Contacts of the helix formed by residues 455 - 474 (chain D) in PDB entry 2NPP
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 VAL 455 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D TRP* 3.7 15.7 - - + -
420D ARG* 3.1 31.4 - - - +
453D ASP* 3.4 1.7 - - - +
454D HIS* 1.3 76.6 - - + +
456D TYR* 1.3 67.8 + - - +
457D ALA* 3.7 12.1 - - + -
458D ILE* 2.9 24.8 + - + +
459D ARG* 3.5 5.5 + - - +
70F ARG 3.5 6.5 - - - +
71F ILE* 3.4 47.6 - - + +
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Residues in contact with TYR 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D HIS 3.3 4.9 + - - -
455D VAL* 1.3 68.4 - - - +
457D ALA* 1.3 73.0 + - - +
459D ARG* 2.6 53.2 + - + +
460D GLU* 2.8 56.4 + - + +
503D PHE* 4.6 23.0 - + - -
69F PHE 4.8 2.0 - - - -
70F ARG* 3.5 11.7 - - - +
71F ILE 3.0 7.8 + - - +
72F GLY 4.2 0.9 - - - -
73F GLY* 3.6 33.7 - - - +
74F LYS* 4.4 30.7 - - + +
77F ASP* 5.3 7.2 + - + -
78F THR* 5.4 2.2 - - + -
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Residues in contact with ALA 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D TRP* 3.5 34.1 - - + -
421D LEU* 5.0 2.4 - - + +
455D VAL* 3.7 9.6 - - + -
456D TYR* 1.3 80.2 - - - +
458D ILE* 1.3 62.3 + - - +
460D GLU* 3.3 12.4 - - - +
461D ALA* 3.2 20.1 + - - +
70F ARG* 2.8 29.9 + - + +
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Residues in contact with ILE 458 (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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417D TRP* 3.5 16.2 - - + +
420D ARG* 3.8 13.9 - - + +
421D LEU* 3.4 42.2 - - + +
424D ILE* 3.5 21.0 - - + +
450D TRP* 3.9 11.4 - - + +
453D ASP* 3.3 26.9 - - + +
455D VAL* 2.9 28.8 + - + +
456D TYR 2.7 3.2 + - - -
457D ALA* 1.3 71.8 - - - +
459D ARG* 1.3 67.8 + - - +
460D GLU 3.0 1.6 - - - -
461D ALA* 2.9 6.3 + - - +
462D ALA* 2.8 19.8 + - - +
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Residues in contact with ARG 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D TRP 3.4 21.1 - - - +
451D LEU* 3.6 20.9 - - - +
452D VAL* 4.1 3.1 - - - +
453D ASP 3.2 26.4 + - - +
454D HIS 3.1 25.1 + - - -
455D VAL 4.1 1.6 - - - +
456D TYR* 2.6 53.0 + - + +
458D ILE* 1.3 73.5 - - - +
460D GLU* 1.3 59.5 + - - +
462D ALA* 3.2 3.7 + - - +
463D THR* 2.9 29.1 + - - -
496D LEU* 4.0 40.3 + - - +
497D HIS* 4.8 11.5 - - - -
499D MET* 5.8 1.6 - - - +
500D THR* 3.3 19.4 + - + +
503D PHE* 5.7 2.8 - - - -
71F ILE 5.1 0.2 + - - -
72F GLY 5.6 1.4 + - - -
73F GLY* 5.5 0.6 - - - -
78F THR* 5.7 0.8 - - - +
277F GLU* 5.9 0.2 + - - -
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Residues in contact with GLU 460 (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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456D TYR* 2.8 51.0 + - + +
457D ALA* 3.3 16.5 - - - +
459D ARG* 1.3 77.3 - - - +
461D ALA* 1.3 62.4 + - - +
463D THR* 3.0 19.0 + - - -
464D SER* 3.1 13.4 + - - -
74F LYS* 4.5 10.2 + - - -
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Residues in contact with ALA 461 (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 LEU* 3.4 33.2 - - + -
424D ILE* 3.6 12.6 - - + +
425D GLU* 5.7 2.5 - - + +
457D ALA 3.2 6.4 + - - +
458D ILE* 2.9 8.8 + - - +
460D GLU* 1.3 82.4 + - - +
462D ALA* 1.3 57.2 + - - +
464D SER* 3.6 9.0 + - - -
465D ASN* 2.9 26.7 + - - +
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Residues in contact with ALA 462 (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 ILE* 4.2 5.1 - - + +
447D CYS 4.4 5.6 - - - +
450D TRP* 3.7 30.5 - - + -
451D LEU* 3.8 20.0 - - + +
458D ILE 2.8 11.5 + - - +
459D ARG 3.4 9.6 - - - +
460D GLU 3.1 0.4 - - - -
461D ALA* 1.3 75.5 - - - +
463D THR* 1.3 64.8 + - - +
465D ASN* 3.1 20.2 - - - +
466D LEU* 3.2 15.6 + - - +
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Residues in contact with THR 463 (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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451D LEU* 3.7 15.1 - - - +
459D ARG 2.9 15.4 + - - -
460D GLU* 3.2 10.2 - - - -
462D ALA* 1.3 75.3 - - - +
464D SER* 1.3 67.1 + - - +
466D LEU* 3.0 20.6 + - - +
467D LYS 3.7 2.4 + - - -
500D THR* 4.3 6.8 - - - +
503D PHE* 3.6 11.9 - - + +
504D CYS* 3.5 29.2 - - - +
507D VAL* 3.5 30.4 - - + +
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Residues in contact with SER 464 (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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460D GLU* 3.1 9.1 + - - -
461D ALA* 3.7 12.3 - - - -
463D THR* 1.3 80.0 - - - +
465D ASN* 1.3 64.2 + - - +
467D LYS* 3.1 15.8 + - - +
468D LYS* 3.4 19.8 + - - +
