Contacts of the helix formed by residues 423 - 440 (chain A) in PDB entry 4LZ6
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 PHE 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A MET* 6.0 4.5 - - + -
365A LEU* 3.7 20.2 - - + +
403A LEU* 3.6 33.2 - - + -
407A VAL* 5.1 9.2 - - + -
419A VAL* 2.7 48.0 - - + -
420A TRP 2.7 10.1 + - - -
422A ALA* 1.3 72.8 - - + +
424A PRO* 1.4 65.4 - - + +
425A ILE 2.9 1.3 - - - -
426A ALA* 2.5 29.6 + - - -
427A ASP* 3.2 20.7 + - - +
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Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 3.3 19.7 - - + +
365A LEU* 3.0 35.0 - - + +
367A CYS 4.9 5.0 - - - +
368A VAL* 3.2 28.2 - - + +
420A TRP* 3.0 40.8 - - + +
421A TRP* 5.0 0.7 - - - +
423A PHE* 1.4 83.2 - - + +
425A ILE* 1.3 62.8 - - + +
428A VAL* 3.9 15.4 + - - +
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 3.8 16.6 - - + -
420A TRP* 5.8 2.0 - - + -
421A TRP* 3.2 46.6 + - + +
423A PHE 2.6 5.1 + - - -
424A PRO* 1.3 81.0 - - + +
426A ALA* 1.3 68.5 + - - +
428A VAL* 3.3 23.0 + - + +
429A LEU* 3.6 4.0 + - + +
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ARG 5.3 4.3 - - - +
402A PHE* 4.5 7.4 - - + +
403A LEU* 3.9 25.8 - - + -
406A LEU* 4.1 7.1 - - + +
421A TRP 4.0 0.4 + - - -
422A ALA 3.1 24.8 + - - +
423A PHE* 2.5 11.3 + - - +
425A ILE* 1.3 77.2 - - - +
427A ASP* 1.3 66.8 + - - +
428A VAL 2.9 0.2 + - - -
429A LEU* 3.0 20.8 + - - +
430A SER* 3.3 10.6 + - - -
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Residues in contact with ASP 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 3.0 33.2 - - + +
372A ILE* 4.7 8.1 - - - +
375A GLN* 2.7 29.2 + - - +
398A ARG* 4.0 20.0 + - - +
423A PHE* 3.2 17.3 + - - +
426A ALA* 1.3 80.5 - - - +
428A VAL* 1.3 49.5 + - - +
430A SER* 2.8 10.5 + - - -
431A PHE 2.6 32.1 + - - -
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 4.2 4.2 - - + +
371A LEU* 3.7 28.3 - - + -
424A PRO 3.9 12.5 + - - +
425A ILE* 3.3 19.2 + - + +
426A ALA 2.9 2.4 + - - -
427A ASP* 1.3 77.3 - - - +
429A LEU* 1.3 57.4 + - + +
431A PHE* 2.9 7.5 + - + +
432A ILE* 2.6 57.5 + - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PHE* 2.9 72.0 - - + -
425A ILE 4.4 3.6 - - - +
426A ALA* 3.0 14.8 + - - +
428A VAL* 1.3 81.1 - - + +
430A SER* 1.3 69.4 + - - +
432A ILE* 4.3 7.9 - - - +
433A LEU* 2.6 39.0 + - + +
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Residues in contact with SER 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN* 3.7 16.6 - - - -
394A LEU* 4.4 4.3 - - - +
397A SER* 4.4 8.5 + - - -
398A ARG* 3.2 39.4 + - - +
402A PHE* 5.4 0.3 - - - +
426A ALA 3.3 4.5 + - - -
427A ASP* 2.8 25.1 + - - -
429A LEU* 1.3 80.7 - - - +
431A PHE* 1.3 50.7 + - - +
433A LEU* 3.5 5.5 - - - +
434A THR* 2.7 36.0 + - - -
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 3.6 57.7 - - + -
374A ALA* 5.2 8.3 - - + -
375A GLN* 3.1 20.7 + - + +
427A ASP 2.6 11.6 + - - +
428A VAL* 2.9 12.4 + - - +
430A SER* 1.3 68.4 - - - +
432A ILE* 1.3 93.0 + - + +
434A THR* 2.8 20.8 + - + +
435A VAL* 2.7 48.7 + - + +
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL* 2.6 60.7 + - + +
429A LEU* 4.0 5.6 - - - +
431A PHE* 1.3 83.8 - - + +
