Contacts of the helix formed by residues 572 - 586 (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 ASP 572 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534D ALA* 2.9 18.1 - - - +
537D ARG* 4.0 12.8 - - - +
570D ASP* 3.2 4.7 + - - +
571D GLN* 1.3 87.6 - - - +
573D VAL* 1.3 65.0 + - - +
574D ASP 2.7 26.7 + - - -
575D VAL* 3.4 20.3 + - + +
576D LYS* 3.0 27.5 + - - +
49F ARG* 4.6 11.4 + - - -
109F GLU* 5.3 2.0 - - - +
110F ARG* 2.4 36.1 + - - -
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Residues in contact with VAL 573 (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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571D GLN* 3.7 7.0 + - - +
572D ASP* 1.3 74.7 + - - +
574D ASP* 1.3 64.4 + - - +
576D LYS* 3.5 16.6 - - - +
577D TYR* 3.2 21.9 + - + +
108F ARG* 6.2 8.1 - - + +
109F GLU* 4.4 24.9 - - + +
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Residues in contact with ASP 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D PHE* 4.4 6.5 - - + -
572D ASP* 2.7 14.0 + - - +
573D VAL* 1.3 75.3 - - - +
575D VAL* 1.3 59.3 + - - +
576D LYS 3.0 1.8 - - - -
577D TYR* 2.6 27.7 + - - +
578D PHE* 2.9 31.8 + - + -
76F PRO* 5.6 0.4 - - - -
106F ARG* 4.2 8.8 + - - +
107F TYR* 3.8 24.7 - - - +
108F ARG 5.9 0.2 - - - -
109F GLU* 4.6 6.6 + - - +
110F ARG* 2.7 42.6 + - - +
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Residues in contact with VAL 575 (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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534D ALA* 3.5 41.5 - - + +
537D ARG* 3.7 14.1 - - + +
538D PHE* 3.5 21.0 - - + +
541D ALA* 5.1 1.1 - - + +
567D LEU* 3.8 27.4 - - + +
570D ASP* 3.3 29.8 - - + +
572D ASP* 3.4 7.8 + - + +
574D ASP* 1.3 75.2 - - - +
576D LYS* 1.3 62.6 + - - +
578D PHE* 3.5 1.4 + - - +
579D ALA* 3.2 23.4 + - - +
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Residues in contact with LYS 576 (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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567D LEU 4.0 9.9 - - - +
568D THR* 3.3 25.0 - - - +
569D GLN* 5.6 0.7 - - - +
570D ASP* 3.0 26.5 + - - +
571D GLN* 4.6 6.5 + - - +
572D ASP 3.0 17.4 + - - +
573D VAL* 3.5 14.3 - - - +
574D ASP 3.0 0.2 - - - -
575D VAL* 1.3 79.8 - - - +
577D TYR* 1.3 60.5 + - - +
579D ALA* 3.8 2.3 - - - +
580D GLN* 3.4 22.5 + - - +
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Residues in contact with TYR 577 (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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573D VAL 3.2 11.4 + - - +
574D ASP* 2.6 20.9 + - - +
576D LYS* 1.3 76.3 - - - +
578D PHE* 1.3 88.1 + + - +
580D GLN* 3.6 4.3 + - + +
581D GLU* 3.2 42.4 + - + +
4F LYS* 4.9 22.8 - - + +
7F THR* 4.2 16.6 - - + +
8F LYS* 5.9 2.6 - - - +
11F ASP* 4.5 7.3 + - - -
106F ARG* 3.0 33.5 + - - -
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Residues in contact with PHE 578 (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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538D PHE* 3.3 60.6 - + + +
541D ALA* 4.3 6.4 - - + +
542D LYS* 4.0 34.5 - - + -
545D GLN* 4.8 1.4 - - - +
574D ASP* 2.9 32.8 + - + +
575D VAL 4.3 2.2 - - - +
577D TYR* 1.3 95.9 - + - +
579D ALA* 1.3 59.6 + - - +
581D GLU* 3.5 10.0 - - + +
582D ALA* 2.9 27.5 + - - +
76F PRO* 4.5 5.8 - - + -
106F ARG* 5.0 0.9 - - - -
107F TYR* 4.3 21.5 - + - -
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Residues in contact with ALA 579 (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* 4.5 6.3 - - + +
