Contacts of the helix formed by residues 360 - 376 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASN 5.2 2.9 - - - +
358A GLN 3.3 11.0 + - - +
359A ASN* 1.3 75.4 - - - +
361A PRO* 1.3 75.4 - - + +
362A GLU* 3.6 15.4 + - - +
363A TYR* 3.0 35.7 + - - +
364A MET* 3.0 12.0 + - - +
340B GLU* 4.4 9.7 + - + +
343B GLY* 5.7 0.7 - - - -
346B PHE* 4.9 0.7 - - - -
405B PG4 3.9 34.5 - - - -
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Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A SER* 5.7 3.1 - - - +
244A GLN* 3.2 27.7 + - - +
359A ASN 3.7 2.2 - - - +
360A THR* 1.3 85.8 - - - +
362A GLU* 1.4 64.7 + - - +
364A MET* 3.3 1.9 + - + -
365A GLU* 3.0 27.0 + - - +
194C THR* 4.0 19.1 - - + -
222C GLY* 3.5 32.3 - - - -
223C LYS* 4.7 3.6 - - + +
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR* 3.1 16.8 - - - +
361A PRO* 1.4 80.5 - - - +
363A TYR* 1.4 61.3 + - - +
365A GLU* 3.4 4.7 + - - +
366A LYS* 2.9 31.4 + - - +
343B GLY* 4.7 1.8 - - - -
344B PRO* 3.8 33.7 - - + +
346B PHE* 3.5 21.8 - - + -
194C THR* 2.8 41.4 + - - +
195C THR* 5.2 1.7 - - - -
223C LYS* 5.6 2.8 - - - +
404C PG4 6.4 0.2 - - - -
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Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 4.6 0.9 - + - -
232A PRO* 2.7 31.6 + - - +
233A MET* 4.0 1.2 + - - -
234A ARG* 3.8 18.3 + - + -
359A ASN* 3.6 26.0 - - + -
360A THR* 3.0 26.0 + - - +
362A GLU* 1.4 76.7 - - - +
364A MET* 1.3 73.9 + - - +
366A LYS* 3.2 2.5 + - - +
367A ILE* 3.0 37.5 + - + +
335B TYR* 2.7 28.0 + + - -
339B PHE* 3.8 28.5 - + + -
340B GLU* 3.7 28.7 - - + -
346B PHE* 3.6 9.8 - - - -
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Residues in contact with MET 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.6 25.1 - - + -
233A MET* 4.3 1.3 - - + -
237A ILE* 3.6 24.2 - - + -
241A SER* 3.8 10.3 - - - +
244A GLN* 3.8 24.5 - - - +
245A ILE* 3.4 36.2 - - + +
359A ASN* 3.6 33.7 - - + +
360A THR 3.0 16.4 + - - +
361A PRO 3.6 6.5 - - - +
363A TYR* 1.3 86.3 - - - +
365A GLU* 1.3 61.7 + - - +
367A ILE 3.6 0.2 + - - -
368A LYS* 3.1 23.9 + - - +
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN* 4.1 12.6 + - - +
245A ILE* 5.3 0.2 - - - -
361A PRO 3.0 16.3 + - - +
362A GLU* 3.9 4.5 - - - +
364A MET* 1.3 76.5 - - - +
366A LYS* 1.3 58.2 + - - +
368A LYS* 3.1 35.9 + - - +
369A GLN* 2.9 48.9 + - + +
149C LYS* 5.5 7.4 + - - +
190C GLU* 3.8 26.0 - - + +
193C TYR* 5.0 13.8 - - + +
194C THR* 4.5 12.3 - - + +
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLU 2.9 19.8 + - - +
363A TYR 3.2 3.1 + - - +
365A GLU* 1.3 73.2 - - - +
367A ILE* 1.4 59.7 + - - +
369A GLN* 3.2 8.1 + - + +
370A ARG* 2.9 53.3 + - - +
373A GLU* 5.9 0.8 + - - -
332B GLU* 2.7 35.7 + - - -
339B PHE* 3.6 24.0 - - + -
345B ASP 5.3 2.5 + - - +
346B PHE* 3.7 30.7 - - + +
347B LYS* 4.7 4.0 - - - +
74C SER* 6.0 0.2 - - - -
149C LYS* 3.9 34.9 - - + +
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 4.1 16.8 - - + -
231A PHE* 3.6 39.5 - - + -
232A PRO* 4.1 14.1 - - + -
363A TYR* 3.0 40.0 + - + +
366A LYS* 1.4 73.7 - - - +
368A LYS* 1.3 56.6 + - - +
370A ARG* 3.2 8.2 + - - +
371A LEU* 2.9 32.7 + - + +
335B TYR* 3.6 36.8 - - + -
339B PHE* 4.0 15.7 - - + -
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Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 4.0 3.7 - - + -
244A GLN* 4.4 7.4 - - - -
245A ILE* 4.1 25.1 - - + -
248A PRO* 3.9 18.2 - - + +
249A ILE* 3.8 17.7 - - + -
364A MET 3.1 17.6 + - - +
