Contacts of the helix formed by residues 308 - 321 (chain E) 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 ASP 308 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E VAL* 4.9 1.2 - - - +
191E THR* 3.5 29.9 - - - +
304E GLY* 3.4 11.0 + - - -
305E PRO 4.5 2.9 - - - -
306E GLU 3.4 0.6 - - - -
307E GLY* 1.3 70.8 - - - +
309E PHE* 1.3 63.6 + - - +
310E LYS* 3.0 31.5 + - - -
311E MET* 3.1 16.5 + - - +
312E ALA 3.1 14.7 + - - -
447E HIS* 2.5 46.4 + - + +
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Residues in contact with PHE 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E ILE* 4.9 1.9 - - + +
180E ARG* 4.2 24.7 - - - +
191E THR 5.0 2.4 + - - -
193E GLY 6.3 0.7 - - - -
195E LYS* 5.7 8.5 - - + -
206E VAL* 4.2 29.1 - - + +
276E THR* 4.2 7.2 - - + -
307E GLY 2.9 8.6 + - - +
308E ASP* 1.3 69.2 + - - +
310E LYS* 1.3 74.5 + - + +
312E ALA* 3.0 20.7 - - + +
313E GLY* 3.4 3.6 + - - -
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Residues in contact with LYS 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E VAL* 2.7 30.0 + - - +
191E THR 4.2 0.9 - - - -
192E GLU 4.0 12.3 - - - +
193E GLY* 4.0 17.3 - - - +
198E ALA* 5.7 4.0 - - + -
308E ASP* 3.0 18.9 + - - -
309E PHE* 1.3 81.0 - - + +
311E MET* 1.3 53.7 + - - +
312E ALA 2.9 3.4 - - - -
313E GLY* 2.6 27.2 + - - -
314E LEU* 3.0 12.1 + - - +
393E LEU* 2.9 53.7 + - + +
394E SER* 4.5 1.9 - - - +
395E TYR 5.2 1.6 - - - +
400E TYR* 4.1 23.6 - - + +
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Residues in contact with MET 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E PHE 4.1 3.3 - - - +
304E GLY* 4.4 1.3 - - - -
305E PRO* 6.1 0.4 - - + -
308E ASP* 3.1 24.8 + - - +
310E LYS* 1.3 74.9 - - - +
312E ALA* 1.3 68.9 + - - +
314E LEU* 3.9 9.9 - - + +
315E THR* 3.0 19.4 + - - -
329E LEU* 4.2 12.3 - - + -
393E LEU* 5.5 1.7 - - - +
447E HIS* 3.2 25.4 - - + +
448E THR 3.1 28.0 - - - +
449E VAL* 3.9 5.2 - - + -
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Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E ILE* 5.0 2.2 - - + -
274E ALA* 4.7 12.1 - - + -
275E PHE 4.5 4.5 - - - +
276E THR* 4.9 3.1 - - + -
302E GLY* 4.0 3.4 - - - -
303E PHE* 3.5 5.2 - - - +
304E GLY* 3.2 34.7 - - - +
308E ASP 3.1 6.1 + - - -
309E PHE* 3.0 20.6 - - + +
310E LYS 2.9 0.2 - - - -
311E MET* 1.3 80.5 - - - +
313E GLY* 1.3 58.9 - - - +
315E THR* 3.0 15.4 + - - -
316E ARG* 3.0 14.5 + - - +
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Residues in contact with GLY 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ILE* 5.2 8.3 - - - -
204E TRP* 5.6 8.1 - - - -
274E ALA* 5.4 1.8 - - - -
309E PHE 3.4 3.4 + - - -
310E LYS 2.6 13.1 + - - -
312E ALA* 1.3 71.7 - - - +
314E LEU* 1.3 48.7 + - - -
315E THR 3.0 4.9 - - - -
316E ARG* 2.6 11.8 + - - -
317E LEU* 2.3 49.4 + - - +
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Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E LYS 3.0 12.2 + - - +
311E MET* 3.8 6.0 + - + -
313E GLY* 1.3 75.1 - - - +
315E THR* 1.3 59.3 + - - +
317E LEU* 4.1 11.9 - - + -
318E LEU* 3.2 27.5 - - + +
391E ILE* 3.1 38.1 - - + +
392E THR* 3.6 21.5 - - - +
393E LEU* 5.2 17.5 - - + -
402E PHE* 5.6 5.6 - - + -
448E THR 5.4 0.2 - - - -
449E VAL* 3.1 30.2 - - + +
