Contacts of the helix formed by residues 416 - 435 (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 LYS 416 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378D PRO* 3.7 31.0 - - + +
381D ARG* 4.4 5.8 - - - +
414D ASP* 3.4 10.9 + - - +
415D ALA* 1.3 86.4 - - + +
417D TRP* 1.3 66.7 + - - +
418D ARG* 3.3 4.9 - - + +
419D VAL* 3.0 31.0 + - + +
420D ARG* 3.4 3.8 + - - +
272F GLN* 5.9 2.9 - - - +
290F ASP* 3.0 31.6 + - - +
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Residues in contact with TRP 417 (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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415D ALA 3.1 3.6 + - - -
416D LYS* 1.3 72.2 - - - +
418D ARG* 1.3 95.5 + - + +
419D VAL 3.0 0.2 - - - -
420D ARG* 2.8 37.7 + - - +
421D LEU* 2.7 56.5 + - + -
455D VAL* 3.7 19.7 - - + -
457D ALA* 3.5 26.7 - - + -
458D ILE* 3.5 13.6 - - + +
67F GLU* 3.4 24.0 + - - -
70F ARG* 3.8 20.2 - - + -
71F ILE* 4.0 14.4 - - + +
289F PHE* 5.6 4.3 - - + +
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Residues in contact with ARG 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D LEU* 3.1 27.7 - - + +
416D LYS* 3.3 4.5 - - + +
417D TRP* 1.3 111.3 - - + +
419D VAL* 1.3 57.2 + - + +
421D LEU* 3.4 8.9 - - + +
422D ALA* 3.2 18.4 + - - +
67F GLU* 2.7 43.4 + - - -
70F ARG* 3.5 24.4 - - - +
292F ALA* 4.6 0.4 - - - +
293F PRO* 3.5 37.1 - - - +
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Residues in contact with VAL 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D PRO* 4.3 14.4 - - + +
381D ARG* 4.5 6.7 - - + +
382D LEU* 3.9 32.3 - - + +
385D ILE* 5.0 6.7 - - + -
411D LEU* 4.0 22.0 - - + +
414D ASP* 2.8 39.7 - - - +
416D LYS* 3.0 14.5 + - + +
417D TRP 3.0 0.4 - - - -
418D ARG* 1.3 76.2 - - + +
420D ARG* 1.3 66.6 + - - +
421D LEU 3.1 0.7 - - - -
422D ALA* 3.3 10.9 + - - +
423D ILE* 3.3 13.2 + - - +
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Residues in contact with ARG 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D LEU 4.1 11.2 - - - +
412D ALA 4.1 9.2 - - - +
413D GLU* 3.8 17.5 - - - +
414D ASP* 3.2 27.0 + - - +
415D ALA* 2.5 31.5 + - - +
416D LYS 3.7 2.0 - - - +
417D TRP* 2.8 22.4 + - - +
419D VAL* 1.3 78.0 - - - +
421D LEU* 1.3 64.8 + - - +
423D ILE* 3.1 6.1 + - - +
424D ILE* 2.9 30.4 + - + +
450D TRP* 5.0 3.8 - - - +
453D ASP* 2.7 45.8 + - - -
454D HIS* 5.6 0.8 + - - +
455D VAL* 3.1 20.6 - - - +
458D ILE* 3.8 7.0 - - + +
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Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D TRP* 2.7 34.4 + - + +
418D ARG* 3.4 15.0 - - + +
420D ARG* 1.3 76.9 - - - +
422D ALA* 1.3 57.3 + - - +
424D ILE* 3.1 4.0 + - + +
425D GLU* 2.9 57.0 + - + +
457D ALA 5.0 2.9 - - - +
458D ILE* 3.4 13.8 - - + +
461D ALA* 3.4 33.0 - - + -
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Residues in contact with ALA 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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382D LEU* 4.6 13.2 - - + +
385D ILE* 3.9 25.9 - - + +
386D SER* 5.2 5.2 - - - +
418D ARG 3.2 10.8 + - - +
419D VAL* 3.6 11.7 - - - +
420D ARG 3.2 0.8 - - - -
