Contacts of the helix formed by residues 335 - 346 (chain J) in PDB entry 5LK5
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 335 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356G GLN* 4.4 9.6 + - - +
19J PRO* 3.5 39.0 - - + +
92J VAL* 4.1 3.1 - - - +
333J THR* 3.5 12.1 + - - +
334J ASN* 1.3 80.8 - - - +
336J GLU* 1.3 62.9 + - - +
337J ALA* 3.0 23.6 + - - +
338J TYR* 3.1 15.5 + - + +
339J ALA* 3.0 18.0 + - - +
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Residues in contact with GLU 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G GLN* 5.9 0.4 - - - +
90J THR* 4.2 13.2 + - + +
92J VAL* 4.0 7.4 - - - +
175J ILE* 3.7 30.4 - - + +
177J ARG* 2.7 47.4 + - - +
183J GLU* 4.4 4.2 - - - +
185J LYS* 5.2 9.4 + - - +
334J ASN 4.3 0.2 + - - -
335J ASP* 1.3 74.1 + - - +
337J ALA* 1.3 63.9 + - - +
339J ALA* 3.3 5.8 + - - +
340J GLU* 3.1 22.5 + - - +
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Residues in contact with ALA 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G ALA* 4.1 26.9 - - + +
353G ALA* 4.3 14.1 - - + +
356G GLN* 3.3 27.9 + - - +
335J ASP* 3.0 7.7 + - - +
336J GLU* 1.3 76.4 - - - +
338J TYR* 1.3 65.1 + - - +
340J GLU* 3.2 4.7 + - - +
341J GLU* 3.0 23.5 + - - +
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Residues in contact with TYR 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J PRO* 4.4 15.0 - - + -
21J VAL* 4.0 22.8 - - + +
24J LYS* 2.6 27.7 + - - -
331J LEU* 4.1 21.5 - - + -
333J THR* 4.0 15.3 - - - -
335J ASP* 3.1 26.9 + - + +
337J ALA* 1.3 78.9 - - - +
339J ALA* 1.3 63.7 + - - +
341J GLU* 3.2 30.7 + - - +
342J PHE* 2.9 32.4 + - + +
345J GLU* 5.3 3.4 + - - -
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Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J VAL* 3.7 30.7 - - + -
94J GLN* 3.0 24.9 + - - +
173J THR* 4.8 2.7 - - + -
175J ILE* 5.5 0.7 - - + -
331J LEU* 3.8 15.0 - - + -
333J THR* 4.1 5.6 - - + +
335J ASP 3.0 11.7 + - - +
336J GLU* 3.3 10.1 + - - +
338J TYR* 1.3 77.2 - - - +
340J GLU* 1.3 57.1 + - - +
342J PHE 3.5 0.3 + - - -
343J GLY* 3.0 23.2 + - - -
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Residues in contact with GLU 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348G GLY 5.4 1.1 - - - +
351G LYS* 2.7 39.0 + - - +
352G ALA* 3.7 21.7 - - + +
185J LYS* 3.5 20.7 + - - +
188J ASN* 3.1 41.3 + - - +
336J GLU 3.1 13.1 + - - +
337J ALA* 3.2 8.9 + - - +
339J ALA* 1.3 74.0 - - - +
341J GLU* 1.3 65.0 + - - +
343J GLY 3.3 0.2 + - - -
344J ASN* 3.0 28.5 + - - +
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Residues in contact with GLU 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G LYS* 4.6 6.6 + - - -
348G GLY 4.5 8.3 - - - -
349G VAL* 3.5 47.4 - - + +
352G ALA* 5.5 1.0 - - + +
337J ALA 3.0 12.5 + - - +
338J TYR* 3.3 34.6 - - + +
340J GLU* 1.3 75.8 - - - +
342J PHE* 1.3 62.5 + - - +
344J ASN* 3.1 5.9 + - - +
345J GLU* 3.0 39.0 + - - +
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Residues in contact with PHE 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J LYS* 3.5 37.2 - - + -
26J GLN* 3.6 39.5 - - + -
94J GLN* 4.1 6.5 - - - -
329J ASN 3.9 15.9 - - - -
330J PHE 4.1 3.8 - - - -
331J LEU* 3.7 40.4 - - + -
338J TYR* 2.9 23.5 + - + +
339J ALA 3.8 3.8 - - - +
341J GLU* 1.3 73.7 - - - +
343J GLY* 1.3 57.9 + - - +
345J GLU* 3.3 16.3 + - + -
346J THR* 2.7 51.4 + - + +
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Residues in contact with GLY 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94J GLN* 3.6 15.9 - - - +
171J LEU* 3.8 17.7 - - - -
188J ASN* 3.9 5.2 - - - -
339J ALA 3.0 11.4 + - - -
340J GLU 3.3 4.2 + - - -
341J GLU 3.2 0.2 - - - -
342J PHE* 1.3 77.4 - - - +
344J ASN* 1.3 57.0 + - - +
346J THR* 3.6 5.4 - - - -
347J TRP* 3.1 15.5 + - - +
348J GLY 3.1 20.4 + - - -
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Residues in contact with ASN 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344G ASN* 3.6 36.7 - - + +
347G TRP* 5.6 2.2 - - - -
348G GLY* 2.9 30.5 + - - +
351G LYS* 4.9 6.1 - - - +
188J ASN* 3.0 22.0 + - - +
340J GLU* 3.0 23.2 + - - +
341J GLU 3.1 6.9 + - - +
343J GLY* 1.3 76.6 - - - +
345J GLU* 1.3 58.7 + - - +
346J THR 3.3 0.2 - - - -
347J TRP* 4.0 13.5 - - - -
348J GLY* 3.4 25.1 - - - -
349J VAL* 3.6 3.1 + - - +
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Residues in contact with GLU 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G LYS* 5.0 4.9 + - - -
345G GLU* 5.0 11.0 - - + -
349G VAL* 3.5 33.5 - - + +
338J TYR* 5.3 4.2 + - - -
341J GLU* 3.0 31.0 + - - +
342J PHE* 3.8 21.1 - - + +
343J GLY 3.3 0.2 - - - -
344J ASN* 1.3 76.7 - - - +
346J THR* 1.3 63.6 + - + +
349J VAL* 3.4 22.1 - - - +
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Residues in contact with THR 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J GLN* 3.7 17.3 - - - +
94J GLN* 5.3 0.2 + - - -
96J THR* 4.9 0.2 - - - +
171J LEU* 4.8 4.0 - - - +
329J ASN* 3.4 40.0 - - - +
342J PHE* 2.7 40.6 + - + +
343J GLY* 3.3 7.5 + - - -
345J GLU* 1.3 81.6 - - + +
347J TRP* 1.3 72.7 + - - +
349J VAL* 3.0 11.7 + - - +
350J THR* 2.9 18.7 + - - +
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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