Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 1L7R
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 PHE 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A SER* 4.5 9.9 - - - -
121A VAL* 4.4 17.5 - - + -
141A MET 3.4 17.5 - - - +
142A ALA 3.5 17.3 - - - +
143A SER* 3.7 20.2 - - - -
149A ALA* 4.2 10.8 - - + -
150A PRO* 3.6 35.4 - - + -
259A ASP* 2.9 18.2 + - - +
260A GLY* 1.3 78.5 - - - +
262A VAL* 1.3 59.8 + - - +
263A GLY 3.4 2.5 - - - -
264A GLU* 3.0 6.7 + - - -
265A SER* 2.8 28.1 + - - -
287A HIS* 3.6 26.2 - + - -
407A LEU* 4.3 16.6 - - + -
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Residues in contact with VAL 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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255A ALA* 4.4 8.3 - - + -
256A GLY 3.1 32.3 - - - +
257A TRP* 4.2 23.8 - - + +
259A ASP* 3.0 18.5 + - - +
260A GLY 3.4 0.4 - - - -
261A PHE* 1.3 76.7 - - - +
263A GLY* 1.3 73.6 + - - +
265A SER* 3.7 5.8 - - - -
266A LEU* 3.0 43.2 + - + +
282A VAL* 5.1 0.2 - - + -
405A THR* 4.2 2.0 - - + -
508A LEU* 3.7 26.2 - - + -
509A ALA* 5.3 3.8 - - + +
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Residues in contact with GLY 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 GLY 5.0 0.8 + - - -
261A PHE 3.4 0.6 - - - -
262A VAL* 1.3 84.9 - - - +
264A GLU* 1.3 62.1 + - - +
266A LEU* 3.6 7.3 + - - +
267A ARG* 3.1 32.4 + - - +
508A LEU* 4.0 30.6 - - - +
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Residues in contact with GLU 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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142A ALA 4.0 1.8 - - - -
143A SER* 3.3 27.3 + - - +
144A ALA 4.7 1.1 + - - +
145A ASP* 3.5 20.3 + - - +
148A ARG* 2.7 46.7 + - + +
149A ALA* 3.3 24.8 - - + +
154A PRO* 4.8 4.2 - - - +
241A PHE* 4.7 6.6 - - - -
261A PHE 3.0 6.2 + - - +
263A GLY* 1.3 75.3 - - - +
265A SER* 1.3 65.4 + - - +
267A ARG* 3.3 22.7 + - - +
268A THR* 3.1 28.4 + - - +
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Residues in contact with SER 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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141A MET* 3.8 5.5 - - - -
142A ALA 2.6 36.0 + - - -
253A ILE* 3.7 14.0 - - - +
254A THR 4.3 5.2 - - - -
255A ALA* 3.7 25.6 - - - +
261A PHE 2.8 22.9 + - - -
262A VAL 3.7 1.6 - - - -
264A GLU* 1.3 71.4 - - - +
266A LEU* 1.3 63.9 + - - +
268A THR* 2.6 26.7 + - - -
269A PHE 3.4 3.3 + - - -
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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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255A ALA* 4.8 2.7 - - + -
257A TRP* 4.3 5.2 - - + -
262A VAL* 3.0 34.3 + - + +
263A GLY* 3.8 6.1 - - - +
265A SER* 1.3 78.8 - - - +
267A ARG* 1.3 62.1 + - + +
269A PHE* 3.1 16.6 + - - +
270A VAL* 3.2 17.5 + - - +
280A LEU* 3.7 32.3 - - + -
282A VAL* 4.0 17.5 - - + -
351A TRP* 3.7 27.7 - - + +
444A THR* 5.6 3.1 - - + -
509A ALA* 3.6 31.4 - - + -
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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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148A ARG* 3.7 33.8 - - - +
241A PHE* 3.5 44.8 - - + -
263A GLY 3.1 17.4 + - - +
