Contacts of the helix formed by residues 256 - 276 (chain B) in PDB entry 4EG8
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 HIS 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ALA* 4.7 9.4 - - + +
254B ALA 3.9 6.7 - - - +
255B PRO* 1.3 75.0 - - - +
257B ILE* 1.3 68.8 + - + +
258B GLY* 2.9 37.6 + - - -
259B HIS* 3.0 43.2 + + - -
260B VAL* 3.1 28.0 + - - +
555B ILE* 6.5 0.7 - - + -
563B PHE 5.8 0.9 - - - +
565B PRO* 4.5 5.4 - - - -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS* 1.3 81.3 - - + +
258B GLY* 1.3 55.4 + - - +
260B VAL* 3.4 2.2 + - + -
261B TYR* 2.8 35.2 + - + +
548B TRP* 4.4 19.3 - - + +
555B ILE* 4.1 28.9 - - + -
563B PHE* 3.5 47.8 + - + +
565B PRO* 3.7 29.7 - - + +
581B LEU* 4.3 20.0 - - + -
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Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 5.5 0.4 - - - -
256B HIS* 2.9 19.0 + - - -
257B ILE* 1.3 80.2 - - - +
259B HIS* 1.3 65.4 + - - +
261B TYR* 3.3 6.7 + - - +
262B SER* 3.1 27.5 + - - -
545B HIS* 4.8 3.8 - - - -
548B TRP* 6.0 1.3 - - - -
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Residues in contact with HIS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 3.3 46.4 + + + +
250B TYR 4.9 5.3 + - - -
253B ALA* 4.6 7.8 - - + +
254B ALA 3.5 13.2 - - - -
255B PRO* 3.4 5.5 - - + +
256B HIS* 3.0 55.9 + + - +
258B GLY* 1.3 75.3 - - - +
260B VAL* 1.3 63.0 + - + +
263B THR* 2.9 32.0 + - - -
315B PHE* 3.5 27.2 - + + -
319B PHE* 4.6 4.7 - - + -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PRO 5.5 0.2 - - - -
256B HIS 3.1 19.0 + - - +
257B ILE* 3.6 7.0 - - + +
259B HIS* 1.3 77.1 - - + +
261B TYR* 1.3 57.4 + - - +
263B THR 3.6 0.2 + - - -
264B LEU* 2.9 14.9 + - - +
318B CYS* 3.7 30.1 - - - -
319B PHE* 4.6 7.2 - - + -
322B MET* 4.0 13.2 - - + -
324B TYR* 2.6 36.9 + - - +
565B PRO* 3.8 35.0 - - + -
581B LEU* 5.2 8.5 - - + -
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 2.8 22.7 + - + +
258B GLY* 3.6 6.1 - - - +
259B HIS 3.2 0.2 - - - -
260B VAL* 1.3 75.5 - - - +
262B SER* 1.3 65.8 + - - +
264B LEU* 3.1 18.2 + - + +
265B ILE* 3.1 31.5 + - + +
545B HIS* 3.1 47.3 - + + +
546B GLY 4.0 6.8 + - - -
548B TRP* 3.5 40.3 + + + +
581B LEU* 4.0 34.3 + - + -
582B LEU* 4.8 4.3 - - + -
585B SER* 4.5 5.7 + - - -
586B GLY 4.4 8.0 + - - -
587B PHE* 3.9 20.1 - - - -
589B ASP 5.5 0.3 + - - -
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 4.6 0.2 - - - -
247B PRO* 3.9 21.1 - - - +
249B TYR* 3.3 18.9 - - - -
258B GLY 3.1 11.4 + - - -
261B TYR* 1.3 78.6 - - - +
263B THR* 1.3 65.3 + - - +
265B ILE* 3.2 6.7 + - - +
266B THR* 3.1 25.4 + - - -
514B VAL* 3.8 5.3 - - - +
516B GLY* 4.4 1.9 + - - -
545B HIS* 2.7 32.9 + - - -
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 4.3 1.6 - - - -
249B TYR* 2.6 32.5 + - - -
