Contacts of the helix formed by residues 258 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 4.6 15.3 - - - +
256A ASN 4.4 1.8 - - - +
257A TRP* 1.3 93.7 - - + +
259A ASP* 1.3 67.0 + - - +
260A HIS* 3.1 29.8 + - + +
261A ASP* 3.1 21.7 + - - +
262A ALA* 3.1 6.6 + - - +
307A LEU 4.8 3.6 - - - +
308A GLY 3.6 25.5 - - - +
309A GLY* 4.8 0.9 - - - -
312A ARG* 4.7 2.5 - - - +
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Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PRO* 1.3 73.8 - - - +
260A HIS* 1.3 57.5 + - - +
262A ALA* 3.2 6.9 + - - +
263A VAL* 2.9 36.2 + - + +
312A ARG* 3.1 23.0 + - - +
320A LEU* 3.9 25.0 - - + +
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Residues in contact with HIS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 6.2 0.4 - - - -
258A PRO* 3.1 21.5 + - + +
259A ASP* 1.3 78.8 + - - +
261A ASP* 1.3 101.8 + - - +
263A VAL* 3.4 8.9 + - - +
264A ARG* 3.1 31.0 + - - +
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PHE* 3.6 14.6 - - + -
257A TRP* 3.7 22.0 - - + -
258A PRO* 3.1 18.1 + - + +
260A HIS* 1.3 106.5 + - - +
262A ALA* 1.3 56.3 + - - +
264A ARG* 2.8 39.0 + - - +
265A ILE* 3.1 33.0 + - - +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 3.7 24.5 - - + +
257A TRP* 4.1 12.5 - - + +
258A PRO 3.1 11.6 + - - +
259A ASP* 3.2 8.5 + - - +
261A ASP* 1.3 76.1 - - - +
263A VAL* 1.3 58.5 + - - +
265A ILE* 4.4 4.0 - - - -
266A LEU* 3.1 34.0 + - - +
312A ARG* 4.2 12.8 - - - +
320A LEU* 4.3 13.0 - - + -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ASP* 2.9 24.4 + - + +
260A HIS* 3.7 8.1 - - - +
261A ASP 3.3 0.2 - - - -
262A ALA* 1.3 75.7 - - - +
264A ARG* 1.3 54.8 + - - +
265A ILE 3.4 0.2 - - - -
266A LEU* 3.8 7.2 - - - +
267A THR* 2.7 41.9 + - - +
320A LEU* 4.2 21.3 - - + +
323A SER* 3.7 47.8 - - - +
324A ALA* 4.1 2.5 - - + +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PHE* 3.6 50.4 + - + +
260A HIS* 3.1 19.0 + - - +
261A ASP* 2.8 42.5 + - - +
263A VAL* 1.3 73.2 - - - +
265A ILE* 1.3 66.0 + - - +
267A THR* 3.3 6.6 + - - -
268A ARG* 3.1 28.8 + - + +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 4.9 1.8 - - + -
237A PHE* 3.5 47.5 - - + +
238A PHE* 3.6 17.7 - - + -
250A LEU* 3.7 30.7 - - + -
253A VAL* 4.3 4.7 - - + -
254A LEU* 3.9 12.1 - - + -
257A TRP* 3.6 27.4 - - + -
261A ASP 3.1 16.7 + - - +
262A ALA 3.9 4.3 - - - +
264A ARG* 1.3 74.9 - - - +
266A LEU* 1.3 65.3 + - - +
268A ARG* 3.3 4.0 + - - +
269A CYS* 3.2 23.2 + - - -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LEU* 3.8 22.9 - - + -
254A LEU* 3.9 18.6 - - + -
262A ALA 3.1 23.2 + - - +
263A VAL* 3.8 2.2 - - - +
265A ILE* 1.3 80.2 - - - +
267A THR* 1.3 55.7 + - - +
269A CYS* 3.3 5.8 + - - +
270A ALA* 3.0 26.7 + - - +
279A ILE* 4.5 7.0 - - + -
281A ILE* 4.2 9.4 - - + -
317A TRP* 4.8 4.3 - - + -
320A LEU* 3.9 35.4 - - + +
321A ALA* 4.5 2.0 - - - +
324A ALA* 3.7 16.4 - - + -
326A LEU* 4.1 19.0 - - + +
348A LEU* 4.3 11.9 - - + -
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A VAL* 2.7 27.7 + - - +
264A ARG* 3.7 7.4 - - - -
265A ILE 3.2 0.2 - - - -
266A LEU* 1.3 74.0 - - - +
268A ARG* 1.3 60.9 + - + +
270A ALA* 3.4 8.5 + - + +
271A GLU* 3.1 43.4 + - + +
323A SER 4.5 0.9 + - - -
324A ALA* 3.7 22.6 - - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE 3.7 22.2 - - - +
238A PHE 3.0 25.5 + - - +
239A GLU* 3.4 12.4 - - - +
240A PRO* 3.7 33.4 - - - +
241A LEU* 3.4 23.4 + - + +
264A ARG 3.1 18.2 + - - +
265A ILE 3.3 8.5 + - - +
267A THR* 1.3 73.8 - - + +
269A CYS* 1.3 62.9 + - - +
271A GLU* 3.3 33.0 + - - +
272A ALA* 3.3 15.9 + - - +
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 4.4 4.3 - - - -
241A LEU* 3.8 15.0 - - - -
248A ILE* 3.3 32.0 - - + +
250A LEU* 4.0 29.2 - - + -
265A ILE* 3.2 19.8 + - - -
266A LEU* 3.4 9.0 - - - +
268A ARG* 1.3 74.5 - - - +
270A ALA* 1.3 65.2 + - - +
272A ALA 3.0 10.7 + - - -
273A LEU* 3.1 11.3 + - - +
279A ILE* 3.5 21.3 - - + -
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU 3.0 13.1 + - - +
267A THR* 3.6 9.4 - - + +
269A CYS* 1.3 76.1 - - - +
271A GLU* 1.3 60.9 + - + +
273A LEU* 3.3 23.8 + - + +
279A ILE* 3.9 6.6 - - - +
324A ALA 4.2 13.0 - - - +
325A GLY 5.4 0.9 - - - +
326A LEU* 4.1 21.1 - - + -
350A PRO* 6.2 1.1 - - + +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 5.3 2.8 - - - +
244A LYS* 3.7 15.4 + - - -
267A THR* 3.1 33.6 + - + +
268A ARG* 3.3 43.3 + - - +
269A CYS 3.2 0.4 - - - -
270A ALA* 1.3 75.2 - - + +
272A ALA* 1.3 58.0 + - - +
273A LEU 3.4 2.8 - - - +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 3.8 14.8 - - + +
243A ARG 3.7 19.1 - - - +
244A LYS* 3.0 28.1 - - - +
245A ALA 3.0 14.0 + - - +
248A ILE* 3.7 14.5 - - + +
268A ARG 3.3 10.9 + - - +
269A CYS 3.0 9.7 + - - +
271A GLU* 1.3 78.5 - - + +
273A LEU* 1.3 58.7 + - - +
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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