264A GLU* 3.3 30.1 + - - +
265A SER 3.3 0.4 - - - -
266A LEU* 1.3 76.9 - - + +
268A THR* 1.3 62.0 + - - +
270A VAL* 3.3 10.2 + - + +
271A ALA* 3.0 23.2 + - - +
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Residues in contact with THR 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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124A TRP* 3.4 28.9 + - - +
142A ALA 5.4 0.2 - - - +
143A SER* 4.8 0.9 - - - -
144A ALA* 3.8 33.7 - - + +
241A PHE* 4.4 3.8 - - + -
244A LEU* 3.9 10.8 - - + -
253A ILE* 3.4 15.8 - - - +
264A GLU 3.1 15.5 + - - +
265A SER* 2.6 21.3 + - - -
267A ARG* 1.3 73.4 - - - +
269A PHE* 1.3 65.0 + - - +
271A ALA* 3.2 1.8 + - - +
272A VAL* 3.1 28.9 + - - +
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Residues in contact with PHE 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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253A ILE* 3.4 14.6 - - + -
265A SER 3.4 3.5 + - - +
266A LEU* 3.1 10.2 + - - +
268A THR* 1.3 81.6 + - - +
270A VAL* 1.3 58.5 + - - +
272A VAL* 3.7 1.4 - - - +
273A LYS* 2.9 53.7 + - + +
278A ALA* 3.6 38.8 - - + -
279A ARG* 3.7 16.8 - - - -
280A LEU* 3.7 25.6 - - + -
334A LYS* 4.4 8.1 - - + -
335A VAL* 3.8 17.9 - - + -
350A ASP* 3.9 3.6 - - - -
351A TRP* 3.7 45.8 - + + -
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Residues in contact with VAL 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 3.2 14.0 + - - +
267A ARG* 3.7 9.6 - - - +
269A PHE* 1.3 77.8 - - - +
271A ALA* 1.3 60.9 + - - +
272A VAL 3.5 0.3 + - - -
273A LYS* 3.6 29.3 - - - +
274A ASP* 4.4 6.9 - - - +
351A TRP* 3.7 33.7 - - + +
352A PRO* 4.2 9.4 - - + -
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Residues in contact with ALA 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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241A PHE* 3.9 23.8 - - + +
244A LEU* 4.0 18.6 - - + +
245A GLY* 3.8 23.5 - - - +
267A ARG 3.0 16.3 + - - +
268A THR 3.6 5.2 - - - +
269A PHE 3.2 0.4 - - - -
270A VAL* 1.3 79.4 - - - +
272A VAL* 1.3 58.9 + - - +
274A ASP* 5.2 2.4 + - - +
275A ASN* 5.5 2.9 - - - +
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Residues in contact with VAL 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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124A TRP* 4.0 26.2 - - + -
244A LEU* 4.1 22.9 - - + +
247A LEU* 5.3 7.0 - - + +
249A THR 4.8 11.4 - - - +
251A ALA* 4.4 6.3 - - + -
253A ILE* 4.3 8.7 - - + -
268A THR 3.1 17.7 + - - +
269A PHE* 3.7 7.0 - - - +
271A ALA* 1.3 80.0 - - - +
273A LYS* 1.3 68.4 + - - +
274A ASP 3.1 4.4 + - - -
275A ASN* 3.2 15.7 + - - +
276A ALA* 3.3 15.1 + - + +
278A ALA* 3.8 16.6 - - + -
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Residues in contact with LYS 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 PHE* 2.9 35.6 + - + +
270A VAL* 3.6 23.7 - - - +
271A ALA 3.8 0.2 - - - -
272A VAL* 1.3 77.2 - - - +
274A ASP* 1.3 76.6 + - - +
276A ALA 3.2 13.4 - - - +
278A ALA* 3.7 18.6 + - + -
334A LYS* 5.5 7.5 - - - -
350A ASP* 3.0 34.3 + - - +
351A TRP 2.8 25.2 + - - +
352A PRO* 4.0 8.1 - - - +
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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