421D LEU* 1.3 79.7 - - - +
423D ILE* 1.3 62.8 + - - +
425D GLU* 3.1 11.8 + - - +
426D TYR* 3.0 20.3 + - - +
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Residues in contact with ILE 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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385D ILE* 3.4 36.1 - - + -
408D ILE* 3.7 39.5 - - + +
411D LEU* 3.7 27.8 - - + -
412D ALA* 3.9 6.3 - - + -
419D VAL 3.3 12.1 + - - +
420D ARG 3.1 8.1 + - - +
422D ALA* 1.3 72.9 - - - +
424D ILE* 1.3 68.0 + - - +
426D TYR* 2.8 18.2 + - + +
427D MET* 3.0 16.5 + - - +
450D TRP* 3.8 23.1 - - + -
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Residues in contact with ILE 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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420D ARG* 2.9 12.9 + - + +
421D LEU* 3.3 7.9 - - + +
423D ILE* 1.3 76.6 - - - +
425D GLU* 1.3 62.4 + - + +
427D MET* 3.5 7.5 + - - +
428D PRO* 3.5 10.4 - - - +
450D TRP* 3.4 49.6 - - + -
458D ILE* 3.5 51.1 - - + +
461D ALA* 3.6 32.1 - - + +
462D ALA* 4.2 2.2 - - - +
465D ASN* 3.6 10.4 + - + +
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Residues in contact with GLU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LEU* 2.9 53.2 + - + +
422D ALA* 3.5 10.1 - - - +
423D ILE 3.0 0.4 - - - -
424D ILE* 1.3 79.5 - - + +
426D TYR* 1.3 58.7 + - - +
428D PRO* 3.4 16.3 - - - +
429D LEU* 4.9 2.8 + - - +
461D ALA* 5.7 2.2 - - + +
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Residues in contact with TYR 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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385D ILE* 4.8 7.9 - - + +
388D LEU* 2.9 50.6 + - + +
389D ASP* 3.7 22.2 - - - +
391D VAL* 4.3 0.3 - - - +
400D LEU* 4.0 14.4 - - - +
408D ILE* 3.2 39.7 - - + -
422D ALA 3.0 11.9 + - - +
423D ILE* 2.8 16.8 + - + +
425D GLU* 1.3 78.4 - - - +
427D MET* 1.3 65.8 + - + +
429D LEU* 2.9 14.4 + - + +
430D LEU* 2.9 56.7 + - + +
433D GLN* 4.4 4.3 + - - -
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Residues in contact with MET 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D ILE* 5.2 6.5 - - + -
423D ILE* 3.0 13.2 + - + +
424D ILE 3.7 9.6 - - - +
426D TYR* 1.3 73.8 - - + +
428D PRO* 1.3 67.1 - - + +
429D LEU 2.7 0.9 + - - -
430D LEU* 2.9 37.0 + - + -
431D ALA* 2.4 36.0 + - + +
439D PHE* 4.1 9.0 - - + -
443D LEU* 3.7 31.0 - - + +
446D LEU* 5.5 3.4 - - - -
447D CYS* 3.5 29.6 - - - -
450D TRP* 4.2 15.3 - - + -
465D ASN* 3.9 7.2 - - - +
469D LEU* 5.0 1.1 - - + -
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Residues in contact with PRO 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 ILE 3.5 1.8 - - - +
425D GLU* 3.4 17.5 - - - +
427D MET* 1.3 88.0 - - + +
429D LEU* 1.3 71.9 + - + +
431D ALA* 3.4 6.9 - - + +
432D GLY* 3.1 14.7 + - - -
465D ASN* 3.0 28.0 - - - +
468D LYS* 3.9 42.6 - - + +
469D LEU* 4.0 10.3 - - + -
472D LYS* 4.5 14.1 - - + +
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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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389D ASP* 3.6 48.7 - - + +
425D GLU 5.4 2.0 - - - +
