Contacts of the helix formed by residues 237 - 255 (chain A) in PDB entry 2FK8
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 LEU 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.8 16.3 - - + +
45A ALA 5.2 1.3 - - - +
46A TYR* 3.8 32.5 - - + -
61A LYS* 5.4 1.6 - - + -
64A LEU* 4.0 12.8 - - + -
176A GLN* 3.6 42.8 - - + +
235A LEU* 4.2 13.7 - - + +
236A SER* 1.3 77.6 - - - +
238A ARG* 1.3 63.9 + - - +
239A PRO* 3.4 4.9 - - - -
240A HIS* 3.0 21.3 + - + +
241A TYR 3.1 9.5 + - - -
289A CYS* 2.7 26.4 + - + +
291A LEU* 4.3 13.7 - - + +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 2.6 30.7 + - - -
236A SER* 3.5 7.3 + - - +
237A LEU* 1.3 76.2 - - - +
239A PRO* 1.4 73.0 - - + +
241A TYR* 3.1 4.0 + - - +
242A ILE* 3.0 32.5 + - + +
282A PHE* 3.4 44.7 + - + +
285A GLU* 3.6 44.8 + - - +
287A LEU 3.0 22.8 + - - -
288A ASP* 3.3 23.9 + - - +
289A CYS 4.2 0.2 + - - -
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Residues in contact with PRO 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 4.7 6.7 - - - +
237A LEU* 3.4 6.1 - - - -
238A ARG* 1.4 97.3 - - + +
240A HIS* 1.3 70.2 + - + +
242A ILE* 3.5 15.7 + - + +
243A LYS* 3.3 31.1 + - - +
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Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS* 3.7 3.6 - - - -
45A ALA 3.3 17.7 - - - +
46A TYR* 3.6 30.4 - + - -
47A PHE* 2.9 54.0 + - + +
48A GLU* 4.0 11.4 + - + +
236A SER 5.1 1.6 - - - -
237A LEU* 3.0 23.4 + - + +
239A PRO* 1.3 85.1 - - + +
241A TYR* 1.3 55.3 + - - +
243A LYS* 3.4 10.0 + - - +
244A THR* 2.8 33.8 + - - -
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.9 0.9 + - - -
43A SER* 3.9 4.7 - - - -
44A CYS* 3.3 34.5 + - + -
146A GLU* 2.6 36.8 + - - -
178A SER* 3.6 17.7 + - - -
237A LEU 3.1 7.0 + - - +
238A ARG* 3.1 9.2 + - - +
240A HIS* 1.3 72.8 - - - +
242A ILE* 1.3 61.4 + - - +
244A THR* 4.0 4.3 - - + -
245A LEU* 2.8 55.5 + - + +
248A TRP* 3.9 25.0 - + - -
274A TYR* 4.7 9.5 + - - -
282A PHE* 3.5 32.8 - + + -
289A CYS* 3.8 11.2 - - + -
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Residues in contact with ILE 242 (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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238A ARG* 3.0 22.2 + - + +
239A PRO* 3.5 15.0 - - + +
241A TYR* 1.3 76.2 - - - +
243A LYS* 1.3 64.0 + - + +
245A LEU* 3.4 2.2 + - - +
246A ARG* 3.1 23.2 + - + +
279A GLU* 3.7 22.5 - - + +
282A PHE* 3.7 22.7 - - + +
283A THR* 3.7 39.7 - - + +
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Residues in contact with LYS 243 (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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47A PHE* 3.6 41.9 + - + +
50A PRO* 3.9 34.9 + - - +
239A PRO* 3.3 20.7 + - - +
240A HIS* 3.7 6.5 - - - +
241A TYR 3.3 0.4 - - - -
242A ILE* 1.3 77.6 - - + +
244A THR* 1.3 62.5 + - - +
246A ARG* 3.4 6.2 + - - +
247A ILE* 3.1 30.8 + - + +
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 4.0 1.1 - - - +
44A CYS* 4.3 1.3 - - - -
45A ALA* 2.9 36.0 + - - +
47A PHE* 3.6 8.2 - - - -
54A LEU* 4.1 11.6 - - + +
240A HIS 2.8 22.7 + - - -
241A TYR* 3.6 10.5 - - + -
243A LYS* 1.3 76.5 - - - +
245A LEU* 1.3 58.9 + - - +
247A ILE* 3.3 3.0 + - - +
248A TRP* 2.9 67.8 + - + +
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 2.8 49.0 + - + +
242A ILE 3.9 2.7 - - - +
244A THR* 1.3 70.6 - - - +
246A ARG* 1.3 61.0 + - - +
248A TRP* 3.7 15.4 - - + +
249A GLY* 2.8 27.5 + - - -
274A TYR* 4.8 4.7 - - + -
275A LEU* 4.0 39.5 - - + +
276A ARG* 4.6 1.0 + - - -
278A CYS* 3.7 35.0 - - + -
279A GLU* 3.7 17.0 - - + +
282A PHE* 3.8 17.0 - - + -
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Residues in contact with ARG 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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242A ILE* 3.1 18.1 + - + +
243A LYS* 3.7 7.0 - - - +
245A LEU* 1.3 75.8 - - - +
247A ILE* 1.3 60.1 + - + +
249A GLY 3.3 1.2 + - - -
