Contacts of the helix formed by residues 326 - 340 (chain R) in PDB entry 5L4K
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 GLY 326 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320R ALA* 4.2 9.2 - - - -
325R VAL* 1.3 79.0 - - - +
327R VAL* 1.3 67.3 + - - -
328R GLU 3.1 3.9 + - - -
329R PHE* 3.3 12.9 + - - +
330R ILE* 3.4 9.9 + - - +
59Y GLU* 3.6 13.1 + - - -
65Y TYR* 3.6 21.1 - - - -
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Residues in contact with VAL 327 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316R LEU* 4.7 22.1 - - + +
317R GLY* 5.3 3.1 - - - +
320R ALA* 4.2 17.0 - - + -
326R GLY* 1.3 71.2 - - - -
328R GLU* 1.3 73.8 + - + +
330R ILE* 3.6 5.3 + - - +
331R ASP* 2.9 25.3 + - - +
349R LYS* 5.6 9.6 - - - +
352R GLU* 4.7 15.9 - - - +
65Y TYR* 5.2 0.2 - - - -
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Residues in contact with GLU 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326R GLY 3.1 1.2 + - - -
327R VAL* 1.3 85.1 - - + +
329R PHE* 1.3 64.9 + - - +
331R ASP* 2.9 17.9 + - - +
332R GLN* 3.0 28.1 + - + +
59Y GLU* 6.1 1.8 - - + +
63Y HIS* 3.2 32.0 + - - +
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Residues in contact with PHE 329 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272R PHE* 3.8 17.3 - + - -
300R ARG* 3.4 25.4 - - - -
304R TYR* 3.7 12.1 - - - -
325R VAL* 3.8 25.4 - - + -
326R GLY 3.3 10.0 + - - +
328R GLU* 1.3 79.4 - - - +
330R ILE* 1.3 65.6 + - - +
332R GLN* 3.4 14.7 + - - +
333R GLU* 3.1 43.0 + - + +
55Y GLN* 4.0 40.4 - - + -
56Y LEU* 4.7 8.3 - - + -
59Y GLU* 4.0 35.2 - - + +
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Residues in contact with ILE 330 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304R TYR* 4.0 17.7 - - + +
316R LEU* 4.0 21.3 - - + +
319R MET* 3.5 44.4 - - + +
320R ALA* 3.8 5.6 - - + +
323R PHE* 4.4 9.0 - - + -
325R VAL* 3.8 22.4 - - + -
326R GLY 3.4 4.2 + - - +
327R VAL* 4.0 6.7 - - - +
328R GLU 3.3 0.4 - - - -
329R PHE* 1.3 81.0 - - + +
331R ASP* 1.3 67.5 + - - +
333R GLU* 3.2 4.1 + - - -
334R LEU* 2.8 47.2 + - + +
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Residues in contact with ASP 331 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316R LEU* 3.9 17.6 - - - +
327R VAL 2.9 18.6 + - - +
328R GLU* 2.9 10.5 + - - +
330R ILE* 1.3 78.3 - - - +
332R GLN* 1.3 55.3 + - + +
334R LEU* 4.3 1.9 - - - +
335R SER* 2.7 36.7 + - - -
347R ILE* 4.1 14.1 - - - +
349R LYS* 3.5 29.2 - - - +
414S TYR* 3.2 21.6 + - - -
425S LYS* 3.3 13.2 + - - -
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Residues in contact with GLN 332 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328R GLU* 3.0 32.4 + - - +
329R PHE* 3.6 11.8 - - - +
331R ASP* 1.3 74.8 + - + +
333R GLU* 1.3 67.5 + - + +
335R SER* 2.6 21.2 + - - -
336R ARG* 3.0 10.6 + - - +
55Y GLN* 3.3 25.2 + - - +
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Residues in contact with GLU 333 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300R ARG* 3.2 45.2 + - - -
304R TYR* 3.2 35.4 + - + +
329R PHE* 3.1 27.8 + - + +
330R ILE 3.8 1.8 - - - +
332R GLN* 1.3 82.6 - - + +
334R LEU* 1.3 65.0 + - - +
336R ARG* 2.9 24.2 + - - +
337R PHE* 3.0 37.7 + - + -
52Y PHE* 4.4 6.0 - - - -