426D TYR* 2.9 17.2 + - + +
427D MET 2.7 2.8 + - - -
428D PRO* 1.3 85.0 - - + +
430D LEU* 1.3 56.2 + - - +
431D ALA 2.7 11.5 + - - -
432D GLY* 3.1 6.1 + - - -
433D GLN* 3.1 28.2 + - + +
472D LYS* 5.3 12.7 - - - +
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Residues in contact with LEU 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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400D LEU* 3.4 34.1 - - + -
405D LEU* 3.2 34.5 - - + -
408D ILE* 4.3 4.0 - - + -
426D TYR* 2.9 48.0 + - + +
427D MET* 3.3 26.9 - - + -
429D LEU* 1.3 75.5 - - - +
431D ALA* 1.3 61.8 + - - +
433D GLN* 3.9 8.4 + - - +
434D LEU* 3.4 27.6 + - + +
443D LEU* 4.0 4.7 - - + -
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Residues in contact with ALA 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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427D MET* 2.4 35.9 + - + +
428D PRO 3.4 4.7 - - - +
429D LEU 2.7 2.8 + - - -
430D LEU* 1.3 64.3 - - - +
432D GLY* 1.3 65.5 + - - +
433D GLN 3.1 1.5 + - - -
434D LEU* 3.2 4.7 + - - +
435D GLY 3.1 19.4 + - - +
439D PHE* 3.7 30.9 - - + +
443D LEU* 4.7 2.5 - - - -
469D LEU* 3.7 20.0 - - + -
472D LYS* 5.9 0.2 - - + -
473D PHE* 3.8 10.1 - - + -
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Residues in contact with GLY 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 PRO 3.1 4.8 + - - -
429D LEU 3.1 5.5 + - - -
431D ALA* 1.3 78.9 - - - +
433D GLN* 1.3 60.5 + - - +
435D GLY* 3.5 10.1 + - - -
472D LYS* 4.1 21.0 - - - +
473D PHE* 4.1 17.5 - - - -
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Residues in contact with GLN 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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389D ASP 4.2 6.4 + - - -
392D ASN* 2.6 48.4 + - - +
393D GLU* 5.6 1.8 + - - -
397D ILE* 3.7 27.8 - - + +
400D LEU* 4.0 7.3 - - + +
426D TYR* 4.4 3.3 + - - -
429D LEU* 3.1 26.6 + - + +
430D LEU* 3.9 16.0 - - - +
431D ALA 3.1 1.0 - - - -
432D GLY* 1.3 79.3 - - - +
434D LEU* 1.3 60.6 + - + +
435D GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 434 (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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397D ILE* 3.9 23.1 - - + +
400D LEU* 4.5 5.8 - - + -
401D SER* 3.7 27.8 - - - +
405D LEU* 3.8 34.8 - - + -
430D LEU* 3.4 23.3 + - + +
431D ALA* 3.2 4.4 + - - +
433D GLN* 1.3 76.4 - - - +
435D GLY* 1.3 60.2 + - - +
437D GLU* 3.4 17.0 - - - +
438D PHE* 3.8 34.2 - - + +
439D PHE* 5.4 0.7 - - - +
443D LEU* 4.5 3.8 - - + -
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Residues in contact with GLY 435 (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 3.1 13.5 + - - +
432D GLY 3.5 8.2 + - - -
433D GLN 3.4 2.6 - - - -
434D LEU* 1.3 77.4 - - - +
436D VAL* 1.3 53.4 + - - -
437D GLU* 3.0 13.5 - - - -
438D PHE* 2.9 6.2 + - - +
439D PHE* 2.8 31.2 + - - +
473D PHE* 4.1 0.9 - - - -
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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
------------------------------------------------------------
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