Contacts of the helix formed by residues 258 - 278 (chain B) in PDB entry 4F4W
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 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B SER* 3.0 14.7 + - - +
257B ARG* 1.3 77.1 - - - +
259B LEU* 1.3 66.0 + - - +
260B GLU* 2.9 14.5 + - - +
261B GLU* 2.9 39.4 + - - +
262B ILE* 3.1 15.3 + - - +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG 3.7 4.4 + - - -
258B ASN* 1.3 73.8 + - - +
260B GLU* 1.3 61.5 + - + +
261B GLU 3.2 0.2 + - - -
262B ILE* 3.2 4.4 + - - +
263B LYS* 3.0 46.3 + - + +
317B VAL* 4.2 16.4 - - + -
320B LEU* 3.6 31.0 - - + -
321B GLN* 4.2 30.5 - - + +
324B LEU* 4.0 18.3 - - + +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 2.9 13.1 + - - +
259B LEU* 1.3 79.8 - - + +
261B GLU* 1.3 61.1 + - - +
263B LYS* 2.6 42.1 + - - +
264B PRO* 3.3 19.0 - - - +
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 5.2 0.7 - - - -
254B ARG* 2.6 56.4 + - - +
255B ASN 4.5 0.5 - - - +
256B SER* 2.5 31.8 + - - +
258B ASN* 2.9 26.6 + - + +
260B GLU* 1.3 78.0 - - - +
262B ILE* 1.3 63.3 - - - +
264B PRO* 3.3 10.2 - - - +
265B TYR* 3.5 22.3 - - + -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 3.7 26.5 - - + -
256B SER* 3.7 30.5 - - - +
257B ARG* 4.2 4.9 - - - -
258B ASN 3.1 20.9 + - - +
259B LEU 3.9 2.5 - - - +
261B GLU* 1.3 78.1 - - - +
263B LYS* 1.3 65.3 + - - +
264B PRO* 3.2 1.1 - - - -
265B TYR* 2.9 16.5 + - - +
266B LEU* 3.2 6.5 + - + -
320B LEU* 3.7 27.6 - - + -
324B LEU* 4.7 3.4 - - + -
331B ILE* 4.2 19.1 - - + -
334B ILE* 3.7 26.0 - - + -
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 3.0 43.3 + - + +
260B GLU* 2.6 38.7 + - - +
262B ILE* 1.3 77.2 - - - +
264B PRO* 1.3 63.2 - - + +
266B LEU* 3.1 9.5 + - + +
267B PHE* 2.8 67.1 + - + -
317B VAL* 4.5 14.5 - - + +
320B LEU* 5.2 2.7 - - + -
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU 3.3 17.0 - - - +
261B GLU* 3.3 14.1 - - - +
262B ILE 3.2 6.1 - - - +
263B LYS* 1.3 92.9 - - + +
265B TYR* 1.3 62.8 + - + +
267B PHE* 4.0 7.8 - - + +
268B ARG* 3.0 29.3 + - - +
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B VAL* 3.9 15.2 - - + +
251B THR 4.1 4.5 - - - -
252B MET* 3.4 40.4 - - + -
253B LYS* 2.9 35.0 + - - +
254B ARG* 4.6 1.1 + - - +
261B GLU* 3.5 31.6 - - + -
262B ILE 2.9 5.9 + - - +
264B PRO* 1.3 80.2 - - + +
266B LEU* 1.3 63.9 + - - +
268B ARG* 3.4 32.2 + - - +
269B ALA* 3.1 22.2 + - - +
334B ILE* 3.5 18.4 - - + -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE 3.2 7.9 + - - +
263B LYS* 3.1 10.4 + - - +
265B TYR* 1.3 80.3 - - - +
267B PHE* 1.3 61.2 + - + +
269B ALA* 3.2 6.3 + - - +
270B ILE* 3.0 31.4 + - + +
287B VAL* 4.4 5.6 - - + -
316B SER* 3.7 40.8 - - - +
317B VAL* 4.6 3.6 - - + +
320B LEU* 4.0 26.0 - - + -
334B ILE* 4.1 17.2 - - + +
335B GLY* 3.9 12.8 - - - +
336B VAL* 3.2 35.2 - - + -
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LYS* 2.8 51.1 + - + +
264B PRO* 4.1 6.3 - - + +
266B LEU* 1.3 75.0 - - + +
268B ARG* 1.3 61.0 + - - +
270B ILE* 3.2 6.3 + - + +
271B GLU* 2.9 33.4 + - - +
313B TYR* 3.2 58.4 + + + +
316B SER* 3.9 7.9 - - - -
317B VAL* 3.7 32.5 - - + -
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG* 5.1 2.4 - - - +
250B VAL* 4.2 24.5 - - + +
251B THR 5.5 1.0 + - - -
264B PRO* 3.0 21.2 + - - +
