Contacts of the helix formed by residues 438 - 452 (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 ASP 438 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D GLY 3.8 1.0 + - - -
437D ASP* 1.3 75.8 - - - +
439D ILE* 1.3 64.2 + - - +
440D LEU* 3.1 33.3 + - - +
441D THR* 2.6 29.0 + - - -
442D ILE* 3.1 21.9 + - - +
473D LYS* 3.9 34.4 + - + +
474D LEU 3.2 22.0 + - - +
475D VAL* 3.8 11.9 - - + -
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Residues in contact with ILE 439 (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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354D VAL* 5.8 0.2 - - + -
356D PHE* 4.5 12.3 - - + -
400D LEU* 3.5 34.5 - - + -
425D LEU* 5.1 0.9 - - + -
429D LEU* 3.9 27.4 - - + -
438D ASP* 1.3 73.5 - - - +
440D LEU* 1.3 68.4 + - + +
442D ILE* 3.6 12.2 - - + +
443D LEU* 2.8 37.7 + - + +
470D LEU* 4.0 11.0 - - + -
474D LEU* 2.8 40.9 + - + +
476D PHE* 4.1 14.4 - - + -
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Residues in contact with LEU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D LEU* 4.3 13.5 - - + -
438D ASP* 3.1 13.9 + - - +
439D ILE* 1.3 90.0 - - + +
441D THR* 1.3 61.4 + - - +
443D LEU* 3.9 6.9 - - + +
444D THR* 2.9 34.3 + - - -
466D PRO* 5.5 3.1 - - + -
468D PHE* 3.6 52.5 - - + -
470D LEU* 4.6 7.4 - - + -
472D LYS 6.1 0.9 - - - +
473D LYS* 6.0 3.6 - - - +
474D LEU 6.3 0.4 - - - +
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Residues in contact with THR 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D ARG* 3.7 26.6 - - - +
437D ASP* 4.2 12.8 - - + +
438D ASP* 2.6 33.2 + - - -
440D LEU* 1.3 76.2 - - - +
442D ILE* 1.3 65.1 + - - +
444D THR* 3.3 8.5 + - - -
445D GLU* 3.1 20.8 + - - +
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Residues in contact with ILE 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D LEU* 4.6 3.8 - - + -
428D SER* 3.3 23.7 + - - +
429D LEU* 4.0 35.7 - - + +
432D ARG* 3.8 32.3 - - + +
433D CYS* 4.0 14.4 - - - +
437D ASP* 3.9 16.2 - - + +
438D ASP 3.1 18.1 + - - +
439D ILE* 3.6 14.8 - - + +
441D THR* 1.3 76.2 - - - +
443D LEU* 1.3 58.0 + - - +
445D GLU* 3.1 6.1 + - - +
446D VAL* 3.0 30.9 + - + +
476D PHE* 5.9 0.4 - - + -
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Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D PHE* 4.4 6.7 - - + -
400D LEU* 3.9 27.4 - - + -
402D GLY* 5.0 2.9 - - - -
421D TYR* 3.9 22.7 - - + +
425D LEU* 3.9 24.0 - - + -
439D ILE* 2.8 42.4 + - + +
440D LEU* 4.1 6.7 - - + +
442D ILE* 1.3 69.8 - - - +
444D THR* 1.3 61.0 + - - +
446D VAL* 3.6 12.1 - - + +
447D ASN* 2.9 34.0 + - - +
466D PRO* 3.7 27.4 - - + -
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Residues in contact with THR 444 (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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440D LEU 2.9 22.1 + - - -
441D THR* 3.5 7.8 - - - -
442D ILE 3.2 0.2 - - - -
443D LEU* 1.3 77.6 - - - +
445D GLU* 1.3 62.3 + - - +
447D ASN* 3.2 13.8 + - + +
448D TYR* 3.0 21.3 + - + +
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Residues in contact with GLU 445 (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* 3.0 28.5 + - - +
431D GLU* 4.0 12.3 - - - +
432D ARG* 2.9 40.8 + - - +
441D THR 3.1 8.7 + - - +
442D ILE 3.1 9.7 + - - +
444D THR* 1.3 81.0 - - - +
446D VAL* 1.3 56.7 + - - +
448D TYR* 3.2 8.1 + - + +
449D GLU* 2.8 44.2 + - + +
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Residues in contact with VAL 446 (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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421D TYR* 3.7 36.6 - - + -
424D SER* 3.7 24.0 - - - +
425D LEU* 3.7 33.2 - - + +
428D SER* 3.9 8.5 - - - -
442D ILE 3.0 21.0 + - - +
443D LEU* 3.6 11.9 - - + +
445D GLU* 1.3 74.5 - - - +
447D ASN* 1.3 65.5 + - - +
450D VAL* 2.9 30.3 + - + +
464D PRO* 4.6 3.1 - - + -
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Residues in contact with ASN 447 (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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421D TYR* 5.7 0.2 - - - -
443D LEU* 2.9 18.2 + - - +
444D THR* 3.3 14.4 - - + +
446D VAL* 1.3 76.6 - - - +
448D TYR* 1.3 58.0 + - - +
450D VAL* 4.4 0.3 - - - +
451D SER* 2.6 34.7 + - - -
463D MET* 3.7 20.6 - - + +
464D PRO* 3.3 33.7 + - - +
465D GLN* 5.0 0.2 - - - +
466D PRO* 3.7 24.6 - - - +
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Residues in contact with TYR 448 (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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444D THR* 3.0 13.3 + - + +
445D GLU* 3.2 13.2 + - + +
447D ASN* 1.3 76.4 - - - +
449D GLU* 1.3 86.7 + - + +
451D SER* 3.4 7.6 + - - -
452D ASN* 3.3 33.4 + - + +
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Residues in contact with GLU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D SER* 3.5 23.1 - - - +
427D GLN* 5.4 12.1 + - - +
445D GLU* 2.8 37.0 + - + +
448D TYR* 1.3 94.5 - - + +
450D VAL* 1.3 65.0 + - - +
452D ASN* 3.2 21.1 + - - +
453D LYS* 3.6 13.2 - - - +
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Residues in contact with VAL 450 (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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420D TRP* 3.7 24.5 - - + +
421D TYR* 4.2 1.6 - - - -
424D SER* 3.7 24.2 - - - -
446D VAL* 2.9 23.2 + - + +
449D GLU* 1.3 76.2 - - - +
451D SER* 1.3 60.9 - - - +
452D ASN 3.1 1.1 + - - -
453D LYS* 3.1 25.0 + - + +
462D GLN* 3.6 37.0 - - + +
464D PRO* 3.6 30.3 - - + -
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Residues in contact with SER 451 (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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447D ASN 2.6 24.6 + - - -
448D TYR* 3.6 8.0 - - - -
449D GLU 3.2 0.2 - - - -
450D VAL* 1.3 75.5 - - - +
452D ASN* 1.3 56.4 + - - +
453D LYS 3.4 0.2 - - - -
461D LYS* 3.0 27.7 + - - +
462D GLN 3.9 9.5 + - - -
463D MET* 3.4 27.6 - - - +
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Residues in contact with ASN 452 (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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448D TYR* 3.3 22.9 + - + +
449D GLU* 3.2 15.6 + - - +
450D VAL 3.1 1.6 - - - -
451D SER* 1.3 77.7 - - - +
453D LYS* 1.3 63.0 + - - +
454D ASP* 3.6 10.9 - - - +
461D LYS* 4.0 3.9 + - - +
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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