Contacts of the helix formed by residues 420 - 433 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412D TYR* 3.2 37.6 + + + +
414D ASN* 5.3 2.2 - - + +
417D GLU* 5.2 8.2 + - - -
418D GLY 5.1 3.1 - - - -
419D THR* 1.3 74.3 - - - +
421D TYR* 1.3 63.6 + - - +
423D GLN* 4.4 1.9 - - - +
424D SER* 3.1 26.5 + - - -
450D VAL* 3.7 13.1 - - + +
453D LYS* 3.3 57.2 - - + +
454D ASP* 3.5 33.7 - - - -
455D ASP 3.7 3.8 - - - -
460D GLY 4.7 0.2 - - - -
461D LYS 4.6 0.4 - - - -
462D GLN* 3.4 40.4 - - + +
402H LEU* 3.6 38.8 - - + +
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Residues in contact with TYR 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D PHE* 3.7 12.7 - + - -
357D ILE 4.4 6.3 - - - -
358D GLN* 3.4 14.4 - - - +
402D GLY* 3.2 38.8 + - - -
403D MET 3.8 13.2 - - - -
404D ALA* 3.6 24.0 - - + -
412D TYR 4.9 0.2 + - - -
419D THR* 3.2 1.8 + - - -
420D TRP* 1.3 81.9 - - - +
422D ILE* 1.3 80.0 + - + +
424D SER* 3.3 1.6 + - - -
425D LEU* 2.8 40.4 + - + +
443D LEU* 3.9 12.7 - - + +
446D VAL* 3.7 26.2 - - + -
450D VAL* 4.2 5.4 - - - -
462D GLN* 3.9 7.7 - - - +
464D PRO* 3.8 19.5 - - + -
466D PRO* 5.7 1.2 - - + +
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Residues in contact with ILE 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D ASP* 3.4 30.5 - - + +
270D LEU* 3.7 31.6 - - + -
315D LEU* 3.9 17.5 - - + -
356D PHE* 4.7 10.1 - - + -
358D GLN* 3.7 17.9 - - + +
419D THR* 3.2 18.2 + - - +
421D TYR* 1.3 96.5 - - + +
423D GLN* 1.3 59.5 + - - +
425D LEU* 3.6 13.8 - - + +
426D CYS* 2.9 32.7 + - - -
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Residues in contact with GLN 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A HIS* 3.3 46.0 + - + +
265D LEU* 3.2 24.0 + - - +
266D ASP* 2.9 23.5 + - - +
269D ALA* 3.8 14.5 - - - +
417D GLU* 3.3 27.4 + - + +
418D GLY* 4.0 0.9 - - - -
419D THR 3.0 22.9 + - - +
420D TRP* 4.4 1.8 - - - +
422D ILE* 1.3 75.7 - - - +
424D SER* 1.3 58.7 + - - +
426D CYS* 4.0 2.7 - - - +
427D GLN* 3.0 29.1 + - - +
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Residues in contact with SER 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A HIS* 5.6 0.4 - - - -
420D TRP 3.1 21.1 + - - -
421D TYR 3.8 1.1 - - - -
423D GLN* 1.3 74.8 - - - +
425D LEU* 1.3 58.9 + - - +
427D GLN* 3.3 9.1 + - - +
428D SER* 2.9 31.7 + - - -
446D VAL* 3.7 14.9 - - - +
449D GLU* 3.5 27.4 - - - +
450D VAL* 3.7 15.8 - - - +
453D LYS* 6.1 1.6 - - - -
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D LEU* 4.6 10.3 - - + -
356D PHE* 3.7 43.7 - - + -
421D TYR* 2.8 23.4 + - + +
422D ILE* 3.6 21.1 - - + +
423D GLN 3.4 0.2 - - - -
424D SER* 1.3 77.1 - - - +
426D CYS* 1.3 58.7 + - - +
428D SER* 3.8 0.9 - - - -
429D LEU* 2.9 55.4 + - + +
439D ILE* 5.1 0.7 - - + -
442D ILE* 4.6 4.0 - - + -
443D LEU* 3.9 26.5 - - + -
446D VAL* 3.7 15.4 - - + +
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Residues in contact with CYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D ALA* 3.7 42.2 - - + -
270D LEU* 3.7 25.4 - - - -
