Contacts of the helix formed by residues 352 - 365 (chain B) in PDB entry 1LFD
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 VAL 352 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.8 40.4 - - + +
222B GLN* 4.0 10.3 - - + -
223B LEU* 4.0 23.6 - - + +
344B THR* 4.4 4.9 - - - -
345B SER 3.6 20.9 - - - +
349B ARG* 3.4 30.7 + - + +
350B GLN 3.2 2.4 - - - +
351B GLY* 1.3 77.7 - - - +
353B GLU* 1.3 64.8 + - - +
355B ALA* 3.4 1.5 + - - +
356B PHE* 3.3 29.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.0 13.9 - - + -
349B ARG* 3.0 40.4 + - - +
351B GLY* 4.6 0.2 - - - -
352B VAL* 1.3 77.1 - - - +
354B ASP* 1.3 58.1 + - - +
356B PHE* 3.3 1.2 + - - -
357B TYR* 2.8 68.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ILE* 3.6 24.2 - - - +
351B GLY* 3.5 16.9 + - - +
352B VAL 3.3 0.2 - - - -
353B GLU* 1.3 79.2 - - - +
355B ALA* 1.3 56.5 + - - +
357B TYR* 4.7 3.1 - - - -
358B THR* 2.6 52.5 + - - -
361B ARG* 4.7 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 6.0 0.9 - - + -
279B LEU* 3.5 21.8 - - + +
312B VAL* 4.1 3.0 - - - +
314B VAL* 4.0 19.7 - - + -
342B ILE* 3.7 15.0 - - + +
344B THR* 3.8 17.0 - - + -
351B GLY 2.9 19.0 + - - +
352B VAL* 3.6 5.6 - - - +
354B ASP* 1.3 77.5 - - - +
356B PHE* 1.3 61.2 + - + +
358B THR* 4.0 2.3 - - - -
359B LEU* 3.4 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.7 23.3 - - + +
208B VAL* 3.9 14.4 - - + -
219B LEU* 3.8 26.7 - - + -
220B THR* 4.0 25.6 - - - -
223B LEU* 3.6 34.5 - - + -
253B LEU* 5.3 1.3 - - + -
255B ILE* 3.7 18.4 - - + -
279B LEU* 3.6 30.5 - - + -
352B VAL* 3.3 27.0 + - + +
355B ALA* 1.3 77.6 - - + +
357B TYR* 1.3 66.4 + - + +
359B LEU* 3.3 7.3 + - - +
360B VAL* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.3 16.6 - - + +
244B VAL* 3.2 34.3 - - + +
245B VAL 4.8 4.7 - - - -
246B ILE* 3.5 33.8 - - + +
253B LEU* 4.4 6.1 - - + -
353B GLU* 2.8 61.4 + - + +
354B ASP* 4.1 1.8 - - - +
356B PHE* 1.3 75.4 - - + +
358B THR* 1.3 60.0 + - - +
360B VAL* 3.2 6.7 + - - +
361B ARG* 3.0 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 4.2 1.6 - - + -
340B PRO* 3.8 24.9 - - + -
342B ILE* 3.5 14.3 - - + +
354B ASP* 2.6 40.1 + - - -
355B ALA 4.0 2.0 - - - -
357B TYR* 1.3 76.6 - - - +
359B LEU* 1.3 59.2 + - - +
361B ARG* 3.5 16.2 + - + +
362B GLU* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.9 25.8 - - + -
277B GLY* 3.8 12.6 - - - +
278B PHE 3.6 48.2 - - - +
279B LEU* 3.7 15.3 - - + +
310B PRO* 3.7 20.4 - - + +
312B VAL* 3.7 17.4 - - + +
355B ALA 3.4 11.6 + - - +
356B PHE* 3.3 10.0 + - + +
357B TYR 3.2 0.2 - - - -
358B THR* 1.3 77.8 - - - +
360B VAL* 1.3 58.8 + - - +
362B GLU* 3.2 4.9 + - + +
363B ILE* 3.0 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 3.7 32.2 - - + +
206B LEU* 4.1 12.3 - - + -
246B ILE* 3.8 28.7 - - + -
251B CYS* 4.6 0.9 - - - -
253B LEU* 3.6 26.5 - - + -
356B PHE 3.1 17.8 + - - +
357B TYR 3.4 7.6 - - - +
359B LEU* 1.3 77.6 - - - +
361B ARG* 1.3 57.3 + - - +
363B ILE* 3.3 11.0 + - - +
364B ARG* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 4.0 13.4 - - + +
247B ASP* 2.8 35.3 + - - +
354B ASP* 4.7 5.7 + - - +
357B TYR* 3.0 45.8 + - - +
358B THR* 3.8 18.9 + - + +
360B VAL* 1.3 71.7 - - - +
362B GLU* 1.3 61.8 + - - +
364B ARG* 3.3 32.3 + - - +
365B GLN* 2.9 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PRO* 4.1 13.5 - - + +
311B MET 4.2 22.7 - - - +
312B VAL* 5.1 0.2 - - + -
339B ILE* 6.1 1.1 - - + -
340B PRO* 4.1 16.4 - - + +
358B THR* 3.0 35.7 + - - +
359B LEU* 3.2 13.9 - - + +
360B VAL 3.2 0.2 - - - -
361B ARG* 1.3 78.6 - - - +
363B ILE* 1.3 62.3 + - - +
365B GLN* 3.2 26.7 + - - +
366B HIS* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 3.8 20.6 - - + -
205B LYS 4.4 1.3 - - - +
206B LEU* 4.3 25.1 - - + -
276B GLU* 4.0 17.7 - - + +
277B GLY* 3.7 26.2 - - - +
310B PRO* 3.7 23.8 - - + -
359B LEU 3.0 21.8 + - - +
360B VAL* 3.3 7.2 + - - +
362B GLU* 1.3 75.3 - - - +
364B ARG* 1.3 54.2 + - - +
366B HIS* 3.2 2.5 + - - +
367B LYS* 2.7 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 3.6 27.3 + - - +
246B ILE* 3.9 16.4 + - - +
247B ASP* 2.7 31.2 + - - +
249B GLU* 3.4 29.0 + - - +
360B VAL* 3.0 17.5 + - - +
361B ARG* 3.3 32.2 + - - +
363B ILE* 1.3 77.3 - - - +
365B GLN* 1.3 64.3 + - + +
367B LYS* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ARG* 2.9 39.2 + - - +
362B GLU* 3.2 30.7 + - - +
363B ILE 3.3 0.2 - - - -
364B ARG* 1.3 79.1 - - + +
366B HIS* 1.3 62.5 + - - +
367B LYS 4.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
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