Contacts of the helix formed by residues 420 - 433 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B TYR* 3.1 40.9 + + + -
414B ASN* 5.3 4.8 - - + +
417B GLU* 6.0 1.6 - - - -
418B GLY 5.1 2.9 - - - -
419B THR* 1.3 75.0 - - - +
421B TYR* 1.3 64.1 + - - +
423B GLN* 4.3 1.9 - - - +
424B SER* 3.1 27.7 + - - -
450B VAL* 3.8 13.0 - - + +
453B LYS* 3.3 58.0 - - + +
454B ASP* 3.5 34.8 - - - -
455B ASP 3.7 3.6 - - - -
460B GLY 4.8 0.2 - - - -
461B LYS 4.6 0.4 - - - -
462B GLN* 3.4 41.5 - - + +
402F LEU* 3.5 39.2 - - + +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B PHE* 3.6 14.6 - + + -
357B ILE 4.3 4.5 - - - -
358B GLN* 3.4 14.4 - - + +
402B GLY* 3.2 37.9 - - - -
403B MET 3.8 14.1 + - - -
404B ALA* 3.6 24.2 - - + -
419B THR* 3.2 1.8 + - - -
420B TRP* 1.3 78.3 - - - +
422B ILE* 1.3 83.4 + - + +
424B SER* 3.3 1.6 + - - -
425B LEU* 2.9 40.6 + - + +
443B LEU* 3.9 12.9 - - + +
446B VAL* 3.7 25.1 - - + -
450B VAL* 4.1 6.1 - - - -
462B GLN* 3.8 8.1 - - - +
464B PRO* 3.8 19.5 - - + -
466B PRO* 5.7 1.2 - - + +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ASP* 3.4 30.3 - - + +
270B LEU* 3.8 31.2 - - + -
313B CYS* 5.8 0.2 - - + -
315B LEU* 3.9 13.2 - - + -
356B PHE* 4.7 10.5 - - + -
358B GLN* 3.6 22.2 - - + +
419B THR* 3.2 20.0 + - - +
421B TYR* 1.3 97.5 - - + +
423B GLN* 1.3 59.1 + - - +
425B LEU* 3.3 14.7 + - + +
426B CYS* 2.9 31.8 + - - -
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.2 27.1 + - - +
266B ASP* 3.0 24.3 + - - +
269B ALA* 3.7 15.0 - - - +
417B GLU* 3.5 26.8 + - + +
418B GLY 4.1 0.9 - - - -
419B THR 3.0 21.7 + - - +
420B TRP* 4.3 2.0 - - - +
422B ILE* 1.3 78.4 - - - +
424B SER* 1.3 60.9 + - - +
426B CYS* 3.5 2.9 + - - +
427B GLN* 3.0 26.0 + - - +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TRP 3.1 20.4 + - - -
421B TYR 3.7 2.7 - - - -
423B GLN* 1.3 73.0 - - - +
425B LEU* 1.3 61.4 + - - +
427B GLN* 3.3 8.0 + - - +
428B SER* 2.9 31.4 + - - -
446B VAL* 3.6 17.1 - - - +
449B GLU* 3.6 25.7 - - - +
450B VAL* 3.8 12.7 - - - +
453B LYS* 6.1 1.8 - - - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B LEU* 4.6 9.4 - - + -
356B PHE* 3.7 44.2 - - + -
421B TYR* 2.9 23.8 + - + +
422B ILE* 3.5 20.4 - - + +
424B SER* 1.3 78.1 + - - +
426B CYS* 1.3 57.2 + - - +
428B SER* 3.8 1.2 - - - -
429B LEU* 2.9 55.5 + - + +
439B ILE* 5.2 0.4 - - + -
442B ILE* 4.9 2.5 - - + -
443B LEU* 3.9 27.4 - - + -
446B VAL* 3.7 15.7 - - + +
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Residues in contact with CYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ALA* 3.6 33.4 - - + -
270B LEU* 3.7 26.5 - - - -
273B THR* 3.3 26.7 - - - +
422B ILE* 2.9 20.6 + - - +
423B GLN* 4.2 2.7 - - - +
425B LEU* 1.3 78.9 - - - +
427B GLN* 1.3 63.9 + - - +
429B LEU* 3.8 5.8 - - - +
430B ARG* 2.9 34.2 + - - +
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Residues in contact with GLN 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLN 3.0 17.9 + - - +
424B SER* 3.6 8.2 - - - +
426B CYS* 1.3 77.6 - - - +
428B SER* 1.3 57.3 + - - +
430B ARG* 3.8 8.2 - - - +
431B GLU* 2.9 63.7 + - - +
449B GLU* 5.5 9.9 + - - +
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B SER* 2.9 18.3 + - - -
425B LEU 3.9 0.7 - - - -
427B GLN* 1.3 74.0 - - - +
429B LEU* 1.3 61.4 + - - +
431B GLU* 4.5 3.4 - - - -
432B ARG* 2.8 36.9 + - - +
442B ILE* 3.2 29.4 + - - +
445B GLU* 3.1 29.1 + - - -
446B VAL* 3.9 11.7 - - - -
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B THR* 3.7 21.5 - - + -
274B PHE* 3.7 28.9 - - + -
277B LEU* 4.9 3.1 - - + +
356B PHE* 5.2 1.1 - - + -
425B LEU* 2.9 43.9 + - + +
426B CYS* 3.8 1.6 - - - +
428B SER* 1.3 76.6 - - - +
430B ARG* 1.3 59.1 + - - +
433B CYS* 2.9 56.0 + - - +
434B PRO* 3.7 0.3 - - - +
439B ILE* 3.6 30.1 - - + -
442B ILE* 3.9 10.1 - - + -
476B PHE* 4.5 8.1 - - + -
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Residues in contact with ARG 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ALA* 5.3 2.6 - - - +
272B THR* 4.4 18.5 - - - +
273B THR* 3.5 32.3 - - + +
276B GLU* 4.3 23.9 + - - +
277B LEU* 6.5 0.2 - - - -
426B CYS* 2.9 24.5 + - - +
427B GLN* 3.8 7.1 - - - +
429B LEU* 1.3 77.4 - - - +
431B GLU* 1.3 62.7 + - + +
434B PRO* 3.2 19.7 - - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B GLN* 2.9 51.9 + - + +
428B SER 3.9 2.5 - - - +
430B ARG* 1.3 81.8 - - + +
432B ARG* 1.3 65.5 + - + +
434B PRO* 3.8 6.0 - - - +
435B ARG* 3.5 20.3 - - - +
445B GLU* 4.2 12.6 - - - +
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B SER* 2.8 27.6 + - - +
431B GLU* 1.3 79.1 - - + +
433B CYS* 1.3 66.0 + - - +
434B PRO 3.2 2.2 - - - -
435B ARG* 3.0 31.6 + - - +
437B ASP* 2.7 53.7 + - - +
441B THR* 3.7 18.5 - - - +
442B ILE* 3.8 22.9 - - + +
445B GLU* 2.7 45.6 + - - +
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Residues in contact with CYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 3.9 16.4 - - + -
429B LEU* 2.9 53.2 + - - +
432B ARG* 1.3 71.9 - - - +
434B PRO* 1.4 62.0 - - + +
436B GLY* 2.9 20.5 + - - +
437B ASP 4.6 7.9 - - - -
442B ILE* 3.8 8.7 - - - -
476B PHE* 3.6 43.9 - - - +
477B PRO* 5.0 4.7 - - - +
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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