273D THR* 3.5 17.3 - - - +
422D ILE* 2.9 23.4 + - - +
423D GLN* 4.1 3.6 - - - +
425D LEU* 1.3 71.3 - - - +
427D GLN* 1.3 66.8 + - - +
429D LEU* 3.4 6.6 + - - +
430D ARG* 3.0 33.9 + - - +
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Residues in contact with GLN 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PRO* 3.8 20.2 - - - +
253A LYS* 3.5 30.0 + - - +
255A HIS* 3.4 24.5 + - + -
423D GLN 3.0 17.7 + - - +
424D SER* 3.6 8.8 - - - +
426D CYS* 1.3 77.1 - - - +
428D SER* 1.3 59.0 + - - +
430D ARG* 3.8 3.3 - - - +
431D GLU* 3.0 49.8 + - - +
449D GLU* 5.4 13.5 + - - +
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D SER* 2.9 17.4 + - - -
425D LEU 3.8 1.6 - - - -
427D GLN* 1.3 76.6 - - - +
429D LEU* 1.3 56.5 + - - +
431D GLU* 3.2 3.6 + - - -
432D ARG* 2.7 43.3 + - - +
442D ILE* 3.3 30.0 + - - +
445D GLU* 3.0 28.6 + - - -
446D VAL* 3.9 9.9 - - - -
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D THR* 3.8 20.9 - - + -
274D PHE* 3.5 32.5 - - + -
277D LEU* 4.8 2.9 - - + +
356D PHE* 5.3 0.4 - - + -
425D LEU* 2.9 42.1 + - + +
426D CYS* 3.8 1.6 - - - +
428D SER* 1.3 74.8 - - - +
430D ARG* 1.3 59.5 + - - +
433D CYS* 2.8 58.0 + - - +
439D ILE* 3.9 26.5 - - + -
442D ILE* 4.0 9.8 - - + +
476D PHE* 4.4 9.9 - - + -
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ARG 4.9 5.1 + - - -
249A GLU 3.1 26.8 + - - -
250A LYS 3.7 18.2 + - - -
251A VAL 4.7 1.4 + - - -
252A PRO* 3.7 44.4 + - + +
255A HIS* 5.0 6.5 - - - +
272D THR* 5.4 8.0 - - - +
273D THR* 3.6 27.8 - - + +
276D GLU* 4.4 21.3 + - - +
426D CYS* 3.0 27.0 + - - +
427D GLN* 3.8 2.1 - - - +
429D LEU* 1.3 75.3 - - - +
431D GLU* 1.3 62.5 + - - +
434D PRO* 3.3 19.7 - - - +
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Residues in contact with GLU 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PRO* 3.7 16.3 - - + +
253A LYS* 3.7 21.3 + - - +
427D GLN* 3.0 47.6 + - - +
428D SER 3.8 2.5 - - - +
430D ARG* 1.3 79.8 - - - +
432D ARG* 1.3 63.6 + - + +
434D PRO* 3.9 5.0 - - - +
435D ARG* 3.5 21.3 - - - +
445D GLU* 4.0 14.6 - - - +
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Residues in contact with ARG 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428D SER* 2.7 27.2 + - - +
431D GLU* 1.3 79.4 - - + +
433D CYS* 1.3 64.9 + - - +
434D PRO 3.3 2.2 - - - -
435D ARG* 2.9 37.5 + - - +
436D GLY 3.3 0.2 + - - -
437D ASP* 2.7 56.7 + - + +
441D THR* 3.7 15.7 - - - +
442D ILE* 3.8 23.8 - - + +
445D GLU* 2.9 45.8 + - - +
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Residues in contact with CYS 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D LEU* 3.9 27.4 - - + -
429D LEU* 2.8 56.3 + - - +
432D ARG* 1.3 71.9 - - - +
434D PRO* 1.4 65.6 - - + +
436D GLY* 3.0 15.2 + - - +
437D ASP 4.8 6.3 - - - +
442D ILE* 4.0 9.2 - - - -
476D PHE* 3.8 33.5 - - - +
477D PRO* 5.4 2.9 - - - +
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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
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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