55Y GLN* 5.4 8.5 - - - +
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Residues in contact with LEU 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304R TYR* 3.3 48.7 - - + -
308R LEU* 4.4 12.3 - - + -
316R LEU* 4.8 6.7 - - + -
319R MET* 4.1 20.2 - - + -
330R ILE* 2.8 41.5 + - + +
331R ASP* 4.3 1.8 - - - +
333R GLU* 1.3 73.8 - - - +
335R SER* 1.3 57.4 + - - +
337R PHE* 3.4 3.7 + - + +
338R ILE* 2.9 45.8 + - + +
343R LEU* 5.0 8.7 - - + -
347R ILE* 5.1 9.4 - - + -
354R VAL* 4.9 9.0 - - + -
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Residues in contact with SER 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331R ASP* 2.7 16.7 + - - -
332R GLN* 2.6 25.5 + - - -
334R LEU* 1.3 75.8 - - - +
336R ARG* 1.3 58.2 + - - +
338R ILE* 3.5 3.0 + - - -
339R ALA* 3.0 29.3 + - - +
347R ILE* 4.8 4.2 - - - +
409S MET* 5.1 4.8 - - - +
413S SER* 3.4 27.6 + - - -
414S TYR* 4.5 14.8 + - - -
425S LYS* 5.9 2.1 + - - +
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Residues in contact with ARG 336 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297R ARG* 3.8 26.5 - - - +
332R GLN 3.0 10.9 + - - +
333R GLU* 2.9 21.0 + - - +
335R SER* 1.3 78.5 + - - +
337R PHE* 1.3 83.7 + - + +
339R ALA* 3.4 7.7 + - + +
340R ALA* 3.1 24.5 + - + +
368S ARG* 6.3 1.1 - - - +
409S MET* 6.1 0.9 - - - -
44Y ASP* 4.3 26.1 + - - +
47Y ASN* 5.0 15.7 + - - +
48Y VAL* 4.5 11.2 - - - +
52Y PHE* 4.5 15.4 - - - -
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Residues in contact with PHE 337 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297R ARG* 3.8 40.8 - - + -
300R ARG* 4.1 14.8 - - + -
301R ILE* 3.9 27.8 - - + -
304R TYR* 4.3 15.5 - + - -
333R GLU* 3.0 47.1 + - + +
334R LEU* 4.1 3.8 - - - +
336R ARG* 1.3 100.2 - - + +
338R ILE* 1.3 63.9 + - - +
340R ALA* 3.4 6.0 + - + +
341R GLY 3.2 3.6 + - - -
342R ARG* 3.0 37.5 + - + +
343R LEU* 3.9 12.3 + - + -
52Y PHE* 6.1 0.2 - + - -
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Residues in contact with ILE 338 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334R LEU* 2.9 36.7 + - + +
335R SER* 3.9 5.2 - - - +
337R PHE* 1.3 74.3 - - - +
339R ALA* 1.3 66.6 + - - +
341R GLY* 3.0 14.2 + - - +
342R ARG 4.9 0.7 - - - +
343R LEU* 4.1 22.7 - - + +
344R HIS 5.6 0.9 - - - +
345R CYS* 3.8 34.5 - - - +
346R LYS* 4.4 7.4 - - - +
347R ILE* 4.7 11.4 - - + -
412S LEU* 3.3 26.5 - - - +
413S SER* 3.6 22.4 - - - +
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Residues in contact with ALA 339 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335R SER 3.0 19.1 + - - +
336R ARG* 3.6 9.4 - - + +
338R ILE* 1.3 78.2 - - - +
340R ALA* 1.3 58.7 + - - +
341R GLY 3.2 0.9 + - - -
409S MET* 3.7 37.0 - - + +
412S LEU* 5.2 11.4 - - - +
413S SER* 4.9 1.5 - - - -
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Residues in contact with ALA 340 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297R ARG* 5.5 2.0 - - - +
336R ARG* 3.1 15.4 + - + +
337R PHE* 3.8 9.9 - - + +
338R ILE 3.1 0.6 - - - -
339R ALA* 1.3 75.7 - - - +
341R GLY* 1.3 64.6 + - - +
342R ARG* 3.3 19.7 + - + +
44Y ASP* 4.3 18.6 - - - +
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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