Contacts of the helix formed by residues 533 - 547 (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 533 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495D TYR* 3.8 24.5 - - + -
498D ARG* 3.2 14.4 - - - +
531D ASP* 3.0 8.5 - - - +
532D PRO* 1.3 83.4 - - + +
534D ALA* 1.3 68.2 + - - +
535D ASN* 3.6 16.6 - - + +
536D VAL* 3.3 6.9 + - + +
537D ARG* 3.1 20.2 + - - -
51F PRO* 4.3 17.5 - - + -
79F ASN* 5.0 1.6 - - - +
280F ASP* 2.9 31.4 - - - +
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Residues in contact with ALA 534 (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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532D PRO 3.9 0.8 + - - -
533D VAL* 1.3 73.3 - - - +
535D ASN* 1.3 65.7 + - - +
537D ARG* 2.7 23.2 + - - +
538D PHE* 2.7 26.7 + - + -
572D ASP* 2.9 36.3 - - - +
575D VAL* 3.5 4.8 - - + +
110F ARG* 3.8 14.4 - - - +
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Residues in contact with ASN 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D TYR* 3.1 31.5 - - + -
499D MET* 4.1 5.2 - - - -
533D VAL* 3.2 4.6 - - + +
534D ALA* 1.3 75.0 - - - +
536D VAL* 1.3 63.0 + - - +
538D PHE* 3.1 18.8 + - + -
539D ASN* 2.9 24.8 + - - +
76F PRO 3.5 5.7 + - - -
77F ASP 2.8 33.7 + - - +
78F THR* 3.5 3.4 - - - +
79F ASN* 2.6 34.2 + - - +
110F ARG* 3.7 9.2 + - - -
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Residues in contact with VAL 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D TYR* 3.9 22.7 - - + +
498D ARG* 4.0 5.2 - - + +
499D MET* 3.9 23.3 - - + +
502D LEU* 3.6 16.8 - - + +
528D MET* 4.1 21.3 - - + +
531D ASP* 3.4 45.1 - - + +
533D VAL* 3.3 2.8 + - + +
534D ALA 3.2 0.6 - - - -
535D ASN* 1.3 74.4 - - - +
537D ARG* 1.3 52.8 + - - +
539D ASN* 3.1 1.7 + - - -
540D VAL* 2.6 38.5 + - - +
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Residues in contact with ARG 537 (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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528D MET 4.6 0.9 - - - -
529D ALA 3.3 25.8 - - - +
530D GLY* 4.9 1.3 - - - -
531D ASP 2.7 43.9 + - - +
532D PRO* 3.4 10.9 + - - +
533D VAL 3.1 16.5 + - - +
534D ALA* 2.7 31.9 + - - +
536D VAL* 1.3 74.1 - - - +
538D PHE* 1.3 60.7 + - - +
540D VAL* 2.7 29.2 - - + +
541D ALA* 3.1 6.2 + - - +
567D LEU* 4.3 10.5 - - + +
570D ASP* 2.8 37.2 + - - -
571D GLN* 5.2 4.0 + - - -
572D ASP* 4.0 8.5 - - - +
575D VAL* 3.7 9.0 - - + -
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Residues in contact with PHE 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ALA* 2.7 30.2 + - + -
535D ASN* 3.1 30.5 - - - -
537D ARG* 1.3 75.5 - - - +
539D ASN* 1.3 73.1 + - - +
541D ALA* 3.3 7.5 + - - +
542D LYS* 2.9 36.7 + - + +
574D ASP* 4.4 9.4 - - + -
575D VAL* 3.5 25.6 - - + +
578D PHE* 3.3 40.1 - + + +
76F PRO* 3.3 34.5 - - + -
77F ASP* 4.0 10.8 - - - -
110F ARG* 4.2 13.0 - - - -
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Residues in contact with ASN 539 (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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499D MET* 3.6 23.1 - - + -
502D LEU* 3.7 11.9 - - + -
503D PHE* 3.5 22.3 - - + -
506D ASN* 5.4 1.7 - - - +
535D ASN 2.9 12.5 + - - +
536D VAL* 3.8 4.5 - - - +
538D PHE* 1.3 83.8 - - - +
540D VAL* 1.3 57.1 + - - +
541D ALA 3.0 5.2 - - - -
542D LYS* 3.0 21.7 + - - +
543D SER* 2.8 32.9 + - - -
77F ASP* 2.6 33.5 + - - +
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Residues in contact with VAL 540 (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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502D LEU* 3.4 17.9 - - + +
525D VAL* 2.8 33.1 - - - +
528D MET* 3.4 26.5 - - + +
529D ALA* 3.6 26.7 - - + -
536D VAL 2.6 17.9 + - - +
537D ARG* 2.7 23.3 - - - +
539D ASN* 1.3 71.1 - - - +
