Contacts of the helix formed by residues 375 - 381 (chain P) 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 MET 375 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373P ILE 3.7 0.4 + - - -
374P THR* 1.3 71.8 - - + +
376P LYS* 1.3 71.9 + - + +
378P MET* 3.0 10.5 + - + +
379P ALA* 3.0 21.0 + - - +
386P VAL* 3.6 34.5 - - + +
389P SER* 3.7 27.8 - - - +
390P GLU* 3.6 34.8 - - + +
393P LEU* 6.3 0.4 - - + -
406P VAL* 5.0 6.1 - - - -
411P GLY* 2.7 29.6 + - - +
413P ILE* 4.4 25.6 - - + -
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Residues in contact with LYS 376 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374P THR* 3.4 13.3 - - + +
375P MET* 1.3 80.4 - - - +
377P ARG* 1.3 63.9 + - - +
379P ALA* 3.0 18.7 + - - +
380P GLN* 3.5 16.7 + - - +
386P VAL* 3.8 32.5 - - + +
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Residues in contact with ARG 377 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305O ASN* 3.3 42.7 + - - +
308O GLU* 3.0 43.9 + - - +
309O LEU* 5.7 3.0 - - - +
326O GLU* 4.4 8.1 - - - +
316P ARG* 5.5 6.5 - - - +
373P ILE* 4.5 8.7 - - + -
374P THR* 3.7 19.0 + - - +
375P MET 3.3 0.4 - - - -
376P LYS* 1.3 77.7 - - - +
378P MET* 1.3 64.4 + - - +
380P GLN* 3.2 20.4 + - - +
381P LEU* 3.0 49.5 + - + +
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Residues in contact with MET 378 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363P ILE* 3.7 33.0 - - + -
366P MET* 4.1 33.7 - - + +
373P ILE* 4.4 16.9 - - + +
374P THR 3.2 14.6 + - - +
375P MET* 3.0 21.0 + - + +
377P ARG* 1.3 77.4 - - - +
379P ALA* 1.3 63.2 + - - +
381P LEU* 2.9 14.5 + - - +
382P LEU* 2.9 35.5 + - + +
389P SER* 5.6 1.1 - - - +
393P LEU* 5.1 3.4 - - + -
413P ILE* 4.2 27.4 - - + -
415P PHE* 4.3 9.2 - - + -
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Residues in contact with ALA 379 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375P MET 3.0 9.2 + - - +
376P LYS 3.0 10.3 + - - +
378P MET* 1.3 77.3 - - - +
380P GLN* 1.3 64.6 + - - +
382P LEU* 3.3 1.0 + - - +
383P ASP* 2.7 29.5 + - - -
384P LEU 3.2 26.0 + - - +
385P SER 4.4 1.6 - - - +
386P VAL* 3.8 26.9 - - + -
389P SER* 4.4 11.9 - - - +
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Residues in contact with GLN 380 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316P ARG* 4.2 18.5 + - - +
376P LYS* 3.7 18.4 + - - +
377P ARG* 3.2 23.7 + - - +
378P MET 3.2 0.8 - - - -
379P ALA* 1.3 84.6 - - - +
381P LEU* 1.3 61.8 + - - +
382P LEU 3.2 5.3 + - - -
383P ASP* 3.8 22.9 + - - +
384P LEU 5.1 2.8 + - - +
386P VAL* 4.6 9.3 - - - +
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Residues in contact with LEU 381 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308O GLU* 4.1 7.6 - - + +
309O LEU* 5.0 7.6 - - + -
314P LEU* 4.4 27.1 - - + +
316P ARG* 4.9 14.9 - - - +
362P ASN* 3.2 23.9 + - - +
366P MET* 3.7 27.0 - - + +
370P TYR* 4.7 5.8 - - + +
373P ILE* 4.1 13.7 - - + -
377P ARG* 3.0 53.5 + - + +
378P MET* 2.9 9.0 + - - +
380P GLN* 1.3 79.5 - - - +
382P LEU* 1.3 61.6 + - - +
383P ASP* 5.6 0.7 - - - -
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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