Contacts of the helix formed by residues 256 - 273 (chain B) in PDB entry 1W98
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 PRO 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B MET* 4.1 1.4 - - - +
243B TYR* 3.2 48.9 - - + +
255B TYR* 1.3 87.8 - - + +
257B GLN* 1.3 67.5 + - + +
258B GLN* 3.3 4.7 + - + +
259B ILE* 3.4 22.9 + - + +
260B PHE 3.5 8.1 + - - -
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Residues in contact with GLN 257 (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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255B TYR 3.4 8.1 + - - +
256B PRO* 1.3 71.5 - - + +
258B GLN* 1.3 63.2 + - + +
259B ILE 3.4 0.2 + - - -
260B PHE* 3.5 2.4 - - - +
261B ILE* 3.2 28.7 + - - +
331B LEU* 4.0 23.9 - - + +
339B ASP* 2.7 32.0 + - - +
340B GLU* 3.7 11.0 + - - -
342B ALA* 4.4 0.6 - - - +
343B HIS* 3.1 49.7 + - + +
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Residues in contact with GLN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PRO* 3.3 3.2 - - + +
257B GLN* 1.3 80.7 - - + +
259B ILE* 1.3 61.1 + - + +
261B ILE* 3.7 4.2 - - - +
262B GLN* 3.0 57.6 + - - +
329B SER 3.0 15.8 + - - -
330B LYS* 3.4 12.3 - - - +
331B LEU* 3.1 39.9 + - + +
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B MET* 3.8 18.2 - - + -
243B TYR* 3.6 23.3 - - + +
256B PRO* 3.4 16.9 + - + +
257B GLN 3.4 0.4 - - - -
258B GLN* 1.3 78.8 - - + +
260B PHE* 1.3 67.6 + - - +
262B GLN* 3.2 15.4 + - - +
263B ILE* 3.2 33.9 + - + +
292B PHE* 5.7 3.5 - - + -
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.6 15.5 - - - -
232B VAL* 3.9 16.4 - - + -
235B LEU* 3.8 23.5 - - + +
236B ASN* 3.5 30.7 - - - -
239B MET* 3.8 23.1 - - + +
255B TYR* 3.6 39.3 - + + -
256B PRO 3.5 4.2 + - - +
257B GLN 3.5 8.9 + - - +
259B ILE* 1.3 79.6 - - - +
261B ILE* 1.3 75.0 + - + +
262B GLN 3.2 0.5 + - - -
263B ILE* 3.3 5.9 + - - -
264B ALA* 3.0 24.1 + - + +
343B HIS* 3.6 24.9 - + - -
344B ASN* 4.6 2.9 - - - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.4 16.4 + - - +
257B GLN 3.2 4.6 + - - +
258B GLN* 3.7 17.5 - - - +
260B PHE* 1.3 79.6 - - + +
262B GLN* 1.3 65.3 + - + +
264B ALA* 3.4 5.5 + - - +
265B GLU* 3.1 26.5 + - + +
329B SER* 4.0 28.7 - - - +
330B LYS 4.6 2.5 - - - +
331B LEU* 4.1 22.2 - - + +
332B LYS 5.7 0.4 - - - +
342B ALA 5.6 0.2 - - - +
343B HIS* 3.2 49.4 - - + +
347B THR* 5.9 2.7 - - + +
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Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 3.0 41.8 - - - +
259B ILE* 3.2 17.3 + - - +
260B PHE 3.1 1.4 - - - -
261B ILE* 1.3 80.7 - - + +
263B ILE* 1.3 61.4 + - - +
265B GLU* 3.5 18.3 + - - +
266B LEU 3.6 4.9 + - - -
292B PHE* 3.7 25.3 - - + -
323B ILE* 5.3 0.3 - - - +
328B SER* 3.5 32.5 + - - +
329B SER 3.1 16.3 + - - +
330B LYS* 6.0 0.4 - - - +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 3.9 24.0 - - + -
239B MET* 4.1 11.9 - - - -
259B ILE* 3.2 25.2 + - + +
260B PHE* 3.9 4.7 - - - +
262B GLN* 1.3 74.0 - - - +
264B ALA* 1.3 63.0 + - - +
266B LEU* 3.3 4.5 + - - +
267B LEU* 3.1 21.6 + - + +
288B ALA* 3.7 35.0 - - + +
289B LEU* 3.7 35.0 - - + +
292B PHE* 4.1 28.5 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.7 31.0 - - - +
152B TYR* 6.2 0.9 - - + -
232B VAL* 5.0 5.6 - - + -
235B LEU* 3.9 13.6 - - + +
260B PHE* 3.0 21.0 + - + +
261B ILE* 3.6 6.3 - - - +
263B ILE* 1.3 76.2 - - - +
265B GLU* 1.3 52.2 + - - +
267B LEU* 3.0 8.7 + - - +
268B ASP* 2.7 42.8 + - - +
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Residues in contact with GLU 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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148B ARG* 5.0 2.2 - - - +
261B ILE* 3.1 16.7 + - + +
262B GLN* 3.6 8.5 - - - +
263B ILE 3.2 0.2 - - - -
264B ALA* 1.3 77.6 - - - +
266B LEU* 1.3 59.4 + - - +
268B ASP* 3.8 12.4 + - - +
269B LEU* 3.4 18.7 + - - +
323B ILE* 3.8 20.6 - - + +
328B SER* 3.7 12.4 + - - -
329B SER* 2.7 50.3 + - - -
347B THR* 6.1 0.4 - - - +
349B ARG* 3.1 27.7 + - + +
351B SER* 5.4 1.9 + - - -
