 1.8 - - - -
244A TRP* 2.9 51.8 + - + +
245A ASN* 1.3 71.8 - - - +
247A LYS* 1.3 64.8 + - - +
249A THR* 2.9 14.6 + - - -
250A THR* 3.0 13.6 + - - -
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 4.8 8.5 + - - +
26A CYS* 3.9 10.5 - - + +
29A PRO* 5.7 4.6 - - - +
245A ASN* 3.3 7.2 + - - +
246A CYS* 1.3 79.1 - - - +
248A LYS* 1.3 64.1 + - - +
250A THR* 3.0 14.1 - - + +
251A ASP* 3.0 43.3 + - - +
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 6.5 0.4 - - + -
215A LYS 3.7 2.4 + - - -
216A ASP* 2.9 14.3 + - - +
217A ASN* 2.8 45.2 - - - +
218A GLY* 3.5 12.0 - - - +
245A ASN* 3.0 39.7 + - + +
247A LYS* 1.3 78.6 - - - +
249A THR* 1.3 57.2 + - - +
251A ASP* 3.1 6.9 + - - +
252A MET* 2.9 29.7 + - + +
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Residues in contact with THR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 5.1 1.4 - - - +
218A GLY* 2.7 33.8 + - - +
220A ILE* 4.4 5.2 - - + +
226A THR* 4.0 25.1 - - + -
230A MET* 4.2 18.2 - - + -
244A TRP* 3.1 31.3 + - + -
245A ASN 3.4 3.1 + - - -
246A CYS 2.9 10.8 + - - -
248A LYS* 1.3 73.8 - - - +
250A THR* 1.3 58.8 + - - +
252A MET* 3.1 3.4 + - + +
253A ILE* 2.9 29.8 + - + +
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.5 33.5 + - + +
27A SER 5.4 0.9 - - - +
28A VAL* 4.1 15.4 - - - +
29A PRO* 5.6 4.3 - - + -
230A MET* 4.3 18.8 - - - +
246A CYS* 3.0 8.3 + - - -
247A LYS* 3.0 31.4 - - + +
249A THR* 1.3 78.6 - - - +
251A ASP* 1.3 64.3 + - - +
253A ILE* 3.8 4.8 + - - +
254A LEU* 3.3 28.4 + - + +
275A LEU* 4.2 8.0 - - - +
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Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 4.8 9.6 - - - +
32A GLN* 3.9 20.1 + - - -
247A LYS* 3.0 49.2 + - - +
248A LYS* 3.5 5.8 - - - +
250A THR* 1.3 78.6 - - - +
252A MET* 1.3 66.7 + - - +
254A LEU* 3.1 9.7 + - - +
255A ASN* 3.1 24.9 + - - +
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 3.3 26.7 - - - +
218A GLY* 4.3 1.1 - - - +
219A ILE* 3.0 42.2 - - + -
223A ILE* 5.5 0.4 - - + -
226A THR* 4.8 1.1 - - + -
248A LYS* 2.9 14.3 + - + +
249A THR* 3.4 9.4 - - - +
251A ASP* 1.3 76.5 - - - +
253A ILE* 1.3 95.2 + - + +
255A ASN* 3.4 5.9 + - - +
256A GLU* 3.1 41.5 + - + +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ILE* 4.7 6.5 - - + +
226A THR* 3.7 29.6 - - + -
230A MET* 4.5 9.6 - - - -
249A THR 2.9 15.2 + - - +
250A THR* 4.1 6.5 - - - +
252A MET* 1.3 96.8 - - + +
254A LEU* 1.3 62.9 + - - +
256A GLU* 3.3 10.8 + - + +
257A ILE* 3.3 29.3 + - + +
262A PHE* 4.1 23.1 - - + -
271A ILE* 4.3 22.0 - - + -
275A LEU* 4.4 16.4 - - + -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.8 35.0 - - + -
29A PRO* 4.4 8.5 - - + -
32A GLN* 4.1 34.8 - - + +
35A LEU* 3.5 35.6 - - + +
36A VAL* 4.4 11.7 - - + -
250A THR* 3.3 18.9 + - + +
251A ASP* 3.1 12.1 + - - +
252A MET 3.1 0.6 - - - -
253A ILE* 1.3 75.2 - - - +
255A ASN* 1.3 67.2 + - - +
256A GLU 3.0 1.1 - - - -
257A ILE* 3.0 26.6 + - + +
258A LYS* 3.4 4.0 + - - -
275A LEU* 4.9 6.1 - - + -
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Residues in contact with ASN 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 6.4 0.7 - - - -
251A ASP 3.1 12.5 + - - +
252A MET* 4.0 7.6 - - - +
254A LEU* 1.3 75.4 - - - +
256A GLU* 1.3 55.4 - - - +
258A LYS* 3.1 47.6 + - - +
259A GLN* 3.1 25.5 + - + +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 5.4 1.8 - - - +
223A ILE* 4.3 20.4 - - + -
252A MET* 3.1 33.7 + - - +
253A ILE* 3.3 13.2 - - - +
254A LEU 3.0 0.6 - - - -
255A ASN* 1.3 77.8 - - - +
257A ILE* 1.3 58.6 + - - +
259A GLN* 3.8 14.7 + - - +
261A LYS* 2.7 71.2 + - + +
262A PHE* 4.2 5.0 - - + -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.0 28.5 - - + +
36A VAL* 5.5 0.7 - - + -
39A ILE* 3.9 35.7 - - + -
253A ILE* 3.3 20.4 - - + +
254A LEU* 3.0 23.3 + - + +
256A GLU* 1.3 75.7 - - - +
258A LYS* 1.3 66.5 + - - +
259A GLN 3.0 1.3 - - - -
260A GLY* 3.0 14.6 + - - -
261A LYS 5.1 0.9 - - - +
262A PHE* 3.6 24.0 + - + -
271A ILE* 4.7 0.4 - - + -
275A LEU* 4.1 18.8 - - + -
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.4 26.9 + - - +
35A LEU* 3.9 35.4 - - + +
254A LEU 3.4 1.6 + - - -
255A ASN* 3.1 33.6 + - - +
257A ILE* 1.3 78.6 - - - +
259A GLN* 1.3 67.3 + - - +
260A GLY* 3.3 3.9 + - - -
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ASN* 3.1 31.1 + - + +
256A GLU* 4.0 22.7 - - - +
257A ILE 3.0 1.2 - - - -
258A LYS* 1.3 92.1 + - - +
260A GLY* 1.3 60.0 + - - +
261A 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