Contacts of the helix formed by residues 919 - 933 (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 ARG 919 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654B GLU* 3.0 41.4 + - + +
655B PRO* 5.1 4.0 - - - +
694B GLY 5.3 6.1 + - - -
695B GLN* 5.8 4.6 - - - +
696B TYR 6.1 0.4 - - - +
917B ASN* 4.3 11.2 + - - +
918B ALA* 1.3 77.9 - - - +
920B LEU* 1.3 71.0 + - - +
921B ASP* 3.6 1.8 - - + +
922B GLU* 2.7 34.6 + - + +
923B ARG* 3.3 13.5 + - - +
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Residues in contact with LEU 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ARG* 4.1 19.5 - - + +
653B GLU 5.3 2.5 - - - +
654B GLU* 3.2 17.3 + - - +
655B PRO* 3.5 36.5 - - + +
666B MET 5.5 9.6 - - - +
696B TYR* 3.3 36.8 - - + +
919B ARG* 1.3 77.0 - - - +
921B ASP* 1.3 64.7 + - - +
922B GLU 3.0 1.4 + - - -
923B ARG* 3.1 17.9 + - - +
924B ILE* 3.2 18.6 + - + +
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Residues in contact with ASP 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B GLU* 4.9 1.6 + - - +
691B LEU* 4.8 0.7 - - - -
693B SER* 4.4 2.1 + - - -
695B GLN 4.0 2.9 - - - +
696B TYR* 3.5 17.6 - - - -
697B SER* 2.8 32.8 + - - -
698B ASP* 3.5 4.9 + - - -
699B LEU* 3.0 38.5 + - + +
700B ALA 4.5 1.2 + - - -
715B TYR* 3.4 26.3 + - + +
919B ARG* 3.6 1.8 - - + +
920B LEU* 1.3 79.3 - - - +
922B GLU* 1.3 56.8 + - - +
924B ILE* 3.8 7.2 - - - +
925B PHE* 2.9 31.0 + - - +
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Residues in contact with GLU 922 (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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715B TYR* 4.3 21.5 + - + +
717B PRO* 5.5 7.9 - - + +
910B LYS* 3.7 34.9 + - + +
918B ALA* 3.5 9.5 - - - +
919B ARG* 2.7 45.8 + - + +
920B LEU 3.0 0.8 + - - -
921B ASP* 1.3 77.2 - - - +
923B ARG* 1.3 57.7 + - - +
925B PHE* 3.2 6.4 + - - +
926B ALA* 2.9 29.2 + - - +
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Residues in contact with ARG 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B MET* 3.9 27.6 - - - -
860B LEU* 3.5 22.2 - - - +
910B LYS* 3.4 19.3 + - + +
911B SER 3.2 32.7 + - - +
912B PHE 3.8 1.4 - - - -
913B GLN* 2.6 34.1 + - - +
914B THR* 4.5 8.7 + - - +
916B THR 5.7 1.0 + - - -
918B ALA* 4.6 23.8 + - + +
919B ARG 3.3 6.8 + - - +
920B LEU* 3.1 14.1 + - - +
922B GLU* 1.3 79.1 - - - +
924B ILE* 1.3 64.0 + - + +
926B ALA* 3.0 5.2 + - - +
927B MET* 2.9 30.3 + - - +
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Residues in contact with ILE 924 (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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666B MET* 3.3 41.7 - - - +
699B LEU* 3.7 24.2 - - + +
700B ALA* 3.8 27.4 - - + +
707B ARG* 3.9 7.8 + - - +
856B MET* 4.6 2.2 - - + -
920B LEU* 3.2 17.1 + - + +
921B ASP* 3.8 10.5 - - - +
923B ARG* 1.3 77.7 - - + +
925B PHE* 1.3 56.8 + - - +
927B MET* 2.9 22.4 + - - +
928B CYS* 2.8 36.3 + - - -
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Residues in contact with PHE 925 (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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699B LEU* 3.8 13.2 - - + +
713B VAL* 3.8 29.8 - - + -
714B TYR* 4.3 0.4 - - - -
715B TYR* 3.3 57.2 - + + -
730B LYS* 5.3 8.1 - - - -
921B ASP 2.9 19.3 + - - +
922B GLU* 3.6 5.6 - - - +
924B ILE* 1.3 77.7 - - - +
926B ALA* 1.3 64.8 + - - +
928B CYS* 3.5 5.3 - - + +
929B GLN* 3.0 53.4 + - + +
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Residues in contact with ALA 926 (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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909B GLN* 4.7 3.1 + - + +
910B LYS* 3.9 10.3 - - + -
911B SER* 3.0 33.0 + - - +
922B GLU 2.9 13.9 + - - +
923B ARG 3.0 12.3 + - - +
925B PHE* 1.3 82.7 - - + +
