Contacts of the helix formed by residues 256 - 275 (chain A) in PDB entry 3FZF
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 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ILE 3.1 6.6 + - - +
254A SER 4.6 0.4 - - - -
255A GLU* 1.3 78.7 - - - +
257A LYS* 1.3 64.9 + - - +
258A ARG* 3.6 12.1 + - - +
259A ALA* 2.8 33.1 + - + +
260A VAL* 3.0 27.3 + - - +
287A LEU 4.9 0.5 - - - +
288A TYR* 3.7 30.4 - - + -
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 5.7 0.4 - - - +
255A GLU 3.8 5.4 + - - +
256A ASN* 1.3 74.4 - - - +
258A ARG* 1.3 56.5 + - + +
260A VAL* 3.3 7.8 + - - +
261A ARG* 2.8 34.5 + - - +
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASN* 3.5 10.8 + - - +
257A LYS* 1.3 77.9 - - + +
259A ALA* 1.3 57.4 + - - +
261A ARG* 3.5 9.1 + - - +
262A ARG* 3.0 36.0 + - + +
211B ILE* 3.6 28.1 - - - +
215B MET* 3.6 30.7 - - + +
248B LEU* 3.9 29.2 - - - +
252B ASP* 2.6 44.8 + - - -
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ILE* 4.3 10.1 - - + +
256A ASN* 2.8 33.1 + - + +
258A ARG* 1.3 70.0 - - - +
260A VAL* 1.3 67.2 + - - +
262A ARG* 3.4 2.6 + - - +
263A LEU* 3.0 21.3 + - - +
287A LEU* 3.2 45.6 - - + +
288A TYR* 4.3 7.9 - - + -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL* 4.8 11.1 - - + +
242A ILE* 4.9 4.7 - - + -
253A ILE* 3.3 26.5 - - + +
254A SER* 3.7 21.8 - - - +
256A ASN 3.0 18.1 + - - +
257A LYS* 3.5 6.3 - - - +
259A ALA* 1.3 74.5 - - - +
261A ARG* 1.3 52.7 + - - +
263A LEU* 3.3 4.3 + - - +
264A ARG* 2.7 60.0 + - - +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 5.5 1.4 - - - +
257A LYS 2.8 17.8 + - - +
258A ARG* 3.5 9.6 - - - +
259A ALA 3.2 0.2 - - - -
260A VAL* 1.3 74.2 - - - +
262A ARG* 1.3 59.1 + - - +
264A ARG* 3.2 5.5 + - - +
265A THR* 2.8 31.5 + - - +
212B GLU* 2.6 42.2 + - - -
215B MET* 3.9 31.3 - - + +
216B LYS* 4.0 4.2 - - - +
219B GLU* 2.7 40.3 + - - +
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Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 3.0 22.4 + - - +
259A ALA* 3.8 5.2 - - - +
261A ARG* 1.3 76.1 - - - +
263A LEU* 1.3 62.3 + - - +
265A THR* 4.0 5.5 - - - -
266A ALA* 3.2 23.9 + - - +
284A ILE* 3.2 22.9 - - + +
285A ASP 3.1 26.9 + - - +
286A SER 3.4 13.7 + - - -
287A LEU* 4.0 12.6 + - + +
215B MET* 3.9 14.4 - - + -
218B LEU* 3.7 32.0 + - + +
219B GLU* 4.9 5.8 - - + -
222B ASP* 2.5 46.9 + - - +
241B VAL* 4.1 15.6 - - - +
245B GLN* 3.6 13.7 - - - +
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Residues in contact with LEU 263 (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 VAL* 4.3 9.2 - - + +
241A PHE* 3.9 34.8 - - + +
242A ILE* 4.2 15.3 - - + +
245A PHE* 6.4 0.4 - - + -
253A ILE* 3.8 21.8 - - + -
259A ALA 3.0 18.1 + - - +
260A VAL 3.6 4.0 - - - +
262A ARG* 1.3 74.5 - - - +
264A ARG* 1.3 66.6 + - - +
266A ALA* 3.1 7.3 + - + +
267A CYS* 2.9 36.9 + - - -
282A ILE* 5.1 3.4 - - + -
284A ILE* 4.1 15.5 - - + -
287A LEU* 4.4 10.5 - - + +
293A PHE* 4.1 17.0 - - + -
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Residues in contact with ARG 264 (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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231A GLU* 5.7 9.4 - - - +
234A ASP* 4.5 19.1 - - + +
235A ASN* 2.9 31.1 + - - +
238A VAL* 3.9 35.4 - - + +
260A VAL* 2.7 46.3 + - - +
261A ARG* 4.0 5.3 - - - +
263A LEU* 1.3 72.0 - - - +
265A THR* 1.3 62.4 + - - +
267A CYS* 2.9 3.0 + - - +
268A GLU* 2.8 25.5 + - + +
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Residues in contact with THR 265 (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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261A ARG* 2.8 21.0 + - - +
262A ARG 4.0 3.6 - - - -
264A ARG* 1.3 72.3 - - - +
266A ALA* 1.3 57.8 + - - +
268A GLU* 3.6 7.5 + - + +
269A ARG* 3.1 28.7 + - + +
219B GLU* 2.6 50.6 + - + +
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Residues in contact with ALA 266 (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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262A ARG 3.2 16.1 + - - +
263A LEU* 3.1 5.7 + - + +
265A THR* 1.3 76.1 - - - +
267A CYS* 1.3 61.2 + - - +
269A ARG* 3.3 8.8 + - - +
270A ALA* 2.8 30.3 + - - +
282A ILE* 4.1 32.7 - - + +
284A ILE* 4.1 9.0 - - + -
222B ASP* 5.3 9.9 - - + +
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Residues in contact with CYS 267 (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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234A ASP* 4.5 8.5 - - + +
