Contacts of the helix formed by residues 263 - 278 (chain A) in PDB entry 4LT6
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 ALA 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO* 4.1 27.6 - - + +
34A ASP* 4.3 7.6 - - + +
35A HIS* 5.1 5.2 - - + +
38A THR* 3.4 10.3 - - + +
218A THR* 5.0 2.9 - - - -
262A ALA* 1.3 77.7 - - - +
264A ALA* 1.3 54.7 + - - +
265A SER* 3.1 19.5 - - - +
266A THR* 3.0 7.5 + - - +
267A LEU* 2.8 34.3 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.0 6.9 + - + +
41A LEU* 4.4 6.7 - - + -
218A THR* 4.5 8.2 - - + +
221A LEU* 3.7 39.5 - - + -
222A THR* 3.5 23.6 - - - +
262A ALA 4.2 0.2 + - - -
263A ALA* 1.3 71.7 - - - +
265A SER* 1.3 54.3 + - - +
267A LEU* 2.8 4.4 + - - +
268A VAL* 2.7 39.8 + - - +
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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
----------------------------------------------------------
34A ASP* 3.2 11.8 + - - -
37A TYR* 3.7 26.2 - - - +
38A THR* 2.7 26.5 + - - -
41A LEU* 4.6 3.7 - - - +
263A ALA* 3.4 6.8 - - - +
264A ALA* 1.3 76.4 - - - +
266A THR* 1.3 67.4 + - - -
268A VAL* 3.5 3.5 + - - +
269A HIS* 3.2 18.5 + - - +
351A LEU* 4.1 8.1 - - - +
357A TRP* 4.0 23.0 - - - -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO* 5.5 0.7 - - - +
34A ASP* 4.1 19.8 + - - -
259A TYR* 5.6 1.6 - - + -
262A ALA* 3.6 20.9 - - + -
263A ALA* 3.0 13.4 + - - +
265A SER* 1.3 83.7 + - - +
267A LEU* 1.3 51.7 + - - +
269A HIS* 3.0 3.1 + - - +
270A LYS* 2.7 57.9 + - + +
351A LEU* 4.4 16.2 - - + +
406B ARG* 4.9 12.6 - - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 3.7 31.4 - - - +
222A THR* 3.3 32.3 - - + +
255A THR* 3.8 11.3 - - + +
256A CYS* 4.0 28.7 - - - +
259A TYR* 3.8 34.1 - - + +
262A ALA* 3.7 11.2 - - + +
263A ALA 2.8 21.2 + - - +
264A ALA 2.8 2.4 + - - +
266A THR* 1.3 73.3 - - - +
268A VAL* 1.3 56.6 + - - +
270A LYS* 4.4 2.5 - - - +
271A PHE* 2.9 30.7 + - - +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.0 12.3 - - + -
222A THR* 4.0 14.1 - - + +
225A ALA* 3.8 29.4 - - + -
226A VAL* 4.7 7.0 - - + -
229A TRP* 6.5 0.2 - - + -
264A ALA 2.7 21.9 + - - +
265A SER 3.8 4.7 - - - +
267A LEU* 1.3 68.7 - - - +
269A HIS* 1.3 66.5 + - - +
271A PHE* 3.4 13.5 - - - +
272A PHE* 3.1 42.5 - - + -
347A THR* 4.3 1.1 - - + -
357A TRP* 3.9 22.2 - - + -
360A LEU* 4.4 6.7 - - + -
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Residues in contact with HIS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 3.2 5.0 + - - +
266A THR* 3.0 8.5 + - + +
268A VAL* 1.3 80.2 - - - +
270A LYS* 1.3 88.3 + - + +
272A PHE* 3.0 15.4 + - - +
273A LEU* 3.1 17.7 + - - +
344A LEU* 3.5 22.2 - - + +
347A THR* 2.9 38.4 + - - +
348A ASP* 3.1 29.9 + - - -
351A LEU* 3.5 31.0 - - + -
465B THR* 5.6 2.4 + - - -
468B ARG* 4.4 2.4 + - - -
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A THR* 4.0 4.5 - - + -
259A TYR* 3.5 51.7 + - + +
266A THR* 2.7 43.7 + - + +
267A LEU* 4.0 4.0 - - - +
269A HIS* 1.3 85.4 + - + +
271A PHE* 1.3 57.3 + - - +
273A LEU* 3.0 22.6 + - + +
274A VAL* 2.7 39.4 + - - +
406B ARG* 5.8 6.2 - - - +
457B TYR* 3.3 21.2 + - - -