927B MET* 1.3 54.6 + - - +
929B GLN* 3.6 6.8 + - - +
930B VAL* 3.2 29.6 + - - +
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Residues in contact with MET 927 (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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666B MET* 3.3 35.0 - - + -
707B ARG* 4.0 8.5 - - - +
852B VAL* 3.8 22.6 - - + +
855B SER* 3.7 17.0 - - - +
856B MET* 4.0 12.3 - - - -
860B LEU* 4.6 0.7 - - + -
911B SER* 3.5 27.6 - - - +
912B PHE* 3.8 15.5 - - + -
923B ARG* 2.9 21.1 + - - +
924B ILE* 3.4 15.0 - - - +
926B ALA* 1.3 73.5 - - - +
928B CYS* 1.3 64.8 + - - +
929B GLN 3.2 0.7 - - - -
930B VAL* 3.3 8.6 + - - +
931B LYS* 3.0 28.6 + - - +
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Residues in contact with CYS 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LEU* 5.0 1.6 - - - -
703B GLY* 4.9 7.6 - - - -
707B ARG* 3.2 38.1 - - + +
713B VAL* 4.0 34.1 - - + -
765B ASN* 4.9 1.6 + - - +
924B ILE* 2.8 23.8 + - - +
925B PHE* 3.3 14.1 + - + +
927B MET* 1.3 78.0 - - - +
929B GLN* 1.3 58.7 + - - +
931B LYS* 3.4 4.6 + - - +
932B ASN* 3.0 30.5 + - - +
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Residues in contact with GLN 929 (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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713B VAL 4.6 7.6 - - - +
925B PHE* 3.0 49.8 + - + +
926B ALA* 3.7 7.6 - - - +
927B MET 3.2 0.2 - - - -
928B CYS* 1.3 76.7 - - - +
930B VAL* 1.3 60.2 + - + +
932B ASN* 4.4 7.3 - - - +
933B GLN* 2.8 79.2 + - - +
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Residues in contact with VAL 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B ALA* 3.5 37.5 - - + -
849B ASN* 3.4 21.1 + - - +
852B VAL* 3.9 11.9 - - + -
909B GLN* 3.9 17.9 - - - +
911B SER* 3.9 7.0 - - - +
912B PHE* 5.3 0.9 - - + -
926B ALA 3.2 16.4 + - - +
927B MET* 3.6 9.6 - - - +
928B CYS 3.3 0.4 - - - -
929B GLN* 1.3 79.3 - - + +
931B LYS* 1.3 62.6 + - - +
932B ASN 3.5 0.3 + - - -
933B GLN* 4.1 9.8 + - - +
938B LEU* 3.8 29.3 - - + +
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Residues in contact with LYS 931 (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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707B ARG* 4.4 17.0 - - - +
762B PHE 4.1 3.6 + - - -
763B HIS* 2.9 38.0 + - - +
764B GLY* 3.2 34.8 + - - +
765B ASN* 4.4 7.9 - - - +
784B GLY 3.8 4.5 - - - +
785B TYR* 5.4 0.2 - - - -
849B ASN* 3.5 25.6 - - - +
852B VAL* 4.2 16.6 - - + -
853B ASP* 3.0 29.7 + - - -
927B MET 3.0 19.4 + - - +
928B CYS* 3.7 7.4 - - - +
930B VAL* 1.3 77.8 - - - +
932B ASN* 1.3 56.1 + - - +
933B GLN 5.4 0.2 - - - -
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Residues in contact with ASN 932 (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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711B GLY 3.7 1.5 + - - +
712B SER* 3.3 29.8 - - - -
713B VAL 5.0 0.7 + - - -
765B ASN* 3.5 34.9 + - - +
780B ASN* 5.8 0.3 + - - -
782B ASP 4.0 2.5 - - - +
783B ALA* 3.4 25.8 - - - +
784B GLY 2.6 36.6 + - - +
785B TYR* 5.4 0.4 - - - -
928B CYS 3.0 17.2 + - - +
929B GLN* 4.3 8.6 - - - +
931B LYS* 1.3 78.7 - - - +
933B GLN* 1.3 56.1 + - + +
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Residues in contact with GLN 933 (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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782B ASP 4.7 2.0 - - - +
784B GLY* 3.9 7.8 - - - -
929B GLN* 2.8 68.5 + - - +
930B VAL* 4.2 8.6 - - - +
932B ASN* 1.3 75.7 - - + +
934B PRO* 1.3 76.4 - - + +
935B LEU* 3.7 1.4 + - - -
937B TYR* 3.6 32.9 - - + +
938B LEU* 4.7 11.3 + - + +
941B THR* 4.3 13.6 + - - +
990B SER* 6.2 2.2 - - - -
1048B PHE* 6.4 0.2 - - - -
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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