237A MET* 3.6 36.4 - - + +
238A VAL* 4.0 9.2 - - - -
241A PHE* 3.4 33.9 - - - -
263A LEU* 2.9 26.2 + - - +
264A ARG* 2.9 11.0 + - - +
266A ALA* 1.3 72.7 - - - +
268A GLU* 1.3 58.6 + - - +
270A ALA* 3.1 3.9 + - - -
271A LYS* 2.7 35.9 + - - +
282A ILE* 4.7 1.3 - - - -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 5.3 4.3 - - - +
234A ASP* 2.8 32.2 + - - +
264A ARG* 2.8 17.8 + - + +
265A THR* 3.6 8.5 - - - +
267A CYS* 1.3 76.6 - - - +
269A ARG* 1.3 64.1 + - - +
271A LYS* 3.5 3.7 - - - +
272A ARG* 3.1 42.3 + - - +
401A ATP 2.3 37.5 + - - +
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Residues in contact with ARG 269 (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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265A THR* 3.1 20.6 + - + +
266A ALA* 3.5 8.0 + - - +
268A GLU* 1.3 77.7 + - - +
270A ALA* 1.3 64.9 + - - +
272A ARG* 3.1 21.3 + - + +
273A THR* 3.1 23.6 + - - +
281A SER 4.9 9.9 + - - -
222B ASP 4.5 3.4 + - - -
223B THR* 3.7 55.5 + - - +
225B ILE* 6.0 2.2 - - - +
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Residues in contact with ALA 270 (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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237A MET* 4.3 9.2 - - + -
266A ALA 2.8 19.8 + - - +
267A CYS 3.6 2.9 - - - +
269A ARG* 1.3 74.3 - - - +
271A LYS* 1.3 62.8 + - - +
273A THR* 3.2 7.3 + - - -
274A LEU* 3.0 28.7 + - - +
280A ALA* 3.7 23.4 - - + +
281A SER 5.2 1.1 - - - +
282A ILE* 4.1 21.8 - - + -
297A ILE* 4.6 2.0 - - + -
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Residues in contact with LYS 271 (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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230A GLY* 3.1 27.3 + - - -
233A PHE* 4.3 8.1 - - + -
234A ASP* 2.6 31.6 + - - +
237A MET* 4.0 14.1 - - - +
267A CYS 2.7 20.1 + - - +
268A GLU* 3.5 9.0 - - - +
270A ALA* 1.3 71.3 - - - +
272A ARG* 1.3 62.9 + - - +
274A LEU* 2.9 20.5 + - - +
275A SER* 3.2 11.4 + - - -
302A PHE* 3.5 30.5 - - + -
340A SER* 5.9 0.2 - - - -
343A ILE* 4.8 2.9 - - + -
401A ATP 2.9 51.9 + - + +
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Residues in contact with ARG 272 (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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268A GLU* 3.1 47.5 + - - +
269A ARG* 3.1 10.4 + - - +
271A LYS* 1.3 75.0 - - + +
273A THR* 1.3 61.9 + - - +
275A SER* 3.3 16.8 - - - -
276A SER* 4.2 4.9 + - - -
342A ARG* 5.7 0.4 - - - +
401A ATP 3.5 69.1 + - + +
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Residues in contact with THR 273 (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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269A ARG* 3.1 24.5 + - - +
270A ALA* 3.4 12.7 - - - -
271A LYS 3.0 0.8 - - - -
272A ARG* 1.3 79.5 - - - +
274A LEU* 1.3 48.9 + - - +
275A SER 3.1 0.2 - - - -
276A SER* 3.1 8.1 + - - -
277A SER* 2.8 43.3 + - - +
279A GLN 4.5 6.5 - - - +
280A ALA* 4.3 16.4 - - + -
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Residues in contact with LEU 274 (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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237A MET* 4.5 0.9 - - + -
270A ALA 3.0 19.5 + - - +
271A LYS* 2.9 9.0 + - - +
273A THR* 1.3 71.1 - - - +
275A SER* 1.3 52.3 + - - +
276A SER 3.0 5.8 - - - -
277A SER 3.4 4.3 - - - +
279A GLN* 3.6 32.3 - - - +
280A ALA* 4.2 2.5 - - + -
297A ILE* 3.8 19.7 - - + +
298A THR 3.7 4.7 - - - +
299A ARG* 2.7 70.0 + - - +
302A PHE* 3.5 44.6 - - + -
344A PRO* 4.2 1.2 - - - +
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Residues in contact with SER 275 (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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271A LYS 3.2 5.7 + - - -
272A ARG 3.3 15.0 - - - -
273A THR 3.1 0.4 - - - -
274A LEU* 1.3 78.1 - - - +
276A SER* 1.3 59.7 + - - +
299A ARG* 3.9 1.8 - - - -
302A PHE* 6.1 0.4 - - - -
342A ARG* 3.5 19.4 + - - +
343A ILE* 3.7 7.3 - - - +
344A PRO* 3.4 23.8 - - - +
401A ATP 2.5 40.0 + - - -
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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
------------------------------------------------------------
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