Contacts of the helix formed by residues 360 - 376 (chain C) in PDB entry 4LXZ
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 THR 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C ARG* 4.4 7.7 + - - +
357C ASN 5.5 1.6 - - - +
358C GLN 3.3 11.0 + - - +
359C ASN* 1.3 74.8 - - - +
361C PRO* 1.4 74.3 - - - +
362C GLU* 3.7 9.3 + - - +
363C TYR* 3.2 23.2 + - - +
364C MET* 3.0 20.5 + - - +
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Residues in contact with PRO 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359C ASN 4.4 1.8 - - - +
360C THR* 1.4 85.8 - - - +
362C GLU* 1.4 56.9 + - - +
364C MET* 3.4 19.0 + - + +
365C GLU* 2.9 45.8 + - - +
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Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C THR* 3.2 9.0 + - - +
361C PRO* 1.4 75.5 - - - +
363C TYR* 1.3 61.4 + - - +
365C GLU* 3.3 8.3 + - - +
366C LYS* 3.0 65.0 + - + +
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Residues in contact with TYR 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C TYR* 5.7 0.9 + - - +
231C PHE* 4.9 4.5 - + - -
232C PRO* 2.6 43.5 + - - +
233C MET* 3.8 4.0 + - - -
234C ARG* 3.4 47.6 - - + +
359C ASN* 3.6 28.5 - - - -
360C THR* 3.1 22.7 + - - +
362C GLU* 1.3 76.3 - - - +
364C MET* 1.3 71.6 + - + +
366C LYS* 3.4 4.6 + - - +
367C ILE* 3.2 48.3 + - + +
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Residues in contact with MET 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PHE* 3.8 12.7 - - + -
237C ILE* 4.5 1.6 - - - -
241C SER* 3.7 32.8 - - - +
245C ILE* 3.6 31.1 - - + +
357C ASN* 5.0 0.4 - - - +
359C ASN* 3.8 36.3 - - + +
360C THR 3.0 9.0 + - - +
361C PRO* 3.7 24.0 - - + +
363C TYR* 1.3 81.2 - - + +
365C GLU* 1.3 55.9 + - + +
367C ILE 3.5 0.7 + - - -
368C LYS* 3.1 30.9 + - - +
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Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C PRO* 2.9 30.7 + - - +
362C GLU* 3.3 8.1 + - - +
364C MET* 1.3 74.3 - - + +
366C LYS* 1.3 66.6 + - + +
368C LYS* 3.4 13.2 + - - +
369C GLN* 2.9 32.1 + - - +
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Residues in contact with LYS 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU* 5.8 0.4 - - - -
362C GLU* 3.0 58.3 + - + +
363C TYR* 3.8 6.7 - - - +
365C GLU* 1.3 83.2 + - + +
367C ILE* 1.4 66.1 - - + +
369C GLN* 3.5 19.1 + - - +
370C ARG* 3.1 23.2 + - - +
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Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU* 3.6 38.8 - - + -
231C PHE* 3.6 41.7 - - + -
232C PRO* 4.1 19.3 - - + +
363C TYR* 3.2 45.5 + - + +
366C LYS* 1.4 75.4 - - + +
368C LYS* 1.3 65.9 + - - +
370C ARG* 3.2 7.6 + - - +
371C LEU* 3.0 24.3 + - + +
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Residues in contact with LYS 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PHE* 4.1 9.1 - - + -
244C GLN* 3.2 29.7 + - - +
245C ILE* 4.5 16.2 - - + +
248C PRO* 4.3 13.5 - - + +
249C ILE* 3.9 11.2 - - + -
364C MET 3.1 17.5 + - - +
365C GLU* 3.7 13.8 - - - +