259B HIS 2.9 14.6 + - - -
262B SER* 1.3 77.8 - - - +
264B LEU* 1.3 50.8 + - - +
266B THR* 3.3 6.8 + - - -
267B ASP* 2.8 33.1 + - - +
284B THR* 3.6 11.2 + - - +
319B PHE* 3.3 13.6 - - + -
324B TYR* 3.4 32.3 - - + -
326B ILE* 4.0 20.9 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 2.9 19.7 + - + +
261B TYR* 3.1 9.2 + - + +
263B THR* 1.3 73.1 - - - +
265B ILE* 1.3 60.8 + - - +
267B ASP* 3.1 3.7 + - + +
268B VAL* 2.8 47.8 + - + +
324B TYR* 3.4 24.8 + - + +
578B LYS* 3.8 37.0 - - + +
581B LEU* 4.0 32.1 - - + -
582B LEU* 3.8 27.8 - - + -
716B ILE 6.0 0.2 - - - +
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Residues in contact with ILE 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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261B TYR* 3.1 43.8 + - + +
262B SER* 3.2 5.8 + - - +
264B LEU* 1.3 75.8 - - - +
266B THR* 1.3 62.9 + - - +
268B VAL* 3.3 6.4 + - - +
269B ILE* 3.0 30.9 + - + +
514B VAL* 3.7 21.1 - - + -
543B VAL* 4.9 2.2 - - + -
545B HIS* 3.7 22.9 - - + -
582B LEU* 4.1 15.7 - - + -
587B PHE* 3.7 36.6 - - + -
661B ILE* 3.9 8.1 - - + -
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.9 21.8 - - + +
245B THR 3.1 35.5 + - - +
246B SER* 3.2 15.4 - - - +
262B SER 3.1 13.0 + - - -
263B THR* 3.4 8.7 - - - -
265B ILE* 1.3 77.1 - - - +
267B ASP* 1.3 62.8 + - - +
269B ILE* 3.4 1.9 + - - +
270B GLY* 3.0 20.6 + - - -
282B ALA* 4.4 2.1 - - + +
283B LEU 4.1 8.1 - - - +
326B ILE* 4.1 13.7 - - + -
514B VAL* 3.5 11.4 - - - +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B THR 2.8 20.4 + - - +
264B LEU* 3.5 7.2 - - + +
266B THR* 1.3 74.4 - - - +
268B VAL* 1.3 52.6 + - - +
270B GLY* 3.2 2.8 + - - -
271B ARG* 2.7 64.6 + - - +
274B ARG* 4.3 1.0 + - - -
282B ALA* 5.6 0.9 - - - -
323B ASP 4.2 0.7 - - - +
324B TYR* 3.4 29.9 - - + -
325B SER* 2.7 39.3 + - - +
326B ILE* 3.9 10.6 + - + +
578B LYS* 4.7 1.9 + - - -
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 2.8 31.8 + - + +
265B ILE 3.6 3.8 - - - +
267B ASP* 1.3 70.9 - - + +
269B ILE* 1.3 61.3 + - - +
271B ARG* 3.2 4.0 + - - +
272B TYR* 2.9 28.9 + - - +
582B LEU* 3.5 27.1 - - + -
656B TYR* 4.1 11.9 - - + -
661B ILE* 3.5 24.5 - - + -
715B PRO* 3.7 24.1 - - + +
716B ILE* 3.8 18.8 - - + +
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.7 28.9 - - + -
244B VAL* 4.0 8.7 - - + -
265B ILE* 3.0 26.8 + - + +
266B THR 3.8 3.6 - - - +
268B VAL* 1.3 75.0 - - - +
270B GLY* 1.3 63.5 + - - +
272B TYR* 3.2 5.8 + - - +
273B HIS* 3.1 35.8 + - + +
512B VAL* 4.1 19.1 - - + -
514B VAL* 4.2 11.4 - - + -
656B TYR* 5.0 9.6 - - + +
659B PRO* 3.7 33.7 - - + -
661B ILE* 4.2 13.2 - - + -
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 5.6 0.4 - - - -
244B VAL* 4.0 9.1 - - - +
266B THR 3.0 14.3 + - - -
267B ASP 3.5 3.6 - - - -
269B ILE* 1.3 77.7 - - - +