354B LEU* 6.2 0.2 - - + -
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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 GLN 3.6 2.8 + - - +
263B ILE 3.3 9.1 + - - +
264B ALA 3.2 0.4 - - - -
265B GLU* 1.3 76.5 - - - +
267B LEU* 1.3 59.8 + - - +
269B LEU* 3.2 4.2 + - + +
270B CYS* 3.0 32.9 + - - -
288B ALA* 4.0 13.2 - - + +
291B HIS* 4.2 7.4 - - + -
292B PHE* 3.6 33.4 - - + -
316B MET* 3.1 34.1 - - + -
319B PHE* 3.7 10.8 - - + +
320B ALA* 3.6 32.3 - - + +
323B ILE* 4.3 13.9 - - + +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.2 13.2 - - + +
231B ILE* 3.7 26.7 - - + +
232B VAL* 5.3 2.5 - - + -
235B LEU* 4.1 28.3 - - + -
263B ILE* 3.1 14.5 + - + +
264B ALA* 3.0 9.5 + - - +
266B LEU* 1.3 78.2 - - - +
268B ASP* 1.3 57.6 + - - +
270B CYS* 3.1 10.2 + - + +
271B VAL* 2.9 30.0 + - - +
284B LEU* 3.4 39.0 - - + +
285B ALA* 4.0 13.0 - - - -
288B ALA* 3.6 13.7 - - + -
316B MET* 5.2 1.6 - - - -
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 3.5 27.1 - - + +
148B ARG* 4.1 11.8 + - - -
152B TYR* 2.7 39.6 + - - -
264B ALA* 2.7 27.4 + - - +
265B GLU* 3.9 10.2 - - - +
267B LEU* 1.3 71.4 - - - +
269B LEU* 1.3 59.8 + - - +
271B VAL* 3.4 15.2 - - - +
272B LEU* 3.5 17.9 - - - +
346B GLN* 3.1 21.7 + - - +
347B THR* 4.5 1.7 + - - +
351B SER* 5.1 4.0 - - - +
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Residues in contact with LEU 269 (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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265B GLU 3.4 10.5 + - - +
266B LEU* 3.2 10.2 + - - +
267B LEU 3.1 0.8 - - - -
268B ASP* 1.3 76.5 - - - +
270B CYS* 1.3 65.1 + - - +
272B LEU* 3.0 27.4 + - + +
273B ASP 3.8 2.1 + - - -
319B PHE* 3.8 42.2 - - + +
322B VAL* 4.3 5.6 - - + -
323B ILE* 4.1 12.8 - - + -
351B SER* 3.9 12.8 + - - +
354B LEU* 4.3 22.9 - - + +
355B LEU* 3.7 44.1 - - + +
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Residues in contact with CYS 270 (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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266B LEU* 3.0 27.3 + - - +
267B LEU* 3.1 12.5 + - + +
269B LEU* 1.3 77.9 - - - +
271B VAL* 1.4 55.5 + - - +
273B ASP* 3.2 21.8 + - - +
276B CYS* 3.3 9.9 - - - +
284B LEU* 4.8 9.0 - - + -
315B TRP* 3.5 19.6 - - + -
316B MET* 3.9 24.2 - - - -
319B PHE* 3.7 33.9 - - - -
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Residues in contact with VAL 271 (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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130B ARG* 2.7 36.5 + - - +
134B LEU* 3.6 4.5 - - + +
151B PHE* 4.3 13.0 - - + -
152B TYR* 3.4 21.8 - - + +
155B GLN* 3.7 29.2 - - + +
231B ILE* 3.6 30.7 - - + +
267B LEU 2.9 24.4 + - - +
268B ASP* 3.4 14.4 - - - +
270B CYS* 1.4 67.0 - - - +
272B LEU* 1.3 56.6 + - + +
273B ASP 3.1 4.1 - - - +
276B CYS* 3.8 11.2 - - - -
284B LEU* 5.8 0.8 - - - +
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Residues in contact with LEU 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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127B PRO 4.8 0.3 - - - +
130B ARG* 3.5 8.6 + - - +
131B ALA* 3.1 48.4 - - + +
134B LEU* 4.2 10.3 - - + -
135B ASP* 4.1 19.7 - - + +
138B MET* 4.3 12.1 - - - -
268B ASP 3.5 15.9 + - - +
269B LEU* 3.0 14.5 + - + +
271B VAL* 1.3 83.2 - - + +
273B ASP* 1.3 55.9 + - - +
274B VAL* 3.8 3.3 + - - +
351B SER* 3.3 43.7 - - - +
352B LEU* 4.4 4.3 - - + +
355B LEU* 4.0 17.3 - - + +
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Residues in contact with ASP 273 (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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130B ARG* 3.9 1.1 - - - -
269B LEU 3.8 1.0 + - - -
270B CYS 3.2 16.2 + - - +
271B VAL 3.1 0.2 - - - -
272B LEU* 1.3 78.0 - - - +
274B VAL* 1.3 64.5 + - - +
275B ASP* 2.8 29.1 + - - +
276B CYS* 3.1 18.9 + - - -
315B TRP* 4.1 13.8 + - + -
319B PHE* 3.8 28.2 - - + -
355B LEU* 3.9 12.6 - - + +
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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