541D ALA* 1.3 63.1 + - - +
543D SER* 3.9 2.7 - - - -
544D LEU* 3.4 23.2 + - + +
567D LEU* 4.3 5.4 - - + -
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Residues in contact with ALA 541 (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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537D ARG 3.1 7.6 + - - +
538D PHE* 3.3 13.2 - - - +
540D VAL* 1.3 82.2 - - - +
542D LYS* 1.3 65.6 + - - +
544D LEU* 3.0 21.6 + - - +
545D GLN* 3.3 9.4 + - - +
564D LEU* 5.6 1.3 - - + -
567D LEU* 4.1 18.8 - - + -
575D VAL 5.1 1.6 - - - +
578D PHE* 4.3 21.5 - - + +
579D ALA* 4.5 6.7 - - + +
582D ALA* 4.2 8.1 - - + +
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Residues in contact with LYS 542 (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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506D ASN* 4.8 0.9 - - - +
538D PHE* 2.9 37.5 + - + +
539D ASN* 3.4 24.3 + - - +
541D ALA* 1.3 76.5 - - - +
543D SER* 1.3 61.9 + - - +
545D GLN* 3.1 21.2 + - - +
546D LYS* 3.2 11.6 + - - +
578D PHE* 4.0 39.3 - - + +
76F PRO* 5.4 5.3 - - - +
77F ASP* 4.0 18.8 + - - -
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Residues in contact with SER 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D LEU* 3.3 23.7 - - - +
505D ILE* 5.5 0.7 - - - -
506D ASN* 3.1 30.2 + - - +
525D VAL* 4.2 16.8 - - - -
539D ASN* 2.8 19.4 + - - -
540D VAL* 3.9 8.3 - - - -
542D LYS* 1.3 77.1 - - - +
544D LEU* 1.3 54.2 + - - +
546D LYS* 2.7 23.2 + - - +
547D ILE* 2.9 19.7 + - - +
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Residues in contact with LEU 544 (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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522D LEU* 3.7 26.9 - - + -
525D VAL* 3.1 24.7 - - + +
526D LEU* 3.9 7.6 - - + -
529D ALA* 6.2 0.9 - - + -
540D VAL* 3.4 18.6 + - + +
541D ALA* 3.0 11.0 + - - +
543D SER* 1.3 75.9 - - - +
545D GLN* 1.3 58.1 + - - +
547D ILE* 3.9 7.0 - - + +
548D GLY* 3.0 26.9 + - - -
551D LEU* 5.7 0.7 - - - +
560D VAL* 4.6 18.3 - - + +
563D ILE* 4.2 24.5 - - + -
564D LEU* 4.5 22.2 - - + -
567D LEU* 5.5 4.7 - - + -
586D LEU* 3.7 6.5 - - - +
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Residues in contact with GLN 545 (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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541D ALA 3.3 3.7 + - - +
542D LYS* 3.1 14.2 + - - +
543D SER 3.1 0.8 - - - -
544D LEU* 1.3 79.4 - - - +
546D LYS* 1.3 61.4 + - - +
548D GLY 4.0 1.7 + - - -
549D PRO* 4.1 8.7 - - - +
578D PHE 4.8 1.0 - - - +
581D GLU* 3.8 14.7 - - - +
582D ALA* 3.6 41.2 + - + +
585D VAL* 4.3 28.9 - - + +
586D LEU* 4.2 13.4 - - + +
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Residues in contact with LYS 546 (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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506D ASN* 3.8 40.6 - - + +
509D SER* 5.1 1.1 - - - +
510D GLU* 4.3 23.1 + - - +
542D LYS 3.2 9.1 + - - +
543D SER 2.7 9.8 + - - +
545D GLN* 1.3 76.7 - - - +
547D ILE* 1.3 59.8 + - + +
548D GLY 2.8 9.1 + - - -
549D PRO* 3.6 11.4 - - - +
550D ILE* 4.8 5.4 - - - +
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Residues in contact with ILE 547 (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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505D ILE* 4.1 18.8 - - + +
506D ASN* 4.7 2.7 - - - +
509D SER* 3.5 31.2 - - - +
517D THR* 4.5 11.2 - - + -
522D LEU* 3.8 35.0 - - + +
525D VAL* 4.1 21.1 - - + -
543D SER 2.9 16.9 + - - +
544D LEU* 4.0 11.7 - - + +
546D LYS* 1.3 75.8 - - + +
548D GLY* 1.3 66.7 + - - +
549D PRO 3.7 0.4 - - - -
550D ILE* 3.5 18.5 + - - +
551D LEU* 3.4 17.1 - - + +
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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