Contacts of the helix formed by residues 420 - 433 (chain A) in PDB entry 4PS1
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 TRP 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A TYR* 3.1 41.2 + + + +
414A ASN* 5.2 5.4 - - + +
417A GLU* 5.4 4.6 + - - -
418A GLY 5.1 3.4 - - - -
419A THR* 1.3 75.3 - - - +
421A TYR* 1.3 64.3 + - - +
423A GLN* 4.2 2.0 - - - +
424A SER* 3.1 26.5 + - - -
450A VAL* 3.7 12.4 - - + +
453A LYS* 3.3 55.9 - - + +
454A ASP 3.6 32.8 - - - -
455A ASP 3.7 3.4 - - - -
460A GLY 4.8 0.2 - - - -
461A LYS 4.5 0.4 - - - -
462A GLN* 3.4 39.7 - - + +
402E LEU* 3.6 38.4 - - + +
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Residues in contact with TYR 421 (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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356A PHE* 3.6 18.7 - + + -
357A ILE 4.3 4.5 - - - -
358A GLN* 3.4 15.3 - - + +
402A GLY* 3.3 40.0 - - - -
403A MET 3.9 11.2 - - - -
404A ALA* 3.6 22.7 - - + -
419A THR* 3.2 1.4 + - - -
420A TRP* 1.3 78.9 - - - +
422A ILE* 1.3 82.1 + - + +
424A SER* 3.3 1.7 + - - -
425A LEU* 2.8 36.1 + - + +
443A LEU* 3.8 13.5 - - + +
446A VAL* 3.8 24.9 - - + -
450A VAL* 4.0 6.3 - - - -
462A GLN* 3.8 9.3 - - - +
464A PRO* 3.8 19.5 - - + -
466A PRO* 5.8 1.2 - - + +
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Residues in contact with ILE 422 (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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266A ASP* 3.5 31.4 - - + +
270A LEU* 3.7 33.0 - - + -
313A CYS* 5.8 0.2 - - + -
315A LEU* 3.8 17.3 - - + -
356A PHE* 4.7 10.1 - - + -
358A GLN* 3.7 18.2 - - + +
419A THR* 3.1 19.1 + - - +
421A TYR* 1.3 94.5 - - + +
423A GLN* 1.3 58.9 + - - +
425A LEU* 3.3 14.6 + - + +
426A CYS* 2.9 31.8 + - - -
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Residues in contact with GLN 423 (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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265A LEU* 3.2 26.0 + - - -
266A ASP* 2.8 25.4 + - - +
269A ALA* 3.9 14.5 - - - +
417A GLU* 3.3 28.0 + - + +
418A GLY 4.1 0.7 - - - -
419A THR 3.0 23.6 + - - +
420A TRP* 4.2 2.0 - - - +
422A ILE* 1.3 78.3 - - - +
424A SER* 1.3 62.4 + - - +
426A CYS* 3.6 2.7 + - - +
427A GLN* 3.1 24.9 + - - +
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Residues in contact with SER 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TRP 3.1 21.3 + - - -
421A TYR 3.8 1.6 - - - -
423A GLN* 1.3 72.6 - - - +
425A LEU* 1.3 60.2 + - - +
427A GLN* 3.4 8.6 + - - +
428A SER* 2.9 31.7 + - - -
446A VAL* 3.6 15.5 - - - -
449A GLU* 3.5 27.3 - - - +
450A VAL* 3.7 16.3 - - - +
453A LYS* 6.2 1.3 - - - -
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Residues in contact with LEU 425 (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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270A LEU* 4.5 11.2 - - + -
356A PHE* 3.7 44.0 - - + -
421A TYR* 2.8 22.9 + - + +
422A ILE* 3.6 19.5 - - + +
424A SER* 1.3 77.5 - - - +
426A CYS* 1.3 57.9 - - - +
428A SER* 3.3 2.1 + - - -
429A LEU* 2.9 54.7 + - + +
439A ILE* 4.9 0.7 - - + -
442A ILE* 4.6 4.9 - - + -
443A LEU* 4.0 26.7 - - + -
446A VAL* 3.6 15.4 - - + +
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Residues in contact with CYS 426 (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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269A ALA* 3.6 30.3 - - + -
