Contacts of the helix formed by residues 309 - 319 (chain D) in PDB entry 4LQL
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 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D ILE* 4.1 5.9 - - + +
180D ARG* 4.0 8.7 - - + +
191D THR 4.9 2.4 + - - -
193D GLY 5.8 2.2 - - - -
194D ASP 6.1 0.7 - - - -
195D LYS* 4.6 12.6 - - + -
198D ALA* 6.5 1.3 - - + -
204D TRP* 6.2 0.3 - - - -
206D VAL* 3.3 45.6 - - + +
276D THR* 4.0 7.9 - - - -
307D GLY 2.6 14.2 + - - +
308D ASP* 1.3 70.7 - - - +
310D LYS* 1.3 64.7 + - + +
312D ALA* 3.4 4.2 - - - +
313D GLY* 3.1 24.9 + - - -
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Residues in contact with LYS 310 (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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190D VAL 3.1 10.3 + - - -
191D THR* 3.1 11.5 + - - +
192D GLU* 2.9 47.2 + - - +
193D GLY* 4.6 4.9 - - - +
308D ASP* 2.8 6.6 + - - +
309D PHE* 1.3 81.4 - - + +
311D MET* 1.3 60.0 + - + +
312D ALA 2.8 10.8 + - - -
314D LEU* 3.1 29.5 + - + +
393D LEU* 3.1 40.6 - - + +
394D SER* 4.8 0.9 - - - +
395D TYR 4.7 8.5 - - - +
400D TYR* 4.9 13.0 - - + -
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Residues in contact with MET 311 (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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303D PHE 2.7 25.1 - - - +
304D GLY* 3.2 6.4 - - - -
305D PRO 5.6 0.2 - - - -
308D ASP* 2.8 24.7 + - - +
310D LYS* 1.3 73.6 - - + +
312D ALA* 1.3 50.8 + - - +
314D LEU* 4.8 8.7 - - + -
315D THR* 3.4 16.2 + - - +
329D LEU* 4.6 8.6 - - + +
392D THR* 5.8 0.9 - - - -
447D HIS* 3.0 48.2 - - + +
448D THR* 3.9 4.9 - - - +
449D VAL* 4.7 12.1 - - + +
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Residues in contact with ALA 312 (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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178D ILE* 3.7 15.7 - - + -
274D ALA* 3.3 16.3 - - - +
275D PHE 4.0 4.5 - - - +
276D THR* 4.4 1.1 - - + -
302D GLY* 3.4 5.2 - - - -
303D PHE* 3.4 6.9 + - - +
304D GLY 3.1 23.8 - - - +
308D ASP 3.5 7.9 - - - +
309D PHE* 3.4 13.0 - - - +
310D LYS 2.8 1.8 + - - -
311D MET* 1.3 76.8 - - - +
313D GLY* 1.3 61.7 + - - +
314D LEU 3.2 0.9 - - - -
315D THR 3.9 0.4 - - - -
316D ARG 3.2 19.8 + - - -
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Residues in contact with GLY 313 (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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173D SER* 6.0 0.3 - - - -
176D ILE* 3.8 19.0 - - - +
178D ILE* 4.0 6.7 - - - +
204D TRP* 5.4 12.5 - - - +
274D ALA* 4.4 5.4 - - - -
309D PHE 3.1 11.5 + - - -
310D LYS 4.1 0.2 - - - -
312D ALA* 1.3 79.0 - - - +
314D LEU* 1.3 56.2 + - - +
316D ARG* 3.7 9.7 - - - +
317D LEU* 3.5 17.7 + - - +
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Residues in contact with LEU 314 (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 LYS 3.1 21.6 + - - +
311D MET* 4.8 6.7 - - + -
313D GLY* 1.3 73.5 - - - +
315D THR* 1.3 59.2 + - - +
316D ARG 3.2 1.3 - - - -
317D LEU* 2.8 31.3 + - + +
318D LEU* 2.9 26.6 + - + +
391D ILE* 4.8 6.5 - - + -
392D THR* 4.4 23.3 - - - +
393D LEU* 3.5 37.5 - - + +
449D VAL* 3.7 27.8 - - + +
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Residues in contact with THR 315 (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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301D TYR 5.1 0.7 - - - -
302D GLY* 4.1 3.8 - - - -
303D PHE 3.9 13.6 + - - -
311D MET 3.4 17.8 + - - -
312D ALA 3.6 11.1 + - - +
314D LEU* 1.3 72.9 - - - +
316D ARG* 1.3 66.6 + - - +
318D LEU* 4.5 1.0 - - - +
319D LYS* 3.0 38.7 + - - +
328D ALA 4.4 2.8 + - - -
329D LEU* 3.4 28.6 - - - +
449D VAL* 3.8 12.5 - - - +
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Residues in contact with ARG 316 (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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172D GLU* 5.1 9.4 - - - +
175D HIS* 5.1 3.8 + - - +
176D ILE* 3.5 23.2 - - + +
273D ASP* 3.0 48.7 - - - +
274D ALA* 4.8 1.8 - - + -
300D GLY* 3.2 27.1 + - - -
301D TYR* 4.8 1.2 - - - +
302D GLY* 3.7 8.2 - - - +
312D ALA 3.2 15.0 + - - +
313D GLY* 3.7 8.5 - - - +
315D THR* 1.3 82.0 - - - +
317D LEU* 1.3 63.6 + - - +
319D LYS* 3.1 5.7 + - - +
320D ILE* 3.0 46.5 + - + +
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Residues in contact with LEU 317 (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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169D ALA* 4.3 9.0 - - + +
173D SER* 3.1 28.5 - - - +
176D ILE* 5.8 0.7 - - + -
313D GLY 3.6 11.9 - - - +
314D LEU* 2.8 29.4 + - + +
316D ARG* 1.3 75.9 - - - +
318D LEU* 1.3 62.7 + - + +
320D ILE* 3.2 17.7 + - - +
321D ALA* 3.6 8.0 + - - +
462D LEU* 6.1 4.9 - - + -
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Residues in contact with LEU 318 (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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314D LEU* 2.9 24.5 + - + +
315D THR 4.7 1.3 - - - +
317D LEU* 1.3 68.9 - - + +
319D LYS* 1.3 58.6 + - + +
320D ILE 2.8 11.1 + - - -
321D ALA* 2.9 17.6 + - - +
322D ALA* 3.1 14.5 + - - +
327D THR* 4.3 9.4 - - + -
328D ALA 5.8 0.2 - - - +
391D ILE* 5.7 5.8 - - + -
449D VAL* 4.0 24.7 - - + -
451D THR* 5.5 0.9 - - - -
454D LEU* 3.7 29.5 - - + +
459D LEU* 5.8 4.9 - - + -
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Residues in contact with LYS 319 (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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297D MET* 3.3 37.7 + - - +
300D GLY* 4.6 18.7 - - - +
301D TYR 3.8 16.1 + - - +
315D THR* 3.0 31.7 + - - +
316D ARG* 3.1 8.1 + - - +
318D LEU* 1.3 74.6 - - + +
320D ILE* 1.3 58.8 + - - +
321D ALA 3.4 0.4 - - - -
322D ALA* 3.8 18.0 + - + +
323D ASP* 4.6 1.2 + - - +
327D THR* 4.2 14.1 - - + +
328D ALA 4.4 25.4 + - - +
329D LEU* 5.4 0.8 - - - +
353D ASP* 3.4 19.9 - - - +
355D THR* 4.2 11.4 - - - -
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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
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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