Contacts of the helix formed by residues 352 - 365 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D LEU* 3.6 33.7 - - + +
222D GLN* 4.2 5.4 - - + -
223D LEU* 4.0 18.8 - - + +
344D THR* 4.4 4.9 - - - -
345D SER 3.8 13.9 - - - +
346D ALA* 4.3 11.4 - - - -
349D ARG* 3.4 35.9 + - - +
350D GLN 3.2 3.5 - - - +
351D GLY* 1.3 76.4 - - - +
353D GLU* 1.3 63.2 + - - +
355D ALA* 3.4 3.3 + - - +
356D PHE* 3.1 39.8 + - + -
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Residues in contact with GLU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.8 16.8 - - + -
242D LYS* 4.9 3.5 + - - -
349D ARG* 3.1 33.4 + - - +
351D GLY 3.5 0.4 - - - -
352D VAL* 1.3 73.5 - - - +
354D ASP* 1.3 60.1 + - - +
356D PHE* 4.6 0.7 - - - +
357D TYR* 2.9 72.4 + - + +
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Residues in contact with ASP 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ILE* 3.6 24.4 - - + +
351D GLY* 3.5 18.6 - - - +
353D GLU* 1.3 79.9 - - - +
355D ALA* 1.3 57.9 + - - +
357D TYR* 5.2 1.1 - - - -
358D THR* 2.5 53.6 + - - +
361D ARG* 5.5 1.9 + - - -
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D LEU* 6.0 1.3 - - + -
279D LEU* 3.4 24.1 - - + +
312D VAL* 4.3 3.4 - - - +
314D VAL* 4.0 21.3 - - + -
342D ILE* 3.6 14.1 - - + +
344D THR* 3.9 16.2 - - + -
351D GLY 3.0 17.8 + - - +
352D VAL* 3.6 6.3 - - - +
353D GLU 3.3 0.2 - - - -
354D ASP* 1.3 78.7 - - - +
356D PHE* 1.3 61.2 + - + +
358D THR* 4.1 1.7 - - - -
359D LEU* 3.4 12.1 + - - +
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Residues in contact with PHE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 4.0 22.5 - - + +
208D VAL* 3.9 15.5 - - + -
219D LEU* 3.9 26.5 - - + -
220D THR* 4.0 25.1 - - - -
223D LEU* 3.4 29.6 - - + -
253D LEU* 5.4 0.4 - - + -
255D ILE* 4.0 16.4 - - + -
279D LEU* 3.5 31.0 - - + -
352D VAL* 3.1 31.3 + - + +
353D GLU 4.3 0.4 - - - +
355D ALA* 1.3 79.7 - - + +
357D TYR* 1.3 73.2 + - + +
358D THR 3.2 0.2 - - - -
359D LEU* 3.2 8.0 + - - +
360D VAL* 3.2 23.8 + - - +
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Residues in contact with TYR 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.6 16.8 - - + +
242D LYS* 3.2 26.3 + - - -
244D VAL* 3.7 23.4 - - + +
245D VAL 5.9 0.2 - - - -
246D ILE* 3.8 28.9 - - + +
253D LEU* 3.9 23.3 - - + -
353D GLU* 2.9 55.2 + - + +
354D ASP* 4.7 1.1 - - - +
356D PHE* 1.3 74.2 - - + +
358D THR* 1.3 63.8 + - - +
360D VAL* 3.5 7.9 + - - +
361D ARG* 3.2 34.4 + - - +
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Residues in contact with THR 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D VAL* 4.3 3.4 - - + -
340D PRO* 3.9 34.3 - - + -
342D ILE* 3.6 10.2 - - + +
354D ASP* 2.5 40.5 + - - -
355D ALA 4.1 1.1 - - - -
357D TYR* 1.3 75.0 - - - +
359D LEU* 1.3 61.9 + - - +
361D ARG* 3.1 20.4 + - + +
362D GLU* 2.9 29.6 + - + +
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 4.0 25.4 - - + -
207D VAL 5.0 0.4 - - - +
277D GLY* 3.9 15.7 - - - +
278D PHE 3.6 41.5 - - - +
279D LEU* 3.7 23.1 - - + +
310D PRO 4.0 1.1 - - - -
311D MET* 3.8 18.8 - - - +
312D VAL* 3.7 12.5 - - + +
355D ALA 3.4 11.8 + - - +
356D PHE 3.2 9.6 + - - +
358D THR* 1.3 80.0 - - - +
360D VAL* 1.3 61.6 + - - +
362D GLU* 3.1 6.2 + - + +
363D ILE* 3.0 28.1 + - + +
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Residues in contact with VAL 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D TYR* 3.8 33.9 - - + -
206D LEU* 4.1 14.6 - - + -
246D ILE* 3.9 29.2 - - + -
253D LEU* 4.0 17.5 - - + -
356D PHE 3.2 15.2 + - - +
357D TYR* 3.6 8.3 - - - +
358D THR 3.2 0.2 - - - -
359D LEU* 1.3 77.4 - - - +
361D ARG* 1.3 62.4 + - - +
363D ILE* 3.1 20.0 + - - +
364D ARG* 3.2 24.8 + - - +
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Residues in contact with ARG 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ILE* 4.9 7.5 - - + +
247D ASP* 2.9 41.6 + - - +
354D ASP* 5.5 1.8 + - - -
357D TYR* 3.2 22.4 + - - +
358D THR* 3.1 26.3 + - + +
360D VAL* 1.3 77.6 - - - +
362D GLU* 1.3 61.7 + - + +
364D ARG* 3.5 15.4 + - - +
365D GLN* 3.2 35.1 + - - +
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Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D PRO* 4.1 17.5 - - + +
311D MET 4.3 9.9 + - - +
312D VAL* 4.3 2.9 - - + -
338D GLY 5.1 5.4 - - - +
339D ILE* 5.4 1.4 - - - +
340D PRO* 3.7 37.7 - - + +
358D THR* 2.9 18.7 + - - +
359D LEU* 3.1 10.7 + - - +
361D ARG* 1.3 76.1 - - - +
363D ILE* 1.3 63.2 + - - +
365D GLN* 3.4 31.0 + - - +
366D HIS* 3.1 21.7 + - - +
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Residues in contact with ILE 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D TYR* 3.9 34.5 - - + -
205D LYS 4.9 0.4 - - - +
206D LEU* 4.7 7.0 - - + -
276D GLU* 4.3 18.2 - - + +
277D GLY* 3.9 23.6 - - - +
310D PRO* 3.6 26.5 - - + -
359D LEU* 3.0 20.1 + - + +
360D VAL* 3.1 11.9 + - - +
362D GLU* 1.3 77.6 - - - +
364D ARG* 1.3 56.7 + - - +
366D HIS* 3.1 6.9 + - - +
367D LYS* 2.9 46.9 + - + +
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Residues in contact with ARG 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D TYR* 3.0 24.8 + - + +
246D ILE* 2.9 36.4 + - - +
247D ASP* 3.2 29.9 + - - +
249D GLU* 3.0 30.2 + - - +
251D CYS* 3.5 15.2 - - - -
360D VAL* 3.2 18.4 + - - +
361D ARG* 3.7 12.9 - - - +
363D ILE* 1.3 77.7 - - - +
365D GLN* 1.3 61.8 + - + +
367D LYS* 3.1 28.6 + - + +
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ARG* 3.2 21.5 + - + +
362D GLU* 3.5 33.8 + - - +
363D ILE 3.3 0.2 - - - -
364D ARG* 1.3 77.4 - - + +
366D HIS* 1.3 60.8 + - - +
367D LYS 3.7 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