461B SER* 4.6 13.3 + - - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 5.4 1.6 - - + -
226A VAL* 3.6 33.4 - - + -
229A TRP* 4.0 2.0 - + - -
248A TRP* 4.1 10.3 - + - -
251A LEU* 3.7 26.7 - - + -
252A VAL* 4.1 15.7 - - + -
255A THR* 3.5 26.8 - - + +
267A LEU 2.9 19.5 + - - +
268A VAL* 3.4 8.1 - - - +
270A LYS* 1.3 75.3 - - - +
272A PHE* 1.3 85.3 + + - +
274A VAL* 3.7 0.6 - - - +
275A PHE* 2.9 38.6 + + - +
340A PHE* 3.6 32.1 - + - -
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 5.8 1.8 - - + -
229A TRP* 3.5 58.3 - + + -
268A VAL* 3.1 38.6 - - + -
269A HIS 3.0 6.2 + - - +
271A PHE* 1.3 93.3 - + - +
273A LEU* 1.3 58.6 + - - +
275A PHE 3.9 0.6 - - - +
276A SER* 2.6 37.3 + - - -
340A PHE* 3.6 21.8 - + - +
343A GLY* 3.5 24.9 - - - -
344A LEU* 3.4 20.4 - - - +
347A THR* 3.8 13.0 - - + -
360A LEU* 4.2 8.1 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 4.2 10.1 - - - +
269A HIS* 3.1 14.8 + - - +
270A LYS* 3.0 40.8 + - + +
272A PHE* 1.3 78.5 - - - +
274A VAL* 1.3 66.8 + - + +
276A SER* 3.1 11.2 + - - -
277A LYS* 3.3 50.4 + - + +
344A LEU* 3.8 23.2 - - + +
461B SER* 6.5 0.9 - - - -
468B ARG* 3.6 25.1 - - - +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.6 6.5 - - + -
255A THR* 4.7 5.2 - - + +
258A LEU* 4.6 20.0 - - + -
259A TYR* 3.9 29.4 - - + +
270A LYS 2.7 23.4 + - - +
271A PHE* 3.7 3.8 - - - +
273A LEU* 1.3 77.2 - - + +
275A PHE* 1.3 87.5 + - + +
276A SER 3.1 4.5 + - - -
277A LYS* 3.3 9.8 + - - +
278A TRP* 3.2 30.8 + - + +
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Residues in contact with PHE 275 (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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251A LEU* 3.3 61.7 - - + -
254A ARG* 4.1 15.7 - - + -
255A THR* 3.3 11.4 - - - -
271A PHE* 2.9 37.5 + + - +
272A PHE 3.9 2.5 - - - -
274A VAL* 1.3 82.2 - - + +
276A SER* 1.3 58.2 + - - +
277A LYS 3.6 0.2 - - - -
278A TRP* 3.8 34.8 - + + +
280A TRP* 4.5 12.2 + + - -
284A VAL* 3.7 14.8 - - + -
337A VAL* 5.4 1.0 - - - +
340A PHE* 3.1 44.5 - + + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE 2.6 22.7 + - - -
273A LEU 3.1 6.9 + - - -
274A VAL 3.2 0.2 - - - -
275A PHE* 1.3 78.8 - - - +
277A LYS* 1.3 63.7 + - - +
278A TRP 3.2 2.0 - - - +
337A VAL* 5.3 4.4 - - - +
340A PHE* 4.0 10.5 - - - -
341A LYS* 3.6 46.2 - - - +
344A LEU* 3.8 14.7 - - - +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.3 44.6 + - + +
274A VAL* 3.3 10.0 + - - +
276A SER* 1.3 81.2 + - - +
278A TRP* 1.3 64.0 + - - +
279A GLU* 3.3 7.6 + - - +
464B ASP* 5.0 11.9 + - - +
468B ARG* 4.9 4.6 - - - +
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Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ARG* 4.6 22.4 - - + -
258A LEU* 5.6 1.1 - - + -
274A VAL* 3.2 27.1 + - + +
275A PHE* 3.8 37.2 - + + -
276A SER 3.2 4.4 - - - +
277A LYS* 1.3 76.9 - - - +
279A GLU* 1.3 65.5 + - - +
280A TRP* 3.1 53.3 + + + -
282A ASN* 2.8 32.4 + - + +
283A PRO 3.3 25.6 - - - -
284A VAL* 3.5 21.8 - - + -
285A LEU 5.3 0.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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