365A GLU* 3.1 40.6 + - - +
367A ILE* 1.3 77.2 - - - +
369A GLN* 1.3 61.2 + - - +
371A LEU* 3.2 3.1 + - - +
372A PHE* 2.9 64.6 + - + -
190C GLU* 5.3 0.4 + - - -
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A GLU* 2.9 34.2 + - + +
366A LYS* 3.2 9.8 + - + +
368A LYS* 1.3 85.3 + - - +
370A ARG* 1.4 62.3 + - + +
372A PHE* 3.3 27.3 + - - +
373A GLU* 3.1 28.3 + - + +
376A ARG* 5.0 7.1 + - - +
148C LYS* 5.6 6.0 - - + +
149C LYS* 4.8 25.1 - - + +
150C SER* 5.9 3.1 - - - +
151C GLU* 5.9 0.4 + - - -
190C GLU* 3.0 34.9 + - - +
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Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.8 24.1 - - + +
366A LYS* 2.9 36.6 + - - +
367A ILE* 3.6 7.9 - - - +
369A GLN* 1.4 75.5 - - + +
371A LEU* 1.3 63.0 + - - +
373A GLU* 3.3 27.5 + - - +
374A ASN* 3.3 18.6 + - - +
332B GLU* 2.8 28.0 + - - -
333B LEU 2.7 31.3 + - - +
334B PRO* 3.9 1.6 - - - +
335B TYR* 3.5 25.1 - - - +
339B PHE* 3.5 25.2 - - - -
346B PHE 4.9 1.2 + - - -
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 4.3 16.4 - - + +
229A VAL* 3.9 28.7 - - + -
230A ASN 3.4 27.8 - - - +
231A PHE* 3.6 34.1 - - + -
249A ILE* 3.8 18.4 - - + -
367A ILE* 2.9 20.2 + - + +
368A LYS 3.7 4.0 - - - +
370A ARG* 1.3 77.1 - - - +
372A PHE* 1.4 56.4 + - - +
374A ASN* 3.1 20.4 + - + +
375A LEU* 3.0 33.0 + - + +
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PRO* 3.7 30.1 - - + -
249A ILE* 3.9 17.3 - - + -
252A LYS* 3.8 35.8 - - + +
368A LYS* 2.9 53.0 + - + -
369A GLN* 3.6 34.1 - - - +
370A ARG 3.3 0.2 - - - -
371A LEU* 1.4 76.1 - - - +
373A GLU* 1.4 60.7 + - - +
375A LEU* 3.2 9.0 + - + +
376A ARG* 3.1 34.8 + - + +
190C GLU* 5.8 0.4 - - - -
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LYS* 5.9 0.9 + - - -
369A GLN* 3.1 21.6 + - + +
370A ARG* 3.4 21.4 + - - +
372A PHE* 1.4 74.4 - - - +
374A ASN* 1.4 64.3 + - - +
376A ARG* 3.2 44.1 + - - +
377A MET* 3.8 12.0 - - - +
332B GLU* 5.7 0.9 - - - +
74C SER* 5.4 3.1 + - - -
98C ARG* 4.2 24.6 + - + +
99C PHE* 4.5 2.4 - - - -
150C SER* 3.0 29.5 + - - +
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Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 4.4 8.3 + - - +
219A ILE* 3.7 29.5 - - + +
226A TYR* 3.6 34.9 - - + +
229A VAL* 6.2 4.0 - - + -
370A ARG* 3.3 14.9 + - - +
371A LEU* 3.1 21.1 + - + +
373A GLU* 1.4 82.8 - - - +
375A LEU* 1.3 62.6 + - + +
377A MET* 3.1 21.7 + - - +
378A LEU 4.2 0.3 + - - -
98C ARG* 5.8 1.7 + - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A MET* 4.2 22.0 - - + -
226A TYR 5.0 2.0 - - - +
229A VAL* 4.3 15.5 - - + -
249A ILE* 4.5 9.6 - - + +
252A LYS* 3.7 34.1 - - + -
253A VAL* 3.8 36.3 - - + -
256A MET* 3.4 21.6 - - + +
371A LEU* 3.0 21.1 + - + +
372A PHE* 3.2 14.6 + - + +
374A ASN* 1.3 77.7 - - + +
376A ARG* 1.4 60.2 + - - +
378A LEU* 3.2 23.0 + - + +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LYS* 6.3 4.9 - - + -
256A MET* 4.5 9.7 - - - +
369A GLN* 5.0 7.7 - - - +
372A PHE* 3.1 24.2 + - + +
373A GLU* 3.2 49.9 + - - +
374A ASN 3.2 0.6 - - - -
375A LEU* 1.4 74.3 - - - +
377A MET* 1.3 51.0 + - - +
378A LEU 3.3 4.2 + - - +
97C GLN* 2.9 42.5 + - - +
98C ARG* 2.9 23.9 + - - +
100C ASN* 5.4 1.3 - - - -
150C SER* 3.1 28.3 + - - -
151C GLU* 3.4 38.6 + - - +
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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
------------------------------------------------------------
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