Contacts of the helix formed by residues 261 - 270 (chain A) in PDB entry 1H3F
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 LEU 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A VAL* 3.7 29.4 - - + +
226A GLY 3.2 27.4 - - - +
229A GLY* 3.9 15.7 - - - +
257A VAL* 3.8 9.0 - - + -
258A PRO* 2.8 42.7 + - + +
260A PRO* 1.3 74.3 - - + +
262A LEU* 1.3 64.9 + - - -
263A PRO* 3.2 2.9 - - - -
264A SER* 2.9 31.1 + - - +
265A TYR* 2.9 28.1 + - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.8 3.8 - - + +
258A PRO 3.6 1.8 + - - +
259A ASP* 3.1 26.2 + - + +
261A LEU* 1.3 76.9 - - - +
263A PRO* 1.3 71.4 - - + +
265A TYR* 3.2 3.8 + - - +
266A PHE* 3.0 40.7 + - + -
281A LEU* 4.1 15.9 - - + -
285A PRO* 4.4 6.7 - - + +
288A ALA* 3.8 22.4 - - + -
289A HIS* 3.8 42.0 - - + +
292A LEU* 3.9 24.5 - - + -
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Residues in contact with PRO 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 3.7 4.7 - - - +
260A PRO* 3.4 18.2 - - + +
261A LEU 3.4 0.4 - - - -
262A LEU* 1.3 94.0 - - + +
264A SER* 1.3 60.2 + - - +
266A PHE* 3.5 2.4 + - - +
267A ARG* 3.0 55.5 + - - +
277A ILE* 4.8 11.3 - - + +
281A LEU* 4.1 21.7 - - + -
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Residues in contact with SER 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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224A LEU* 5.1 1.3 - - - +
225A VAL* 5.6 3.1 + - - +
260A PRO 5.1 0.8 + - - -
261A LEU* 2.9 29.2 + - - +
263A PRO* 1.3 77.0 - - - +
265A TYR* 1.3 69.2 + - - +
267A ARG* 3.9 10.0 - - - +
268A LEU* 2.9 46.4 + - - +
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Residues in contact with TYR 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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53A LEU* 4.8 6.1 - - + -
224A LEU* 3.6 20.6 - - + -
225A VAL 2.8 29.6 + - - -
226A GLY 3.8 9.2 - - - -
227A LEU* 4.1 5.8 + - + +
233A MET* 3.4 19.3 - - + +
241A ILE* 5.0 0.2 - - + -
254A LEU* 4.8 4.0 - - + -
257A VAL* 3.8 33.4 - - + -
261A LEU* 2.9 38.7 + - + +
262A LEU* 3.2 5.6 + - - +
264A SER* 1.3 82.2 + - - +
266A PHE* 1.3 59.3 + - - +
269A LEU* 2.8 61.2 + - + +
270A THR* 4.5 0.5 - - - +
292A LEU* 4.3 22.0 - - + -
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Residues in contact with PHE 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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262A LEU* 3.0 43.7 + - + +
263A PRO 3.9 2.2 - - - +
265A TYR* 1.3 78.3 - - - +
267A ARG* 1.3 58.3 + - - +
270A THR* 2.5 46.2 + - + +
272A LEU* 3.7 22.5 + - + +
277A ILE* 3.6 36.3 - - + +
280A LEU* 3.7 28.0 - - + -
281A LEU* 5.0 3.6 - - + -
288A ALA* 3.5 33.0 - - + -
291A VAL* 4.7 0.2 - - + -
292A LEU* 3.7 28.0 - - + -
295A LEU* 4.7 4.0 - - + -
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Residues in contact with ARG 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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18A GLY* 5.1 9.9 - - - -
263A PRO* 3.0 55.5 + - - +
264A SER* 3.9 8.6 - - - +
265A TYR 3.3 0.2 - - - -
266A PHE* 1.3 77.1 - - - +
268A LEU* 1.3 68.1 + - + +
270A THR 3.5 13.5 - - - +
272A LEU 5.8 1.1 - - - -
274A GLU* 3.0 38.9 + - - +
277A ILE* 4.1 12.9 - - + +
278A GLU* 4.7 9.3 + - - -
281A LEU* 6.3 0.2 - - - +
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Residues in contact with LEU 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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18A GLY* 4.3 12.3 - - - +
56A ALA 5.0 1.0 - - - +
57A VAL* 4.0 33.8 - - + +
60A ARG* 4.4 8.1 + - - +
221A MET* 5.2 1.3 - - + -
222A PRO* 3.2 46.7 - - + +
223A LEU 4.5 2.2 - - - +
224A LEU* 4.2 33.2 - - + +
264A SER* 2.9 27.4 + - - +
267A ARG* 1.3 83.7 - - + +
269A LEU* 1.3 65.8 + - - +
270A THR 3.7 0.4 - - - -
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Residues in contact with LEU 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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53A LEU* 3.6 43.3 - - + +
56A ALA* 4.5 9.9 - - + -
57A VAL* 4.2 9.2 - - + -
60A ARG* 3.4 17.9 + - - +
224A LEU* 4.2 12.6 - - + -
265A TYR* 2.8 52.9 + - + +
268A LEU* 1.3 82.0 - - - +
270A THR* 1.3 62.8 + - + +
296A LEU* 3.7 39.1 - - + +
300A TYR* 5.3 1.5 + - + +
309A ILE* 3.8 8.7 - - - +
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Residues in contact with THR 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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60A ARG* 4.0 5.8 + - - +
266A PHE* 2.5 50.9 + - + +
267A ARG* 3.5 12.0 - - - +
269A LEU* 1.3 84.5 - - - +
271A ASP* 1.3 69.6 + - - +
272A LEU* 3.3 21.6 + - - +
292A LEU* 4.4 7.2 - - + -
295A LEU* 4.3 10.3 - - + -
296A LEU* 4.3 10.1 - - + -
309A ILE* 3.6 24.2 - - + -
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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