Contacts of the helix formed by residues 259 - 274 (chain B) in PDB entry 3SSB
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 GLY 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B SER* 2.8 23.0 + - - -
246B GLN* 4.9 1.8 - - - -
257B GLY 3.7 0.2 - - - -
258B ILE* 1.3 80.5 - - - +
260B ARG* 1.3 65.5 + - - -
261B ASP 3.3 2.9 - - - -
262B LYS 3.4 1.6 + - - -
263B LEU* 3.0 22.9 + - - +
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Residues in contact with ARG 260 (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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175B LEU* 3.7 22.8 - - + +
178B PHE* 3.4 64.3 + - - +
186B TRP* 3.8 12.1 - - + -
245B SER* 3.3 16.4 - - - +
246B GLN* 4.0 13.0 + - - +
259B GLY* 1.3 69.0 - - - -
261B ASP* 1.3 67.2 + - - +
263B LEU* 3.3 4.6 + - - +
264B GLY* 2.9 27.2 + - - -
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Residues in contact with ASP 261 (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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87B VAL* 6.1 5.6 - - - +
259B GLY 3.3 0.6 - - - -
260B ARG* 1.3 84.8 + - - +
262B LYS* 1.3 60.2 + - + +
264B GLY* 3.3 2.5 + - - -
265B LYS* 3.0 38.2 + - - +
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Residues in contact with LYS 262 (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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258B ILE* 3.4 40.9 - - + +
259B GLY 3.4 1.8 + - - -
260B ARG 3.3 0.4 - - - -
261B ASP* 1.3 77.5 - - + +
263B LEU* 1.3 65.3 + - - +
265B LYS* 3.4 2.6 + - + +
266B ILE* 3.0 32.3 + - - +
296B TYR* 3.3 29.1 - - + +
302B GLU* 2.7 37.6 + - + +
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ILE* 4.3 15.9 - - + -
175B LEU* 4.5 9.4 - - + -
186B TRP* 4.0 17.3 - - + -
241B ALA* 3.6 42.2 - - + +
244B ILE* 3.9 19.3 - - + -
245B SER* 3.9 14.1 - - - -
258B ILE* 4.8 1.2 - - - +
259B GLY 3.0 15.1 + - - +
260B ARG* 3.4 8.1 - - - +
262B LYS* 1.3 76.4 - - - +
264B GLY* 1.3 56.9 + - - +
266B ILE* 3.7 2.0 - - - +
267B PHE* 2.9 63.9 + - + +
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Residues in contact with GLY 264 (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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83B TYR* 4.6 0.7 - - - -
88B HIS* 3.6 11.2 - - - -
172B PHE* 3.9 6.8 - - - -
175B LEU* 3.6 24.2 - - - -
260B ARG 2.9 12.8 + - - -
261B ASP* 3.7 3.8 - - - -
263B LEU* 1.3 76.7 - - - +
265B LYS* 1.3 56.2 + - - +
267B PHE* 5.1 0.2 - - - -
268B TYR* 2.9 34.0 + - - +
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Residues in contact with LYS 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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87B VAL* 4.6 17.2 + - + +
88B HIS* 4.4 10.7 - - + +
261B ASP* 3.0 26.1 + - - +
262B LYS* 3.8 6.3 - - + +
264B GLY* 1.3 75.4 - - - +
266B ILE* 1.3 63.0 + - - +
268B TYR* 4.0 2.1 - - - +
269B ARG* 3.0 26.2 + - - +
295B LEU* 3.9 20.6 - - + +
296B TYR* 3.5 23.6 - - + +
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.9 1.1 - - + -
258B ILE* 3.6 27.1 - - + -
262B LYS 3.0 18.8 + - - +
263B LEU* 3.7 5.2 - - - +
265B LYS* 1.3 77.1 - - - +
267B PHE* 1.3 69.5 + - + +
269B ARG 3.4 0.2 + - - -
270B ALA* 2.9 25.5 + - - +
288B ALA* 3.5 35.0 - - + +
291B SER* 3.4 7.8 - - - -
292B ALA* 3.9 21.5 - - + -
295B LEU* 4.1 7.0 - - + -
296B TYR* 3.9 22.2 - - + -
302B GLU* 4.5 0.4 - - + -
306B VAL* 4.0 13.2 - - + -
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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
