Contacts of the helix formed by residues 258 - 269 (chain A) in PDB entry 1LHA
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A SER* 6.3 2.7 - - - -
196A ASP 2.5 34.3 - - - +
197A ALA* 4.0 7.2 - - + -
198A GLY* 3.7 24.2 - - - -
254A VAL* 4.4 2.9 - - + -
255A THR* 2.8 9.4 + - - +
257A GLU* 1.3 95.1 - - + +
259A GLN* 1.3 61.2 + - - +
260A PRO* 3.7 1.1 - - - -
261A VAL* 2.8 43.3 - - + +
262A TYR* 3.2 19.8 - - + -
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Residues in contact with GLN 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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254A VAL* 3.9 15.6 - - + +
255A THR 3.2 3.9 + - - +
256A GLU* 3.2 25.5 + - - +
258A PHE* 1.3 76.5 - - - +
260A PRO* 1.3 62.9 - - + +
261A VAL 2.8 2.2 + - - -
262A TYR* 2.7 29.5 + - - +
263A LYS* 2.7 47.0 + - - +
274A VAL* 3.9 23.4 + - - +
275A GLY 4.7 0.6 - - - +
276A THR* 3.7 32.0 + - - +
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Residues in contact with PRO 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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256A GLU* 3.7 12.8 - - - +
257A GLU 5.0 4.0 - - - +
258A PHE* 3.9 1.1 - - - -
259A GLN* 1.3 94.1 - - + +
261A VAL* 1.3 67.0 + - + +
263A LYS* 3.3 37.0 + - - +
264A GLU* 3.8 11.4 + - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLY* 5.7 2.7 - - - -
199A PHE* 5.6 4.5 - - + -
257A GLU 5.5 1.1 - - - +
258A PHE* 2.8 49.4 - - + +
259A GLN 2.8 5.1 + - - -
260A PRO* 1.3 76.2 - - + +
262A TYR* 1.3 70.6 + - + +
263A LYS 3.0 5.7 + - - -
264A GLU* 3.1 11.5 + - - +
265A LEU* 2.7 32.1 - - + +
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Residues in contact with TYR 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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169A PHE* 4.8 2.9 - + - -
193A PHE* 3.9 19.1 - + - -
195A THR* 3.6 20.9 - - + +
197A ALA 3.1 27.4 + - - -
198A GLY* 3.3 10.7 + - - -
199A PHE* 3.6 27.9 - + + +
252A PHE* 3.5 34.7 - + + -
254A VAL* 3.9 20.0 - - + -
258A PHE* 3.2 25.8 - - + -
259A GLN 2.7 13.3 + - - +
261A VAL* 1.3 86.4 - - + +
263A LYS* 1.3 55.1 + - - +
265A LEU* 3.5 15.5 - - + +
266A LYS* 2.9 30.9 + - - +
274A VAL* 4.0 4.7 - - + -
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Residues in contact with LYS 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 GLN* 2.7 38.3 + - - +
260A PRO* 3.3 27.2 - - - +
261A VAL 3.0 0.4 + - - -
262A TYR* 1.3 75.7 - - - +
264A GLU* 1.3 59.1 + - - +
266A LYS* 2.9 12.8 + - - +
267A ASN* 2.7 32.9 + - - +
274A VAL* 3.6 22.7 - - + -
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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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260A PRO 4.1 11.2 - - - +
261A VAL* 3.1 9.0 + - - +
263A LYS* 1.3 79.9 - - + +
265A LEU* 1.3 64.5 + - + +
267A ASN* 3.3 21.2 + - - +
268A LEU* 3.2 29.8 + - - +
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Residues in contact with LEU 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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169A PHE* 4.2 9.0 - - + -
199A PHE* 2.9 46.0 - - + -
236A ILE* 5.9 7.0 - - + -
252A PHE* 4.3 7.4 - - + -
261A VAL* 2.7 31.9 - - + +
262A TYR* 3.5 30.1 - - + +
264A GLU* 1.3 81.8 - - + +
266A LYS* 1.3 58.7 + - - +
268A LEU* 3.4 9.1 + - + +
269A ILE* 3.0 40.1 + - + +
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Residues in contact with LYS 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 THR* 3.7 15.4 + - - -
251A ILE 3.7 0.2 - - - -
252A PHE* 2.7 54.4 - - + +
262A TYR 2.9 19.5 + - - +
263A LYS* 2.9 11.8 + - - +
265A LEU* 1.3 74.4 - - - +
267A ASN* 1.3 52.7 + - - +
268A LEU 3.0 4.0 - - - -
269A ILE* 2.6 36.2 + - + +
270A PRO* 4.2 1.9 - - - +
272A SER* 3.1 28.0 - - - +
273A ALA 2.9 31.9 + - - +
274A VAL* 3.1 20.0 - - + -
434A ARG* 5.1 2.9 + - - -
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Residues in contact with ASN 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 LYS 2.7 15.2 + - - +
264A GLU* 3.3 27.2 + - - +
266A LYS* 1.3 72.1 - - - +
268A LEU* 1.3 60.6 + - + +
269A ILE 4.9 0.2 - - - -
270A PRO* 5.0 0.5 - - - +
431A ALA* 3.5 16.1 - - - +
432A TYR* 2.6 57.7 + - - +
434A ARG* 5.5 6.6 + - - +
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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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236A ILE* 4.9 28.0 - - + +
240A VAL* 4.2 8.8 - - - +
264A GLU* 3.2 14.5 + - + +
265A LEU* 3.7 10.8 - - + +
266A LYS 3.0 0.8 - - - -
267A ASN* 1.3 82.1 - - - +
269A ILE* 1.3 60.1 + - + +
270A PRO* 3.1 14.9 - - - +
432A TYR* 3.2 39.7 - - + -
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Residues in contact with ILE 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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169A PHE* 5.2 9.6 - - + -
236A ILE* 4.4 17.5 - - + +
239A LEU* 5.1 9.0 - - + -
240A VAL* 4.2 23.8 - - + +
243A LEU* 4.1 22.9 - - + -
250A THR* 4.7 0.9 - - - +
252A PHE* 4.8 17.9 - - + -
265A LEU* 3.0 24.9 + - + +
266A LYS 2.6 15.0 + - - +
268A LEU* 1.3 79.7 - - + +
270A PRO* 1.3 67.1 - - + +
272A SER* 2.7 46.7 + - - +
434A ARG* 5.4 0.2 + - - -
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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