271B ARG* 1.3 61.7 + - - +
273B HIS* 3.3 2.8 + - - -
274B ARG* 3.0 35.8 + - - +
280B VAL* 3.7 21.2 - - - +
282B ALA* 5.0 2.0 - - - -
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 2.7 42.3 + - - +
268B VAL* 3.2 4.9 + - - +
270B GLY* 1.3 73.3 - - - +
272B TYR* 1.3 63.6 + - - +
274B ARG* 3.1 11.9 + - - +
275B VAL* 2.8 26.3 + - - +
323B ASP* 3.1 30.5 + - - -
324B TYR 3.8 1.0 + - - -
325B SER* 3.7 21.4 - - - +
715B PRO* 3.6 29.6 - - + -
718B PRO* 3.3 26.3 - - - +
804B GOL 3.2 51.7 + - - +
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL 2.9 13.6 + - - +
269B ILE* 3.2 7.4 + - - +
271B ARG* 1.3 75.6 - - - +
273B HIS* 1.3 72.3 + + - +
275B VAL* 3.1 6.5 + - + +
276B LYS* 2.9 41.1 + - + +
649B PRO 4.7 0.2 + - - -
653B ASP* 2.5 41.6 + - - +
656B TYR* 3.5 60.8 - + + -
657B LEU* 4.1 5.6 - - + -
712B LEU* 4.3 11.6 - - + +
715B PRO* 3.6 17.4 - - + +
741B PHE* 3.6 30.4 - + - -
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.7 1.3 - - + -
242B PHE* 3.1 49.8 - + + -
269B ILE* 3.1 30.9 + - + +
270B GLY 3.3 0.2 + - - -
272B TYR* 1.3 91.3 - + - +
274B ARG* 1.3 60.4 + - - +
276B LYS* 3.4 4.8 + - - +
277B GLY 3.3 4.0 + - - -
278B GLU* 2.5 55.1 + - - +
280B VAL* 3.6 20.9 - - + -
656B TYR 4.9 5.1 + - - -
657B LEU* 3.7 30.9 - - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 4.3 2.8 + - - -
270B GLY* 3.0 25.0 + - - +
271B ARG* 3.1 15.0 + - - +
273B HIS* 1.3 74.4 - - - +
275B VAL* 1.3 63.9 + - - +
277B GLY* 3.0 15.2 + - - -
278B GLU 3.9 9.4 - - - +
280B VAL* 3.5 35.9 + - + +
282B ALA* 4.7 3.0 - - - +
325B SER* 2.9 37.9 + - - -
327B ASP* 2.8 39.6 + - - -
736B LYS* 3.7 21.4 - - - -
804B GOL 3.6 17.9 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG 2.8 20.0 + - - +
272B TYR* 3.5 11.2 - - + +
274B ARG* 1.3 75.3 - - - +
276B LYS* 1.3 56.9 + - - +
277B GLY 3.0 0.4 + - - -
711B LEU* 3.7 38.1 - - + +
712B LEU* 6.0 0.2 - - + -
714B SER* 3.6 16.8 - - - +
715B PRO* 4.5 5.8 - - + -
735B ARG 4.5 7.0 - - - +
736B LYS* 4.4 8.1 - - + -
737B GLY* 2.7 32.1 + - - -
741B PHE* 4.3 12.9 - - + -
804B GOL 4.0 23.1 - - - +
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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
----------------------------------------------------------
-1B SER* 2.6 46.3 + - - -
0B MET 3.8 13.8 + - - -
237B LYS* 3.6 9.2 - - + +
272B TYR* 2.9 26.7 + - + +
273B HIS* 3.5 11.8 - - - +
274B ARG 3.2 0.2 - - - -
275B VAL* 1.3 75.6 - - - +
277B GLY* 1.3 58.8 + - - +
278B GLU* 4.0 23.6 + - - +
653B ASP* 2.7 25.2 + - - +
657B LEU* 4.1 7.7 - - - +
738B ILE* 3.1 39.8 + - + +
741B PHE* 4.1 17.0 - - + -
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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
------------------------------------------------------------
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