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Residues in contact with THR 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E MET* 5.5 3.8 - - - -
301E TYR 4.9 1.7 + - - -
302E GLY* 5.0 0.4 - - - -
303E PHE 4.4 11.9 + - - -
311E MET 3.0 19.3 + - - -
312E ALA 3.0 7.0 + - - -
313E GLY 3.0 0.6 - - - -
314E LEU* 1.3 78.1 - - - +
316E ARG* 1.3 56.5 + - - +
317E LEU 3.6 0.2 - - - -
319E LYS* 3.1 39.9 + - - +
327E THR* 4.9 0.2 - - - +
328E ALA 3.5 11.5 + - - +
329E LEU* 3.6 18.9 - - - +
449E VAL* 3.4 14.1 - - - +
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ILE* 3.9 25.5 - - + +
273E ASP* 3.2 33.2 - - - +
274E ALA* 4.6 0.9 - - + -
300E GLY* 3.8 19.4 + - - -
301E TYR 4.5 1.6 - - - -
302E GLY* 3.4 36.8 - - - +
312E ALA 3.0 5.0 + - - +
313E GLY* 2.6 16.6 + - - +
315E THR* 1.3 73.2 - - - +
317E LEU* 1.3 58.3 + - - +
318E LEU 3.6 0.2 - - - -
319E LYS* 4.0 7.7 - - - +
320E ILE* 3.1 52.0 + - + +
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Residues in contact with LEU 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ALA* 4.0 10.0 - - + +
173E SER* 3.1 34.3 - - - +
176E ILE* 6.2 2.5 - - + -
204E TRP* 6.0 4.9 - - + -
313E GLY* 2.3 37.0 + - - +
314E LEU* 4.2 13.0 - - + +
316E ARG* 1.3 68.9 - - + +
318E LEU* 1.3 63.7 + - + +
320E ILE* 3.0 26.5 + - - +
321E ALA* 3.4 5.5 + - - +
462E LEU* 6.4 3.4 - - + -
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E LEU* 3.2 46.5 + - + +
316E ARG 3.6 0.2 - - - -
317E LEU* 1.3 77.7 - - + +
319E LYS* 1.3 64.0 + - - +
321E ALA* 4.0 2.2 + - - +
322E ALA* 4.0 4.0 + - - +
327E THR* 3.6 16.1 + - + +
391E ILE* 6.2 0.9 - - + -
449E VAL* 4.3 13.9 - - + -
451E THR* 4.6 8.1 - - - -
454E LEU* 3.8 25.7 - - + +
459E LEU* 5.8 8.3 - - + -
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Residues in contact with LYS 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E MET* 4.3 13.2 - - - +
300E GLY* 5.9 2.2 - - - -
301E TYR 4.8 14.1 - - - +
315E THR* 3.1 36.3 + - - +
316E ARG* 4.2 9.0 - - - +
317E LEU 3.1 0.4 - - - -
318E LEU* 1.3 74.9 - - - +
320E ILE* 1.3 53.0 + - - +
321E ALA 2.5 4.8 + - - -
322E ALA* 2.3 45.0 + - - +
326E GLN 5.1 1.6 - - - +
327E THR* 2.2 50.9 + - + +
328E ALA* 3.2 11.9 + - - +
353E ASP* 3.5 22.6 - - - -
355E THR* 4.5 1.9 + - - +
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Residues in contact with ILE 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LYS* 4.8 12.8 - - + +
168E VAL* 4.0 17.2 - - - +
169E ALA* 4.4 8.9 - - + +
172E GLU* 4.0 28.3 - - + -
173E SER* 5.6 1.3 - - - +
316E ARG* 3.1 43.9 + - + +
317E LEU* 3.0 16.1 + - - +
319E LYS* 1.3 75.7 - - - +
321E ALA* 1.3 56.0 + - - +
322E ALA 4.9 1.1 - - - -
323E ASP* 4.9 5.2 - - - -
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Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MET* 6.2 0.2 - - - +
165E HIS* 4.1 38.0 - - + +
166E VAL* 5.0 1.8 - - + +
168E VAL* 5.1 2.9 - - - -
169E ALA* 3.8 20.2 - - + -
317E LEU 3.4 6.2 + - - +
318E LEU* 4.5 1.1 - - - +
319E LYS 2.5 6.5 + - - -
320E ILE* 1.3 73.5 - - - +
322E ALA* 1.3 56.9 + - - -
323E ASP* 3.4 8.8 + - - +
454E LEU* 4.4 24.7 - - + +
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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