270A LEU* 3.6 31.6 - - - -
273A THR* 3.4 25.1 - - - +
422A ILE* 2.9 20.7 + - - +
423A GLN* 4.2 3.1 - - - +
425A LEU* 1.3 75.5 - - - +
427A GLN* 1.3 59.6 + - - +
429A LEU* 3.8 5.6 - - - +
430A ARG* 2.9 40.9 + - - +
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Residues in contact with GLN 427 (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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423A GLN 3.1 18.5 + - - +
424A SER* 3.7 8.2 - - - +
425A LEU 3.3 0.2 - - - -
426A CYS* 1.3 75.8 - - - +
428A SER* 1.3 58.6 + - - +
430A ARG* 3.3 9.7 + - - +
431A GLU* 2.9 62.9 + - - +
449A GLU* 5.5 11.0 - - - +
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Residues in contact with SER 428 (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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424A SER* 2.9 17.2 + - - -
425A LEU 3.8 2.9 - - - -
427A GLN* 1.3 76.4 - - - +
429A LEU* 1.3 60.2 + - - +
431A GLU* 4.5 3.1 - - - -
432A ARG* 2.8 38.5 + - - +
442A ILE* 3.4 27.5 + - - +
445A GLU* 2.8 30.0 + - - -
446A VAL* 3.9 10.5 - - - -
449A GLU* 6.5 0.4 - - - -
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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
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273A THR* 3.7 23.1 - - + -
274A PHE* 3.7 27.8 - - + -
277A LEU* 4.8 2.4 - - + +
356A PHE* 5.3 0.2 - - + -
425A LEU* 2.9 44.4 + - + +
426A CYS* 3.8 1.6 - - - +
428A SER* 1.3 73.7 - - - +
430A ARG* 1.3 60.6 + - - +
433A CYS* 2.9 57.4 + - - +
439A ILE* 3.7 28.3 - - + -
442A ILE* 3.9 9.2 - - + +
476A PHE* 4.3 10.8 - - + -
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Residues in contact with ARG 430 (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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269A ALA* 6.2 2.2 - - - +
272A THR* 4.8 14.1 - - - +
273A THR* 3.4 31.2 - - + +
276A GLU* 4.3 21.9 + - - +
426A CYS* 2.9 24.3 + - - +
427A GLN* 3.8 8.1 - - - +
429A LEU* 1.3 76.3 - - - +
431A GLU* 1.3 62.8 + - + +
434A PRO* 3.3 20.3 - - - +
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Residues in contact with GLU 431 (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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427A GLN* 2.9 50.3 + - + +
428A SER* 4.0 2.6 - - - +
430A ARG* 1.3 79.5 - - + +
432A ARG* 1.3 67.2 + - + +
434A PRO* 3.8 5.1 - - - +
435A ARG* 3.6 20.5 - - - +
445A GLU* 4.2 13.3 - - - +
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Residues in contact with ARG 432 (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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428A SER* 2.8 24.0 + - - +
431A GLU* 1.3 83.5 - - + +
433A CYS* 1.3 64.5 + - - +
434A PRO 3.2 2.5 - - - -
435A ARG* 3.0 31.3 + - - +
436A GLY 3.3 7.1 + - - -
437A ASP* 2.7 48.2 + - - +
441A THR* 3.7 19.3 - - - +
442A ILE* 3.8 22.7 - - + +
445A GLU* 2.7 46.9 + - - +
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Residues in contact with CYS 433 (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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277A LEU* 3.9 27.4 - - + -
429A LEU* 2.9 45.8 + - - +
432A ARG* 1.3 76.8 - - - +
434A PRO* 1.4 64.9 - - + +
436A GLY* 2.9 15.5 + - - +
437A ASP 4.7 7.9 - - - -
442A ILE* 3.9 9.2 - - - -
476A PHE* 3.7 35.1 - - - +
477A PRO* 5.2 4.2 - - - +
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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