250A ASP* 2.8 58.8 + - - +
276A ARG* 3.8 6.1 + - - +
279A GLU* 2.6 46.3 + - - +
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.6 31.9 - - + -
54A LEU* 3.9 33.0 - - + +
243A LYS* 3.1 21.1 + - + +
244A THR* 3.8 3.1 - - - +
246A ARG* 1.3 77.4 - - + +
248A TRP* 1.3 57.9 + - - +
250A ASP* 3.3 7.1 + - - +
251A THR* 2.9 42.3 + - - +
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Residues in contact with TRP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.4 50.2 + + + +
36A GLN* 4.3 7.4 - - + +
41A THR 3.7 18.2 + - - -
42A TYR* 3.9 20.9 - + - -
43A SER* 3.4 36.8 - - - -
54A LEU* 3.6 25.6 - - + +
58A GLN* 3.9 3.2 - - - +
241A TYR* 3.9 21.1 - + - -
244A THR* 2.9 33.2 + - + +
245A LEU* 3.7 15.0 - - + +
247A ILE* 1.3 74.2 - - - +
249A GLY* 1.3 62.6 + - - +
251A THR* 3.1 1.7 + - - -
252A LEU* 2.9 21.8 + - - +
274A TYR* 5.4 3.4 - + - -
275A LEU* 3.6 25.4 - - + -
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Residues in contact with GLY 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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245A LEU 2.8 20.4 + - - -
248A TRP* 1.3 74.0 - - - +
250A ASP* 1.3 62.7 + - - +
252A LEU 3.5 0.2 + - - -
253A GLN* 3.1 25.1 + - - +
272A MET* 3.8 6.6 - - - +
275A LEU* 3.8 21.5 - - - +
276A ARG* 3.6 19.5 + - - -
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Residues in contact with ASP 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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246A ARG* 2.8 38.1 + - - +
247A ILE* 3.7 6.4 + - - +
249A GLY* 1.3 77.3 - - - +
251A THR* 1.3 57.7 + - - +
253A GLN* 3.5 5.4 + - - +
254A SER* 3.0 28.6 + - - -
276A ARG* 3.0 28.9 + - - +
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Residues in contact with THR 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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33A ALA 5.8 0.2 - - - +
34A LEU 3.3 16.2 - - - +
35A PHE* 3.9 18.4 + - - +
36A GLN 5.6 1.1 - - - +
247A ILE* 2.9 28.0 + - - +
248A TRP 3.1 3.1 + - - -
250A ASP* 1.3 73.1 - - - +
252A LEU* 1.3 65.1 + - - +
254A SER* 2.7 25.8 + - - +
255A ASN* 2.9 18.9 + - - +
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Residues in contact with LEU 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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31A PHE* 4.1 14.1 - - + -
34A LEU* 3.7 20.3 + - + +
35A PHE* 3.8 14.3 - - + +
248A TRP 2.9 19.1 + - - +
249A GLY 4.0 0.2 - - - +
251A THR* 1.3 73.1 - - - +
253A GLN* 1.3 63.6 + - - +
255A ASN 3.0 13.0 + - - -
256A LYS 3.1 9.7 + - - -
259A ALA* 3.8 26.0 - - + -
268A TYR* 3.6 15.1 - - + +
271A TYR* 3.7 30.3 - - + -
272A MET* 3.9 18.4 - - + -
275A LEU* 3.9 15.0 - - + -
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Residues in contact with GLN 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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249A GLY 3.1 18.2 + - - +
250A ASP* 3.7 5.6 + - - +
252A LEU* 1.3 76.5 - - - +
254A SER* 1.3 61.9 + - - +
256A LYS* 3.1 21.8 + - + +
268A TYR* 3.5 19.2 + - - +
272A MET* 3.8 15.8 - - + +
276A ARG* 3.4 20.8 + - - +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP 3.0 14.3 + - - -
251A THR* 2.7 25.0 + - - +
253A GLN* 1.3 75.8 - - - +
255A ASN* 1.3 65.1 + - - +
256A LYS 3.4 2.4 + - - -
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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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33A ALA 5.0 0.8 + - - -
34A LEU* 2.6 55.6 + - + +
251A THR* 2.9 23.7 + - - +
252A LEU 3.0 6.4 + - - +
254A SER* 1.3 82.6 + - - +
256A LYS* 1.3 58.0 + - - +
257A ASP 3.5 2.2 - - - -
258A LYS* 3.2 25.1 + - + +
259A ALA* 2.9 26.7 + - - +
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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
------------------------------------------------------------
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