507D VAL* 4.9 8.3 - - - -
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Residues in contact with ASN 465 (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 ILE* 3.6 14.6 + - + +
427D MET* 3.9 4.2 - - - +
428D PRO* 3.0 40.2 - - - +
447D CYS* 3.6 30.0 - - - +
450D TRP* 4.2 4.9 - - - -
461D ALA 2.9 16.9 + - - +
462D ALA* 3.1 15.9 - - - +
464D SER* 1.3 77.1 - - - +
466D LEU* 1.3 62.3 + - - +
468D LYS* 3.2 7.8 + - - +
469D LEU* 3.1 25.9 + - - +
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Residues in contact with LEU 466 (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 CYS* 4.8 6.7 - - + +
448D MET* 3.4 25.6 - - + -
451D LEU* 3.8 22.9 - - + -
462D ALA 3.5 13.7 - - - +
463D THR 3.0 8.1 + - - +
465D ASN* 1.3 78.6 - - - +
467D LYS* 1.3 63.1 + - - +
469D LEU* 2.9 24.4 + - + +
470D VAL* 2.9 19.8 + - + +
482D ILE* 3.9 30.9 - - + +
486D VAL* 4.3 1.6 - - + -
504D CYS* 3.8 19.7 - - - -
508D LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 467 (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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463D THR 3.7 2.0 + - - -
464D SER* 3.1 8.5 + - - +
466D LEU* 1.3 78.6 - - - +
468D LYS* 1.3 65.5 + - + +
470D VAL* 3.3 8.7 + - - +
471D GLU* 3.0 51.9 + - + +
507D VAL* 3.1 26.5 - - + +
508D LEU* 4.4 3.3 - - - +
510D GLU* 3.4 34.0 + - - +
511D VAL* 4.3 22.2 - - + -
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Residues in contact with LYS 468 (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 PRO* 3.9 31.4 - - + +
464D SER* 3.4 17.0 + - - +
465D ASN* 3.2 11.3 + - - +
466D LEU 3.2 0.8 - - - -
467D LYS* 1.3 80.9 - - + +
469D LEU* 1.3 61.7 + - - +
471D GLU* 3.5 21.0 + - - +
472D LYS* 3.3 22.9 + - - +
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Residues in contact with LEU 469 (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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427D MET* 4.9 0.4 - - + -
428D PRO* 4.0 16.6 - - + +
431D ALA* 3.7 29.2 - - + -
439D PHE* 3.2 35.4 - - + -
444D ASN* 5.6 0.2 - - - +
447D CYS* 4.3 4.0 - - + -
448D MET* 6.1 0.2 - - + -
465D ASN* 3.1 29.0 + - - +
466D LEU* 2.9 21.4 + - + +
468D LYS* 1.3 73.2 - - - +
470D VAL* 1.3 55.2 + - - +
471D GLU 3.0 1.3 - - - -
472D LYS* 2.7 10.5 + - + +
473D PHE* 2.7 41.9 + - + +
477D TRP* 3.9 17.9 - - + -
482D ILE* 4.9 0.7 - - + -
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Residues in contact with VAL 470 (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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466D LEU 2.9 15.6 + - - +
467D LYS* 3.5 6.1 - - - +
469D LEU* 1.3 74.5 - - - +
471D GLU* 1.3 57.6 + - - +
474D GLY* 2.9 27.7 + - - -
475D LYS* 4.2 10.0 + - - +
477D TRP* 4.0 13.7 - - + -
478D ALA* 4.0 27.6 - - + -
482D ILE* 4.9 2.5 - - + -
508D LEU* 3.5 26.9 - - + -
511D VAL* 3.6 28.3 - - + +
512D CYS* 4.1 8.3 - - - -
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Residues in contact with GLU 471 (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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467D LYS* 3.0 41.4 + - + +
468D LYS* 3.6 26.0 - - - +
469D LEU 3.0 0.4 - - - -
470D VAL* 1.3 77.1 - - - +
472D LYS* 1.3 65.6 + - + +
474D GLY* 4.6 1.2 + - - -
511D VAL* 4.4 16.3 - - + +
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Residues in contact with LYS 472 (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 PRO* 4.5 16.4 - - + +
429D LEU* 5.3 12.1 - - - +
432D GLY* 4.1 27.8 - - - +
468D LYS 3.3 10.7 + - - +
469D LEU* 2.7 14.1 + - + +
471D GLU* 1.3 85.7 - - + +
473D PHE* 1.3 72.1 + - + +
474D GLY 3.7 0.4 + - - -
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Residues in contact with PHE 473 (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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431D ALA* 3.8 22.0 - - + -
432D GLY* 4.1 15.5 - - - -
435D GLY* 4.7 0.7 - - - -
436D VAL* 3.4 46.2 - - + +
439D PHE* 3.6 31.2 - + + -
469D LEU* 2.7 25.3 + - + -
472D LYS* 1.3 81.5 - - + +
474D GLY* 1.3 55.9 + - - +
476D GLU* 5.8 0.7 - - - +
477D TRP* 3.6 56.1 - + + +
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Residues in contact with GLY 474 (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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470D VAL* 2.9 21.5 + - - -
471D GLU 4.6 0.6 + - - -
472D LYS 3.7 1.6 - - - -
473D PHE* 1.3 72.7 - - - +
475D LYS* 1.3 68.0 + - - -
476D GLU* 3.2 10.3 - - - -
477D TRP* 2.9 18.2 + - - +
478D ALA* 3.1 10.4 + - - +
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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