Contacts of the helix formed by residues 258 - 272 (chain B) in PDB entry 1TW2
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 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B ASN 4.3 1.8 - - - +
257B TRP* 1.3 93.8 - - + +
259B ASP* 1.3 67.0 + - - +
260B HIS* 2.9 23.3 + - + +
261B ASP* 3.0 29.8 + - - +
262B ALA* 3.1 6.6 + - - +
307B LEU 4.4 5.2 - - - +
308B GLY* 3.5 25.5 - - - +
309B GLY* 5.0 0.4 - - - -
312B ARG* 4.7 0.4 - - - +
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Residues in contact with ASP 259 (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 PRO* 1.3 71.2 - - - +
260B HIS* 1.3 58.1 + - + +
262B ALA* 3.3 2.8 + - - +
263B VAL* 3.0 35.1 + - + +
312B ARG* 3.2 26.2 + - - +
316B LYS* 6.1 0.9 - - - +
320B LEU* 3.9 13.8 - - + +
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Residues in contact with HIS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 2.9 26.0 + - + +
259B ASP* 1.3 77.7 - - + +
261B ASP* 1.3 94.4 + - - +
263B VAL* 3.6 7.7 + - - +
264B ARG* 3.3 29.8 + - + +
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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
----------------------------------------------------------
238B PHE* 3.4 8.1 - - + -
257B TRP* 3.7 35.0 - - + -
258B PRO* 3.0 17.5 + - + +
260B HIS* 1.3 106.0 + - - +
262B ALA* 1.3 56.0 + - - +
264B ARG* 3.2 31.8 + - - +
265B ILE* 3.0 32.2 + - - +
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Residues in contact with ALA 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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254B LEU* 3.9 23.4 - - + +
257B TRP* 4.0 6.5 - - + +
258B PRO 3.1 11.7 + - - +
259B ASP 3.8 6.1 - - - +
261B ASP* 1.3 75.1 - - - +
263B VAL* 1.3 60.9 + - - +
265B ILE* 3.6 5.6 + - - +
266B LEU* 2.9 35.3 + - - +
312B ARG* 3.9 24.5 - - - +
320B LEU* 4.3 9.6 - - + -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP* 3.0 20.9 + - + +
260B HIS* 3.8 7.6 - - - +
262B ALA* 1.3 74.1 - - - +
264B ARG* 1.3 61.6 + - + +
266B LEU* 3.3 6.3 + - - +
267B THR* 2.9 38.8 + - - +
320B LEU* 3.8 22.9 - - + +
323B SER* 3.7 48.5 - - - +
324B ALA* 4.0 1.0 - - - +
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 3.5 55.3 + - + +
260B HIS* 3.3 18.4 + - + +
261B ASP* 3.2 33.4 + - - +
263B VAL* 1.3 78.5 - - + +
265B ILE* 1.3 63.1 + - - +
267B THR* 3.3 7.6 + - - -
268B ARG* 3.0 28.8 + - - +
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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
----------------------------------------------------------
185B VAL* 4.8 0.9 - - + -
237B PHE* 3.4 50.3 - - + +
238B PHE* 3.5 17.5 - - + -
250B LEU* 3.9 27.6 - - + -
253B VAL* 4.5 2.0 - - + -
254B LEU* 4.0 11.4 - - + -
257B TRP* 3.6 28.3 - - + -
261B ASP 3.0 20.9 + - - +
262B ALA* 3.7 7.4 - - - +
264B ARG* 1.3 77.9 - - - +
266B LEU* 1.3 60.6 + - - +
268B ARG* 3.3 3.8 + - - +
269B CYS* 3.1 30.1 + - - -
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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
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250B LEU* 3.6 26.7 - - + -
254B LEU* 4.0 14.1 - - + -
262B ALA 2.9 24.1 + - - +
263B VAL* 3.8 1.1 - - - +
264B ARG 3.3 0.2 - - - -
265B ILE* 1.3 76.5 - - - +
267B THR* 1.3 57.2 + - - +
269B CYS* 3.4 5.1 + - - +
270B ALA* 3.0 27.2 + - - +
279B ILE* 4.2 16.2 - - + -
281B ILE* 4.5 2.2 - - + -
317B TRP* 5.8 0.2 - - + -
320B LEU* 4.0 41.5 - - + +
321B ALA* 4.9 5.4 - - - +
324B ALA* 3.6 19.5 - - + -
326B LEU* 4.0 13.8 - - + +
348B LEU* 4.4 10.1 - - + -
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 2.9 25.6 + - - +
264B ARG* 3.5 8.5 - - - -
266B LEU* 1.3 76.2 - - - +
268B ARG* 1.3 62.0 + - - +
270B ALA* 3.1 8.6 + - + +
271B GLU* 2.9 49.8 + - + +
323B SER 4.9 0.7 + - - -
324B ALA* 3.9 19.6 + - - +
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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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237B PHE 3.4 16.2 - - - +
238B PHE 3.0 24.9 + - - -
239B GLU* 3.0 34.9 + - - +
240B PRO* 3.3 36.0 - - + +
241B LEU* 3.3 22.7 + - + +
264B ARG* 3.0 15.7 + - - +
265B ILE 3.5 9.6 - - - +
267B THR* 1.3 77.9 - - - +
269B CYS* 1.3 61.1 + - - +
271B GLU* 3.2 31.3 + - - +
272B ALA* 3.3 14.7 + - - +
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Residues in contact with CYS 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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185B VAL* 4.2 9.9 - - - -
237B PHE* 6.3 0.2 - - - -
241B LEU* 3.7 9.6 - - - -
248B ILE* 3.4 33.5 - - + +
250B LEU* 3.9 33.0 - - - -
265B ILE* 3.1 27.2 + - - -
266B LEU* 3.5 8.3 - - - +
267B THR 3.2 0.2 - - - -
268B ARG* 1.3 75.0 - - - +
270B ALA* 1.3 64.7 + - - +
272B ALA 3.3 1.7 + - - -
273B LEU* 3.3 18.5 + - - +
279B ILE* 3.7 18.1 - - + +
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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 LEU 3.0 14.7 + - - +
267B THR* 3.1 11.6 + - + +
269B CYS* 1.3 75.8 - - - +
271B GLU* 1.3 61.5 + - + +
273B LEU* 3.4 19.8 + - - +
279B ILE* 3.7 7.1 - - - +
324B ALA 4.4 8.3 - - - +
325B GLY 5.6 0.7 - - - +
326B LEU* 4.0 23.3 - - + -
350B PRO* 6.5 0.2 - - + -
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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
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240B PRO* 5.5 1.4 - - - +
244B LYS* 3.6 18.7 + - - -
267B THR* 2.9 37.4 + - + +
268B ARG* 3.2 39.9 + - - +
269B CYS 3.2 0.4 - - - -
270B ALA* 1.3 77.5 - - + +
272B ALA* 1.3 58.3 - - - +
273B LEU 3.3 2.3 + - - +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.8 23.3 - - + +
243B ARG 3.6 20.2 - - - +
244B LYS* 3.0 18.7 - - - +
245B ALA 2.9 26.5 + - - -
248B ILE* 4.0 6.5 - - + -
268B ARG 3.3 14.3 + - - +
269B CYS 3.3 3.3 + - - +
270B ALA 3.3 0.4 - - - -
271B GLU* 1.3 77.4 - - - +
273B LEU* 1.3 57.4 + - - +
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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