Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 4TR8
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 ARG 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A GLY 3.4 4.2 + - - -
260A ASP* 1.4 70.4 - - - +
262A GLN* 1.3 91.4 + - - +
264A LEU* 3.8 2.3 - - - +
265A ARG* 2.9 45.4 + - - +
329A LEU* 2.9 41.2 + - + +
330A GLY* 4.4 4.2 + - - +
332A ILE* 3.2 39.2 + - + -
333A GLY 5.4 0.6 - - - -
334A THR 3.6 15.7 + - - +
335A GLU* 2.8 22.8 + - - +
337A VAL* 4.1 14.6 - - + -
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Residues in contact with GLN 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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260A ASP* 3.4 8.0 + - - +
261A ARG* 1.3 99.6 + - - +
263A GLN* 1.3 61.1 + - - +
265A ARG* 3.3 3.5 + - + +
266A GLU* 2.9 66.5 + - + +
335A GLU* 4.5 0.8 + - - +
1001A NA 4.0 6.7 - - - -
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Residues in contact with GLN 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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260A ASP* 2.9 32.1 + - + +
262A GLN* 1.3 74.7 - - - +
264A LEU* 1.4 57.1 + - - +
266A GLU* 3.5 8.3 + - - +
267A ALA* 2.9 31.6 + - + +
270A ARG* 4.8 3.7 + - - +
305A GLU* 5.6 4.2 + - - +
306A GLU 5.3 1.8 + - - -
307A VAL* 3.6 35.2 - - + +
308A GLN* 4.4 9.2 + - - +
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Residues in contact with LEU 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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257A VAL* 5.8 2.5 - - + -
259A GLY* 4.0 14.1 - - - -
260A ASP 2.9 21.6 + - - +
261A ARG 3.8 3.1 - - - +
263A GLN* 1.4 73.2 - - - +
265A ARG* 1.4 58.9 + - - +
267A ALA* 3.2 3.7 + - - +
268A PHE* 2.8 47.3 + - + -
291A LEU* 3.6 31.2 - - + -
293A ILE* 5.0 0.4 - - + -
307A VAL* 3.9 23.6 - - + -
309A VAL* 4.4 6.5 - - + -
329A LEU* 4.1 9.2 - - + -
337A VAL* 3.6 28.5 - - + -
339A PHE* 4.1 15.9 - - + -
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Residues in contact with ARG 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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261A ARG* 2.9 38.4 + - - +
262A GLN* 3.8 6.1 - - + +
264A LEU* 1.4 71.1 - - - +
266A GLU* 1.3 59.7 + - + +
268A PHE 3.4 0.2 + - - -
269A SER* 2.9 36.3 + - - -
326A LEU* 2.9 60.7 + - + +
327A ASP* 5.2 2.2 + - - +
329A LEU* 3.6 27.7 - - + +
330A GLY* 3.6 11.3 - - - +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLN* 2.9 55.2 + - + +
263A GLN* 3.9 6.3 - - - +
265A ARG* 1.3 76.9 - - + +
267A ALA* 1.3 58.3 + - - +
269A SER* 3.5 6.0 + - - -
270A ARG* 3.0 53.9 + - - +
81B SER 5.5 1.1 - - - +
83B PRO* 6.2 0.2 - - - +
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Residues in contact with ALA 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 GLN 2.9 19.2 + - - +
264A LEU 3.7 2.9 - - - +
266A GLU* 1.3 72.9 - - - +
268A PHE* 1.3 65.4 + - - +
270A ARG* 3.4 2.9 + - - +
271A THR* 3.0 31.3 + - - +
293A ILE* 3.6 21.5 - - + -
305A GLU* 3.5 32.1 - - - +
307A VAL* 3.7 9.4 - - + -
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Residues in contact with PHE 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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264A LEU* 2.8 32.6 + - + +
265A ARG* 4.5 0.2 - - - -
267A ALA* 1.3 71.6 - - - +
269A SER* 1.4 57.6 + - - +
271A THR* 3.1 5.6 + - - -
272A ALA* 2.9 31.5 + - - +
282A ILE* 3.5 23.8 - - + -
284A LEU* 4.4 13.5 - - + -
291A LEU* 4.3 12.6 - - + -
293A ILE* 3.8 29.4 - - + -
322A VAL* 3.4 18.5 - - + +
325A LEU* 3.9 30.1 - - + -
326A LEU* 3.7 9.0 - - + -
329A LEU* 3.5 28.3 - - + -
339A PHE* 4.5 13.9 - + - -
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Residues in contact with SER 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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265A ARG* 2.9 22.9 + - - -
266A GLU* 3.8 7.6 - - - -
267A ALA 3.3 0.2 - - - -
268A PHE* 1.4 76.8 - - - +
270A ARG* 1.3 62.2 + - - +
272A ALA* 3.4 18.5 - - - +
273A ILE* 3.6 11.7 + - - +
326A LEU* 3.8 18.7 - - - +
81B SER* 5.6 3.6 - - - -
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Residues in contact with ARG 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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263A GLN* 4.8 4.9 + - - +
266A GLU* 3.0 37.0 + - - +
267A ALA* 3.4 14.5 + - - +
269A SER* 1.3 73.7 - - - +
271A THR* 1.3 63.6 + - + +
273A ILE* 3.2 30.9 + - - +
274A LEU 4.5 0.2 + - - -
305A GLU* 2.7 43.0 + - - +
81B SER* 2.9 50.5 + - - +
82B LEU* 3.8 20.8 - - - +
83B PRO* 3.7 25.8 - - - +
104B SER* 3.6 6.4 + - - -
106B PHE* 3.8 19.1 - - + -
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Residues in contact with THR 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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267A ALA 3.0 17.8 + - - +
268A PHE* 3.1 8.7 + - - -
270A ARG* 1.3 75.0 - - + +
272A ALA* 1.4 59.9 + - - +
274A LEU 3.1 12.6 + - - -
282A ILE* 4.2 4.5 - - - +
293A ILE* 3.2 31.9 - - + +
295A ALA* 3.1 24.2 - - - +
303A ALA* 3.6 21.2 - - + +
304A GLU 4.3 4.9 - - - +
305A GLU* 3.8 34.5 - - + +
106B PHE* 5.6 1.8 - - + -
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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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268A PHE 2.9 20.2 + - - +
269A SER* 3.4 11.2 - - - +
271A THR* 1.4 73.4 + - - +
273A ILE* 1.3 64.4 + - - +
274A LEU 3.1 0.2 - - - -
275A SER* 2.8 30.1 + - - +
280A ARG* 3.3 23.2 + - - +
282A ILE* 4.5 1.8 - - - -
322A VAL* 3.5 27.4 - - + -
326A LEU* 5.0 0.2 - - + -
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Residues in contact with ILE 273 (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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269A SER 3.7 8.1 - - - +
270A ARG* 3.4 20.2 - - - +
271A THR 3.1 0.8 + - - -
272A ALA* 1.3 77.1 - - - +
274A LEU* 1.3 72.4 + - + +
275A SER 3.8 3.5 + - - +
280A ARG* 5.3 1.1 - - - +
297A ASN* 5.0 0.5 + - - -
74B LYS* 4.3 24.5 - - + +
77B ASP* 3.6 42.8 - - + +
78B ILE* 3.8 23.6 - - + +
81B SER* 3.7 16.8 - - - +
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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