265B TYR* 3.7 34.8 - - - +
266B LEU 3.3 0.2 - - - -
267B PHE* 1.3 77.8 - - - +
269B ALA* 1.3 63.3 + - - +
271B GLU* 3.2 8.3 + - + +
272B GLU* 3.0 51.4 + - + +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG* 3.7 39.5 - - + +
250B VAL* 5.0 6.1 - - + -
265B TYR 3.1 13.4 + - - +
266B LEU* 3.2 11.4 + - - +
268B ARG* 1.3 76.6 - - - +
270B ILE* 1.3 58.7 + - - +
273B SER* 2.8 33.3 + - - -
334B ILE 4.8 2.9 - - - +
335B GLY* 4.5 7.2 - - - -
336B VAL* 3.9 7.9 - - + -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 3.0 19.6 + - + +
267B PHE* 3.5 14.4 - - + +
269B ALA* 1.3 76.4 - - - +
271B GLU* 1.3 57.4 + - - +
273B SER* 3.2 3.1 + - - -
274B TYR* 2.8 47.5 + - + -
309B LYS* 4.3 2.9 - - + -
312B ALA* 3.7 26.0 - - + +
313B TYR* 4.0 21.8 - - + -
316B SER* 3.4 37.0 - - - +
336B VAL* 3.8 22.7 - - + -
338B PHE* 4.3 4.7 - - + -
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE 2.9 23.7 + - - +
268B ARG* 3.2 10.5 + - + +
270B ILE* 1.3 73.5 - - - +
272B GLU* 1.3 60.1 + - + +
274B TYR* 3.1 3.5 + - - +
275B TYR* 2.9 28.3 + - - +
309B LYS* 3.0 35.5 + - - +
313B TYR* 2.3 38.9 + - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG* 2.5 49.8 + - - +
268B ARG* 3.0 49.7 + - + +
269B ALA 4.1 2.5 - - - +
271B GLU* 1.3 72.9 - - + +
273B SER* 1.3 65.5 + - - +
275B TYR* 3.4 10.2 + - - +
276B LYS* 3.1 22.9 + - - +
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 3.9 6.2 - - - +
247B GLY* 3.6 8.9 - - - -
248B ARG* 3.5 24.6 + - - +
269B ALA 2.8 24.3 + - - -
270B ILE 3.4 4.3 - - - -
272B GLU* 1.3 77.4 - - - +
274B TYR* 1.3 56.5 + - - +
276B LYS* 3.2 7.2 + - - +
277B LEU* 2.8 32.5 + - - +
336B VAL* 3.7 5.0 - - - +
338B PHE* 3.8 26.2 - - - -
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 2.8 30.6 + - + +
271B GLU 3.1 3.8 + - - +
273B SER* 1.3 72.8 - - - +
275B TYR* 1.3 66.7 + - - +
277B LEU* 3.6 24.7 - - + +
278B ASP* 3.1 22.7 + - - +
280B ARG 5.5 2.0 - - - -
282B PRO* 3.7 11.7 - - + +
307B ILE* 2.7 46.8 + - - +
308B SER* 3.4 0.7 + - - -
309B LYS* 3.6 42.0 - - + -
312B ALA* 3.6 8.9 - - + +
338B PHE* 3.5 28.3 - + - -
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLU 2.9 13.3 + - - +
272B GLU* 3.5 13.2 - - - +
274B TYR* 1.3 78.5 - - - +
276B LYS* 1.3 68.2 + - + +
278B ASP* 3.3 13.9 + - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ARG* 4.2 25.3 - - - +
246B ILE* 3.7 24.1 - - + +
272B GLU 3.1 13.6 + - - +
273B SER* 3.5 7.6 - - - +
275B TYR* 1.3 82.5 - - + +
277B LEU* 1.3 66.4 + - - +
278B ASP* 3.2 3.6 + - - +
280B ARG* 3.0 42.0 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 3.8 23.8 - - + -
273B SER 2.8 23.2 + - - +
274B TYR* 3.3 44.6 + - + +
276B LYS* 1.3 72.6 - - - +
278B ASP* 1.3 69.6 + - - +
280B ARG* 3.0 47.8 + - + +
282B PRO* 4.1 14.1 - - + -
338B PHE* 4.3 10.8 - - + -
341B PHE* 3.4 34.3 - - + -
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TYR* 3.1 14.1 + - - +
275B TYR 3.3 9.4 + - - +
276B LYS 3.1 8.0 - - - +
277B LEU* 1.3 78.1 - - - +
279B LYS* 1.3 93.8 + - - +
280B ARG* 3.5 6.9 + - - +
281B ILE* 6.0 0.2 - - - +
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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
------------------------------------------------------------
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