367C ILE* 1.3 75.4 - - - +
369C GLN* 1.4 61.9 + - - +
371C LEU* 3.3 1.2 + - - -
372C PHE* 3.0 53.4 + - + -
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Residues in contact with GLN 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C GLU 2.9 17.5 + - - +
366C LYS* 3.5 21.0 - - - +
367C ILE 3.3 0.2 - - - -
368C LYS* 1.4 76.4 - - - +
370C ARG* 1.3 61.5 + - - +
372C PHE* 3.3 5.9 + - - +
373C GLU* 2.8 49.1 + - + +
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Residues in contact with ARG 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU* 3.8 46.7 + - + +
217C ARG* 4.9 10.9 - - - +
366C LYS 3.1 10.3 + - - +
367C ILE 3.5 8.3 - - - +
369C GLN* 1.3 79.6 - - - +
371C LEU* 1.4 57.2 + - - +
373C GLU* 3.3 22.4 + - - +
374C ASN* 2.9 45.9 + - - +
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Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PHE* 5.6 0.2 - - + -
216C LEU* 3.6 18.2 - - + +
229C VAL* 3.7 31.0 - - + -
230C ASN 3.4 26.0 - - - +
231C PHE* 3.6 32.5 - - + -
249C ILE* 3.8 26.0 - - + -
367C ILE* 3.0 19.2 + - + +
370C ARG* 1.4 70.8 - - - +
372C PHE* 1.3 55.4 + - - +
374C ASN* 3.1 14.7 + - + +
375C LEU* 2.8 43.6 + - + +
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PRO* 3.5 36.1 - - + -
249C ILE* 3.6 25.1 - - + -
252C LYS* 3.4 43.4 + - + +
368C LYS* 3.0 40.3 + - + +
369C GLN* 3.6 6.3 - - - +
371C LEU* 1.3 76.6 - - - +
373C GLU* 1.3 60.4 + - + +
375C LEU* 3.3 4.8 + - + -
376C ARG* 3.1 30.2 + - - +
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Residues in contact with GLU 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C GLN* 2.8 53.7 + - + +
370C ARG* 3.4 23.0 + - - +
371C LEU 3.3 0.2 - - - -
372C PHE* 1.3 74.3 - - + +
374C ASN* 1.4 65.1 + - - +
376C ARG* 3.4 26.5 + - - +
377C MET* 3.7 11.4 + - - +
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Residues in contact with ASN 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C LEU 4.6 2.6 + - - -
219C ILE* 3.6 28.9 - - + +
226C TYR* 3.8 36.1 - - + +
229C VAL* 6.2 3.6 - - + -
370C ARG* 2.9 41.4 + - - +
371C LEU* 3.1 17.5 + - + +
373C GLU* 1.4 76.4 - - - +
375C LEU* 1.3 60.3 + - + +
377C MET* 3.1 26.5 + - - +
378C LEU* 4.2 0.9 + - - +
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C MET* 3.8 29.2 - - + -
226C TYR 5.1 0.7 - - - +
229C VAL* 4.2 12.6 - - + -
249C ILE* 4.2 7.9 - - + +
252C LYS* 3.7 37.0 - - + +
253C VAL* 3.8 30.3 - - + +
256C MET* 3.5 16.0 - - + +
371C LEU* 2.8 32.0 + - + +
372C PHE* 3.3 9.2 + - + +
374C ASN* 1.3 73.4 - - + +
376C ARG* 1.3 60.3 + - - +
377C MET 3.1 1.3 + - - -
378C LEU* 3.3 27.1 + - + +
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LYS* 3.4 19.1 - - - +
256C MET* 4.2 8.5 - - + +
372C PHE* 3.1 19.6 + - - +
373C GLU* 3.5 17.0 + - - +
374C ASN 3.3 0.4 - - - -
375C LEU* 1.3 74.3 - - - +
377C MET* 1.4 59.4 + - + +
378C LEU 3.4 0.4 - - - -
379C PRO* 3.2 17.2 - - - +
380C HIS* 3.4 17.5 + - - -
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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