Contacts of the helix formed by residues 724 - 741 (chain B) in PDB entry 2NUP
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 ASN 724 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B PRO 3.6 5.7 + - - -
718B SER* 3.0 32.3 + - - +
720B HIS* 3.3 21.0 + - + +
723B HIS* 1.3 76.2 - - - +
725B PRO* 1.3 62.1 - - - +
726B VAL* 3.5 8.7 + - - +
727B GLN* 2.9 42.8 + - + +
728B VAL* 3.2 12.0 + - - +
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Residues in contact with PRO 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B HIS 5.6 1.3 - - - +
722B GLN 3.8 9.7 - - - +
723B HIS 2.9 24.5 - - - +
724B ASN* 1.3 74.7 - - - +
726B VAL* 1.3 66.8 + - + +
728B VAL* 3.4 10.6 - - + +
729B GLN* 3.1 24.1 + - - +
1020B PRO* 4.2 28.5 - - + -
1022B THR* 5.5 8.7 + - - -
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Residues in contact with VAL 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ASN* 3.0 7.0 + - - +
725B PRO* 1.3 80.9 - - + +
727B GLN* 1.3 74.5 + - - +
729B GLN* 3.5 4.7 + - - +
730B LYS* 3.0 23.3 + - + +
1022B THR* 6.0 4.5 - - - -
1051B ILE* 4.6 15.3 - - + +
1053B TYR* 4.3 30.3 - - + -
1055B ILE* 3.7 29.8 - - + -
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Residues in contact with GLN 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B TYR* 3.2 29.9 - - - +
717B PRO* 3.5 34.5 + - - +
719B TYR* 3.5 23.4 - - + -
724B ASN* 2.9 43.1 + - + +
726B VAL* 1.3 79.0 - - - +
728B VAL* 1.3 56.7 + - - +
730B LYS* 3.4 17.7 - - - +
731B LEU* 2.8 32.4 + - - +
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Residues in contact with VAL 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B SER* 5.7 6.3 - - - +
719B TYR* 3.5 27.9 + - + +
720B HIS 3.2 27.4 - - - +
721B HIS* 4.0 17.5 - - - +
724B ASN 3.2 7.4 + - - +
725B PRO* 3.4 10.8 - - + +
726B VAL 3.1 0.2 - - - -
727B GLN* 1.3 77.3 - - - +
729B GLN* 1.3 66.5 + - + +
731B LEU* 3.3 2.4 + - - +
732B GLN* 3.0 23.1 + - + +
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Residues in contact with GLN 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B PRO 3.1 13.0 + - - +
726B VAL* 4.1 4.3 - - - +
728B VAL* 1.3 82.4 - - + +
730B LYS* 1.3 61.9 + - - +
732B GLN* 3.2 9.2 - - + +
733B LYS* 3.0 39.5 + - + +
1022B THR* 3.1 39.9 + - - +
1023B ASP* 4.6 8.9 + - - +
1049B PHE* 5.2 5.5 - - - -
1051B ILE* 3.5 26.3 - - + +
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Residues in contact with LYS 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B TYR 3.3 22.4 + - - -
716B TYR* 3.7 9.2 - - + -
717B PRO* 4.9 2.2 - - - +
726B VAL* 3.0 20.0 + - + +
727B GLN* 3.4 26.9 + - - +
728B VAL 3.1 0.2 - - - -
729B GLN* 1.3 74.0 - - - +
731B LEU* 1.3 66.1 + - - +
732B GLN 3.1 0.3 + - - -
733B LYS* 3.2 2.9 + - - +
734B GLU* 2.9 53.5 + - - +
925B PHE* 5.3 9.3 - - - -
990B SER* 5.7 6.5 - - - -
991B VAL* 5.5 7.4 - - - -
1051B ILE* 4.0 29.3 - - + +
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Residues in contact with LEU 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TYR* 4.6 4.5 - - + -
524B SER* 4.5 8.7 - - - +
525B VAL* 4.7 7.0 - - + -
637B PHE* 5.1 4.0 - - + -
690B PHE* 4.7 7.2 - - + -
692B LEU* 3.4 21.1 - - + -
716B TYR* 3.5 38.6 - - + +
719B TYR* 3.3 33.4 - - + +
727B GLN 2.8 19.9 + - - +
728B VAL 3.7 2.0 - - - +
730B LYS* 1.3 72.5 - - - +
732B GLN* 1.3 58.2 + - - +
735B LEU* 2.8 57.5 + - + +
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Residues in contact with GLN 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B SER* 3.9 21.3 - - - +
527B GLN* 5.8 3.1 - - - +
528B SER* 3.0 30.0 + - - +
531B ASP* 5.3 3.8 + - - -
532B ASN* 5.9 0.4 - - - +
728B VAL* 3.0 15.6 + - + +
729B GLN* 3.2 15.7 - - + +
730B LYS 3.0 0.2 - - - -
731B LEU* 1.3 78.9 - - - +
733B LYS* 1.3 77.5 + - - +
735B LEU* 3.2 6.1 + - - +
736B GLN* 3.0 36.3 + - - +
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Residues in contact with LYS 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B GLN* 3.0 26.8 + - + +
730B LYS* 4.0 2.7 - - - +
732B GLN* 1.3 97.0 - - - +
734B GLU* 1.3 65.1 + - + +