433A LEU* 1.3 66.7 + - - +
435A VAL* 2.9 27.8 + - + +
436A VAL* 3.2 10.1 + - + +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ILE* 4.9 7.6 - - + +
394A LEU* 3.8 12.1 - - + -
397A SER* 3.9 20.6 - - - +
402A PHE* 5.0 7.0 - - + -
429A LEU* 2.6 28.2 + - + +
430A SER* 3.5 2.9 - - - +
432A ILE* 1.3 76.2 - - - +
434A THR* 1.3 52.1 + - - +
435A VAL 2.9 1.2 + - - -
436A VAL* 3.1 22.9 + - + +
437A LEU* 2.7 64.2 + - + +
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Residues in contact with THR 434 (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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374A ALA* 4.9 2.7 - - + -
375A GLN* 3.6 29.1 - - + +
378A ALA* 3.3 24.2 - - + +
382A TYR* 5.6 0.2 - - - -
394A LEU* 3.2 25.3 - - - +
430A SER 2.7 16.7 + - - -
431A PHE* 2.8 31.7 + - + +
433A LEU* 1.3 69.7 - - - +
435A VAL* 1.3 66.0 + - - +
437A LEU* 3.6 8.3 + - - +
438A LEU* 3.3 23.1 - - + +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 2.7 61.7 + - + +
432A ILE* 2.9 12.5 + - + +
433A LEU 2.9 1.4 + - - -
434A THR* 1.3 70.7 - - - +
436A VAL* 1.3 54.5 + - - +
438A LEU* 2.8 34.9 + - - +
439A TYR* 3.5 33.7 + - + +
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ILE* 3.2 9.1 + - + +
433A LEU* 3.1 29.6 + - + +
435A VAL* 1.3 72.6 - - - +
437A LEU* 1.3 69.3 + - + +
438A LEU 2.8 11.5 + - - -
439A TYR* 3.9 8.9 - - + +
440A ARG* 3.0 29.9 + - - +
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A TYR* 2.1 37.3 + - + +
390A GLN* 3.9 26.4 - - + +
393A ILE* 5.0 11.0 - - + -
394A LEU* 3.2 44.0 - - + +
433A LEU* 2.7 35.9 + - + +
434A THR* 4.0 9.9 - - - +
435A VAL 3.1 1.0 + - - -
436A VAL* 1.3 80.2 - - + +
438A LEU* 1.3 55.0 + - + +
440A ARG* 3.4 23.9 - - + +
441A ASP* 3.3 6.9 - - - +
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Residues in contact with LEU 438 (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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323A PHE* 3.4 41.1 - - + -
374A ALA* 5.8 2.2 - - + -
378A ALA* 4.8 13.2 - - + -
381A LEU* 6.0 0.9 - - + +
382A TYR* 3.1 29.6 - - + +
434A THR* 3.3 18.2 - - + +
435A VAL* 2.8 9.6 + - - +
436A VAL 2.8 1.4 + - - -
437A LEU* 1.3 79.9 - - + +
439A TYR* 1.3 59.9 + - + +
440A ARG 2.7 4.7 - - - -
441A ASP 2.6 32.8 + - - +
442A ARG* 3.4 0.9 + - - -
444A VAL* 4.3 18.8 - - + -
445A PHE* 6.5 0.9 - - + -
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Residues in contact with TYR 439 (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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435A VAL* 3.5 39.6 + - + +
436A VAL* 3.5 6.9 + - + +
438A LEU* 1.3 73.2 - - + +
440A ARG* 1.3 61.7 + - - +
441A ASP 3.2 0.2 - - - -
442A ARG* 3.6 51.2 + - - +
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Residues in contact with ARG 440 (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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390A GLN* 5.0 3.4 - - - +
436A VAL* 3.0 27.1 + - - +
437A LEU* 3.4 27.6 - - + +
439A TYR* 1.3 81.5 - - - +
441A ASP* 1.3 66.8 + - - +
442A ARG* 4.1 0.9 + - - +
443A ASN* 4.6 1.9 + - - -
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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