Contacts of the helix formed by residues 253 - 266 (chain A) in PDB entry 1LTQ
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 LYS 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO* 6.5 0.4 - - + -
117A THR* 4.1 31.2 + - + +
246A ARG* 3.7 0.4 - - - +
252A ARG* 1.3 76.5 - - - +
254A ASP* 1.3 66.5 + - - +
255A ASP* 2.9 20.1 + - + +
256A VAL* 3.1 10.8 + - + +
257A VAL* 3.0 19.6 + - - +
281A GLN* 3.9 11.9 - - - +
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Residues in contact with ASP 254 (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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212A GLY* 3.4 28.5 - - - +
246A ARG* 2.6 34.8 + - - +
253A LYS* 1.3 69.9 - - - +
255A ASP* 1.3 55.4 + - - +
257A VAL* 3.8 2.7 - - - -
258A LYS* 2.8 44.6 + - - +
279A ARG* 2.8 38.0 + - - +
281A GLN* 3.7 7.6 - - - +
282A VAL* 4.0 15.8 - - + +
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Residues in contact with ASP 255 (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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116A TRP* 5.0 5.7 - - - +
117A THR* 4.4 18.7 + - - +
253A LYS* 3.7 11.2 - - + -
254A ASP* 1.3 78.4 - - - +
256A VAL* 1.3 67.5 + - + +
259A GLU* 3.5 14.7 + - - +
281A GLN* 2.8 47.8 + - - +
282A VAL* 5.2 2.5 - - - -
285A MSE 3.8 20.8 - - - +
288A ARG* 3.5 24.0 + - - -
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 3.5 39.9 - - + +
253A LYS* 3.1 13.8 + - + +
255A ASP* 1.3 85.0 - - + +
257A VAL* 1.3 66.6 + - - +
259A GLU* 3.2 6.2 + - - +
260A GLU* 3.1 23.3 + - + +
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Residues in contact with VAL 257 (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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211A SER 5.5 0.7 - - - +
212A GLY* 5.5 2.7 - - - -
246A ARG* 3.4 46.4 - - + +
250A ASP* 3.0 29.6 - - - +
252A ARG* 3.9 13.9 - - + +
253A LYS 3.0 16.2 + - - +
254A ASP* 3.7 4.5 - - - +
256A VAL* 1.3 77.3 - - - +
258A LYS* 1.3 60.2 + - + +
260A GLU* 3.5 3.4 + - - +
261A ILE* 2.7 51.8 + - + +
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Residues in contact with LYS 258 (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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165A ASP* 2.7 34.2 + - - +
210A VAL* 4.0 23.6 - - + +
211A SER 5.3 0.4 - - - +
212A GLY* 3.8 24.0 - - - +
254A ASP* 2.8 30.8 + - - +
257A VAL* 1.3 77.9 - - + +
259A GLU* 1.3 58.0 + - - +
261A ILE* 3.5 9.7 + - - +
262A PHE* 2.9 26.2 + - - +
277A ASP* 3.1 22.2 + - - +
282A VAL* 3.7 26.1 - - + +
285A MSE 3.6 16.2 - - + -
286A TRP* 4.4 10.6 - - + -
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Residues in contact with GLU 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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144A ARG* 4.9 8.4 + - - -
149A LEU* 5.9 1.2 - - - +
150A PRO* 4.4 8.8 - - - +
255A ASP 3.5 11.5 + - - +
256A VAL* 3.2 9.4 + - - +
258A LYS* 1.3 75.1 - - - +
260A GLU* 1.3 66.7 + - - +
262A PHE* 3.1 5.1 + - - +
263A TRP* 2.9 61.6 + - + +
285A MSE 3.9 25.6 - - - +
288A ARG* 5.1 3.6 + - - -
289A ILE* 3.6 28.8 - - + +
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Residues in contact with GLU 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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247A GLU* 5.7 1.9 - - - +
252A ARG* 2.8 41.8 + - - +
256A VAL* 3.1 17.6 + - + +
257A VAL* 3.7 2.9 - - - +
259A GLU* 1.3 76.9 - - - +
261A ILE* 1.3 74.9 + - + +
262A PHE 3.2 0.2 + - - -
263A TRP* 3.3 5.3 + - - +
264A LYS* 3.0 31.6 + - + +
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Residues in contact with ILE 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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210A VAL* 4.7 13.9 - - + -
244A CYS* 3.5 31.4 - - + -
245A GLN* 4.7 16.8 - - - +
246A ARG* 5.5 0.7 - - - -
247A GLU* 5.6 8.1 - - - +
252A ARG* 5.7 0.4 - - - +
257A VAL* 2.7 41.3 + - + +
258A LYS* 3.6 9.6 - - - +
260A GLU* 1.3 90.0 - - + +
262A PHE* 1.3 56.0 + - - +
264A LYS* 5.0 0.2 - - - -
265A HIS* 2.9 42.0 + - + +
266A ILE* 3.0 18.9 - - + +
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Residues in contact with PHE 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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152A TYR* 3.8 20.9 - + - -
163A ILE* 3.9 16.6 - - + -
258A LYS 2.9 15.6 + - - +
259A GLU* 3.1 10.7 + - - +
261A ILE* 1.3 76.1 - - - +
263A TRP* 1.3 82.6 + + - +
266A ILE* 3.0 24.7 + - + -
267A ALA* 2.8 44.3 + - + -
272A VAL* 3.4 34.8 - - + -
286A TRP* 3.7 22.7 - + + -
289A ILE* 3.7 22.4 - - + -
291A VAL* 4.0 10.1 - - + -
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Residues in contact with TRP 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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150A PRO* 3.7 42.1 - - + +
151A VAL 4.0 1.6 - - - -
152A TYR* 3.7 40.8 - + + -
259A GLU* 2.9 56.7 + - + +
260A GLU* 4.1 5.4 - - - +
262A PHE* 1.3 97.5 - + - +
264A LYS* 1.3 60.8 + - - +
267A ALA* 4.0 9.4 - - + +
268A PRO* 3.3 17.3 - - - +
289A ILE* 4.3 10.1 - - + -
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Residues in contact with LYS 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 GLU* 3.0 21.8 + - + +
263A TRP* 1.3 81.7 - - - +
265A HIS* 1.3 79.7 + - + +
268A PRO* 3.5 14.2 - - - +
269A HIS* 4.7 3.1 + - - -
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Residues in contact with HIS 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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242A MSE 3.6 15.3 - - - +
244A CYS* 4.0 15.1 - - - +
247A GLU* 5.0 11.2 - - - -
261A ILE* 2.9 30.3 + - + +
264A LYS* 1.3 96.0 - - + +
266A ILE* 1.3 63.9 + - + +
268A PRO* 4.3 0.2 - - - -
269A HIS* 3.1 26.6 - - - +
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Residues in contact with ILE 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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161A ALA* 6.1 0.2 - - + -
163A ILE* 4.3 14.1 - - + -
208A VAL* 4.1 12.3 - - + -
210A VAL* 5.0 4.5 - - + -
242A MSE 3.1 24.0 - - + -
244A CYS* 3.8 4.3 - - + -
261A ILE* 3.0 42.6 - - + +
262A PHE* 3.0 29.5 + - + +
264A LYS 3.9 0.2 - - - -
265A HIS* 1.3 78.6 - - - +
267A ALA* 1.3 67.9 + - - +
268A PRO* 3.2 2.7 - - - -
269A HIS* 2.8 15.9 + - - -
270A PHE* 3.0 33.3 + - + -
272A VAL* 4.7 4.9 - - + -
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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