736B GLN* 3.3 15.6 + - + +
737B ARG* 3.2 20.8 + - - +
1048B PHE* 4.5 3.8 - - - -
1049B PHE* 3.8 62.8 + - + +
1051B ILE* 4.3 8.1 - - + -
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Residues in contact with GLU 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B PHE* 6.1 0.7 - - - -
714B TYR* 3.4 16.5 - - + +
715B TYR 5.2 0.9 + - - +
716B TYR* 2.4 46.7 + - - +
730B LYS* 2.9 45.4 + - + +
731B LEU 3.8 0.2 - - - +
733B LYS* 1.3 74.5 - - + +
735B LEU* 1.3 60.6 + - - +
737B ARG* 3.5 3.1 + - - +
738B TYR* 3.0 28.3 + - - +
990B SER* 5.6 4.7 - - - -
1048B PHE* 3.3 32.5 - - + -
1049B PHE 6.1 0.7 - - - +
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Residues in contact with LEU 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B PHE* 6.1 0.7 - - + -
524B SER* 5.0 0.9 - - - +
525B VAL* 3.9 33.7 - - + +
528B SER* 3.7 26.2 - - - +
637B PHE* 4.3 18.2 - - + -
690B PHE* 4.5 7.6 - - + -
731B LEU* 2.8 40.4 + - + +
732B GLN* 3.5 5.4 - - - +
734B GLU* 1.3 74.7 - - - +
736B GLN* 1.3 60.9 + - - +
738B TYR* 4.0 21.5 - - + -
739B LEU* 2.8 48.5 + - + +
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Residues in contact with GLN 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B SER* 5.4 0.6 + - - -
531B ASP* 6.0 0.9 - - - +
532B ASN* 3.3 35.5 + - - +
535B LEU* 5.1 3.0 - - - +
732B GLN* 3.0 23.6 + - - +
733B LYS* 3.3 23.0 + - + +
735B LEU* 1.3 78.0 - - - +
737B ARG* 1.3 64.2 + - - +
739B LEU* 3.9 0.5 - - - +
740B THR* 2.9 41.9 + - - +
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Residues in contact with ARG 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ASP* 3.4 26.1 + - - -
733B LYS 3.2 4.9 + - - +
734B GLU 3.7 0.2 - - - +
735B LEU 3.3 0.2 - - - -
736B GLN* 1.3 79.1 - - - +
738B TYR* 1.3 64.0 + - - +
740B THR* 3.1 4.5 + - - -
741B ARG* 2.9 53.0 + - - +
781B PRO* 3.5 15.8 + - - +
782B ASP* 2.7 45.9 + - - +
1047B PRO* 3.4 38.3 - - - +
1048B PHE* 3.5 38.8 - - + -
1049B PHE 6.0 0.2 - - - +
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Residues in contact with TYR 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B PHE* 4.8 1.8 - + - -
537B PRO* 5.9 0.2 - - - +
633B ARG* 3.2 45.3 + - - +
635B SER* 2.8 28.7 + - - -
688B ASP* 2.5 42.5 + - + +
690B PHE* 3.8 25.6 - + + -
714B TYR* 3.5 26.2 - + + +
734B GLU 3.0 16.1 + - - +
735B LEU* 3.6 13.2 - - + +
737B ARG* 1.3 81.0 - - - +
739B LEU* 1.3 74.5 + - + +
741B ARG* 3.5 35.4 - - - +
1048B PHE* 5.0 0.2 - - - -
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Residues in contact with LEU 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B PHE* 4.2 9.9 - - + -
525B VAL 5.5 0.2 - - - +
528B SER* 3.9 25.6 - - - +
529B LEU* 4.0 27.1 - - + +
532B ASN* 3.7 29.6 - - + +
535B LEU 3.8 1.6 - - - +
536B LEU* 3.4 27.2 - - + +
537B PRO* 3.6 13.4 - - - +
633B ARG* 4.2 14.8 + - - +
735B LEU* 2.8 34.6 + - + +
736B GLN 3.9 2.0 - - - +
738B TYR* 1.3 89.0 - - + +
740B THR* 1.3 59.9 + - - +
741B ARG 3.7 0.2 - - - -
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Residues in contact with THR 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ASN* 3.8 20.2 - - + +
535B LEU* 3.6 41.8 - - + +
537B PRO* 4.6 2.9 - - - +
736B GLN* 2.9 28.6 + - - +
737B ARG* 3.8 3.3 + - - -
739B LEU* 1.3 78.9 - - - +
741B ARG* 1.3 66.5 + - - +
742B LYS 4.0 0.2 + - - -
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Residues in contact with ARG 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B PRO* 3.1 19.3 - - - +
633B ARG* 5.1 5.0 - - - +
688B ASP* 5.0 1.6 + - - -
712B SER* 4.0 7.1 + - - -
714B TYR* 3.2 27.8 + - - -
737B ARG* 2.9 47.2 + - - +
738B TYR* 3.5 37.9 + - - +
739B LEU 3.7 0.2 - - - -
740B THR* 1.3 78.6 + - - +
742B LYS* 1.3 72.6 + - - +
743B ILE* 4.7 0.7 - - + +
780B ASN* 3.3 38.0 - - - +
781B PRO* 4.0 9.6 - - + -
782B ASP* 3.0 29.0 + - - +
1048B PHE* 4.7 4.6 - - - -
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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
------------------------------------------------------------
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