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168B ILE* 4.0 17.1 - - + +
171B ILE* 3.8 31.9 - - + -
172B PHE* 4.0 19.0 - - + -
237B ILE* 4.4 4.5 - - + -
241B ALA* 4.7 5.2 - - + -
244B ILE* 3.9 17.5 - - + -
263B LEU* 2.9 44.2 + - + +
266B ILE* 1.3 86.4 - - + +
268B TYR* 1.3 60.6 + - - +
270B ALA* 3.6 6.1 - - + +
271B LEU* 2.9 31.5 + - - +
284B LEU* 4.1 27.8 - - + -
288B ALA* 4.5 7.2 - - + -
310B PHE* 4.2 21.3 - + - -
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Residues in contact with TYR 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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84B TYR* 4.3 11.9 - + - -
88B HIS* 3.6 55.7 + + + +
90B ARG* 3.0 48.4 + - - +
148B VAL* 4.9 4.3 - - + -
172B PHE* 3.6 11.9 - + + -
264B GLY 2.9 24.0 + - - +
265B LYS* 4.0 3.1 - - - +
267B PHE* 1.3 72.2 - - - +
269B ARG* 1.3 64.4 + - + +
271B LEU* 3.4 8.1 + - + +
272B THR* 2.8 54.6 + - + +
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Residues in contact with ARG 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 LYS 3.0 18.8 + - - +
266B ILE 3.7 2.0 - - - +
268B TYR* 1.3 76.9 - - + +
270B ALA* 1.3 60.4 + - - +
272B THR* 3.7 5.2 - - - -
273B GLN* 2.8 64.4 + - + +
274B TYR* 4.5 4.0 + - - -
291B SER* 3.6 28.0 - - - +
294B ASP* 2.9 36.8 + - - +
295B LEU* 3.9 20.4 - - + +
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Residues in contact with ALA 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 ILE 2.9 17.0 + - - +
267B PHE* 3.6 9.2 - - + +
269B ARG* 1.3 73.5 - - - +
271B LEU* 1.3 58.5 + - - +
274B TYR* 3.0 13.9 + - - -
275B LEU* 2.9 36.5 + - + +
284B LEU* 4.9 6.1 - - + -
287B ALA* 3.9 22.9 - - + +
288B ALA* 4.1 6.5 - - + +
291B SER* 3.0 14.8 + - - +
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Residues in contact with LEU 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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84B TYR* 5.8 0.4 - - + +
145B THR* 5.4 0.4 - - + -
148B VAL* 3.9 28.0 - - + -
149B THR* 3.9 17.7 - - + +
152B THR* 3.5 12.3 - - - +
153B ALA* 3.5 43.3 + - + +
155B LEU* 4.5 2.5 - - + -
168B ILE* 3.9 28.0 - - + -
172B PHE* 4.7 9.2 - - + -
267B PHE 2.9 17.7 + - - +
268B TYR* 3.5 9.6 - - + +
269B ARG 3.2 0.2 - - - -
270B ALA* 1.3 78.1 - - - +
272B THR* 1.3 62.8 + - + +
275B LEU* 4.0 21.0 + - + +
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Residues in contact with THR 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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90B ARG* 4.0 3.1 - - - +
152B THR* 3.7 31.9 - - + +
268B TYR* 2.8 59.6 + - + +
269B ARG* 3.4 7.8 + - - -
271B LEU* 1.3 80.2 - - + +
273B GLN* 1.3 75.0 + - - +
275B LEU 5.9 0.2 - - - -
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Residues in contact with GLN 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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269B ARG* 2.8 50.3 + - + +
272B THR* 1.3 94.0 + - - +
274B TYR* 1.3 80.2 + - + +
275B LEU 5.2 1.1 - - - -
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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
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269B ARG* 4.5 5.0 + - - -
270B ALA* 3.0 6.3 + - - +
273B GLN* 1.3 99.1 - - + +
275B LEU* 1.3 68.2 + - - +
276B THR* 3.7 12.1 - - - +
279B SER* 4.6 0.9 + - - -
287B ALA* 3.6 29.2 - - + +
290B GLN* 3.4 25.3 + - + +
291B SER* 3.3 25.4 - - - -
294B ASP* 2.5 36.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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