564D LEU* 3.2 23.4 - - + +
567D LEU* 3.8 26.7 - - + -
568D THR* 3.8 14.1 - - + +
575D VAL 3.2 16.9 + - - +
576D LYS 3.8 4.3 - - - +
577D TYR 3.2 0.8 - - - -
578D PHE* 1.3 74.9 - - - +
580D GLN* 1.3 64.3 + - - +
581D GLU 2.9 4.9 + - - -
582D ALA* 3.0 10.7 + - - -
583D LEU* 3.0 11.4 + - - +
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Residues in contact with GLN 580 (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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568D THR* 3.9 21.5 - - + +
576D LYS 3.4 13.3 + - - +
577D TYR* 4.1 6.1 - - + +
579D ALA* 1.3 78.5 - - - +
581D GLU* 1.3 60.5 + - - +
583D LEU* 3.6 14.1 + - - +
584D THR* 2.8 37.0 + - - +
589D ALA* 5.6 6.2 - - - +
4F LYS* 4.9 17.5 - - - +
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Residues in contact with GLU 581 (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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545D GLN* 3.8 13.9 - - - +
577D TYR* 3.2 42.6 + - + +
578D PHE* 3.5 13.9 - - + +
579D ALA 2.9 0.4 - - - -
580D GLN* 1.3 77.0 - - - +
582D ALA* 1.3 66.8 + - - +
583D LEU 3.1 2.0 + - - -
584D THR* 3.3 19.0 + - - +
585D VAL* 3.3 25.8 + - + +
4F LYS* 5.2 8.5 - - - +
8F LYS* 6.1 1.2 - - - -
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Residues in contact with ALA 582 (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* 4.2 11.9 - - + +
545D GLN* 3.6 31.3 + - + -
564D LEU* 3.7 22.7 - - + -
578D PHE 2.9 18.1 + - - +
579D ALA* 3.0 6.0 + - - +
581D GLU* 1.3 76.3 - - - +
583D LEU* 1.3 61.5 + - - +
585D VAL* 3.7 1.6 + - - +
586D LEU* 3.1 30.8 + - - +
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Residues in contact with LEU 583 (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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561D LYS* 4.8 5.8 - - + +
564D LEU* 3.2 36.3 - - + -
565D GLU* 3.7 15.7 - - - +
568D THR* 3.6 28.9 - - + -
579D ALA 3.0 10.8 + - - +
580D GLN* 3.7 16.4 - - - +
582D ALA* 1.3 73.9 - - - +
584D THR* 1.3 68.3 + - - +
586D LEU* 2.8 14.5 + - - -
587D SER 3.1 9.5 + - - -
588D LEU* 3.4 31.4 + - + +
589D ALA* 4.4 22.4 - - + -
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Residues in contact with THR 584 (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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580D GLN* 2.8 30.3 + - - +
581D GLU* 3.3 14.6 + - - +
583D LEU* 1.3 77.5 - - - +
585D VAL* 1.3 63.7 + - + +
587D SER* 3.7 9.8 + - - +
589D ALA* 5.0 13.6 + - - +
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Residues in contact with VAL 585 (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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545D GLN* 4.3 28.0 - - + +
581D GLU* 3.3 27.0 + - - +
582D ALA 4.3 2.7 - - - +
583D LEU 2.8 1.8 + - - -
584D THR* 1.3 76.6 - - + +
586D LEU* 1.3 62.6 + - + +
587D SER* 3.0 14.9 + - - -
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Residues in contact with LEU 586 (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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544D LEU 3.7 19.3 - - - +
545D GLN* 4.2 15.9 - - + +
548D GLY* 3.8 23.1 - - - -
549D PRO* 4.0 15.0 - - + -
556D LEU* 4.3 28.5 - - + +
560D VAL* 4.6 2.0 - - + -
564D LEU* 4.3 18.2 - - + -
582D ALA 3.1 18.1 + - - +
583D LEU 2.8 8.4 + - - +
585D VAL* 1.3 74.7 - - + +
587D SER* 1.3 71.0 + - - +
588D LEU* 3.0 22.9 + - + +
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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