Contacts of the helix formed by residues 934 - 943 (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 PRO 934 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 5.4 1.1 - - - +
412B HIS* 3.7 51.8 - - + +
782B ASP 3.5 19.5 - - - +
783B ALA 3.9 6.5 - - - +
784B GLY* 4.0 6.3 - - - -
932B ASN 4.0 1.1 - - - +
933B GLN* 1.3 88.6 - - + +
935B LEU* 1.3 69.4 + - - +
936B VAL* 2.7 15.5 + - + +
937B TYR* 2.9 28.8 + - + -
938B LEU* 3.5 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 935 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 3.3 43.5 - - + +
410B LEU* 3.3 33.7 - - + +
841B GLN* 3.6 22.0 - - + +
842B ALA* 3.8 20.4 - - - +
845B GLY* 4.3 8.7 - - - -
933B GLN 3.7 2.8 + - - -
934B PRO* 1.3 69.3 - - - +
936B VAL* 1.3 63.9 + - - +
938B LEU* 3.0 19.0 + - + +
939B MET* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 936 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B HIS* 5.8 2.0 - - + -
841B GLN* 6.2 0.2 - - - +
934B PRO* 2.7 14.5 + - + +
935B LEU* 1.3 76.4 - - - +
937B TYR* 1.3 105.4 + - + +
939B MET* 3.4 5.8 + - - +
940B LEU* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 937 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B HIS* 5.3 5.5 + - - -
782B ASP* 5.8 6.1 - - + -
933B GLN* 3.6 29.7 - - - +
934B PRO* 2.9 30.4 + - + +
936B VAL* 1.3 103.4 - - + +
938B LEU* 1.3 67.0 + - - +
940B LEU* 3.9 11.6 - - + +
941B THR* 2.9 31.3 + - - +
989B GLY* 5.1 11.9 - - - -
1045B GLN 4.7 2.1 + - - -
1046B ARG* 3.8 23.2 - - + +
1047B PRO* 3.4 28.5 - - + +
1048B PHE* 6.0 9.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 938 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844B SER* 4.5 2.0 - - - +
845B GLY* 3.3 36.8 - - - +
848B ALA* 4.2 12.3 - - + -
849B ASN* 5.5 2.0 - - - +
906B LEU* 4.9 5.2 - - + -
909B GLN* 4.4 4.0 - - - +
930B VAL* 3.8 40.4 - - + +
933B GLN* 4.7 13.7 + - + +
934B PRO 3.5 4.6 + - - +
935B LEU* 3.0 21.4 + - + +
937B TYR* 1.3 78.8 - - - +
939B MET* 1.3 63.2 + - - +
941B THR* 3.6 3.6 - - - -
942B THR* 2.8 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 939 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B GLN* 3.3 52.7 - - + +
844B SER* 4.4 7.9 - - - -
902B PHE* 3.8 36.3 - - + -
906B LEU* 6.5 0.7 - - - -
935B LEU* 3.0 32.0 + - + +
936B VAL* 3.6 9.0 - - - +
938B LEU* 1.3 84.3 - - - +
940B LEU* 1.3 62.3 + - + +
942B THR* 4.6 6.7 - - + +
943B HIS* 2.8 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 940 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B GLN* 6.2 0.2 - - - +
936B VAL* 2.9 45.8 + - + +
937B TYR* 3.9 9.2 - - + +
938B LEU 3.4 0.2 - - - -
939B MET* 1.3 79.3 - - + +
941B THR* 1.3 61.8 + - - +
943B HIS 4.3 3.1 - - - +
944B PRO* 3.2 22.5 - - - +
945B SER* 4.1 16.6 - - - +
987B ASP* 3.7 39.3 - - - +
988B ALA* 3.5 10.5 - - - -
989B GLY* 3.6 19.1 - - - -
1046B ARG* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 941 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909B GLN* 4.3 20.0 - - + +
933B GLN* 4.3 11.3 + - - +
937B TYR* 2.9 21.4 + - - +
938B LEU* 3.6 4.5 - - - -
940B LEU* 1.3 79.4 - - - +
942B THR* 1.3 67.2 + - - +
944B PRO* 3.4 11.8 - - - +
988B ALA* 3.8 15.2 + - - +
989B GLY* 5.5 0.2 - - - -
990B SER* 5.2 4.7 + - - -
1068B ASN* 4.3 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 942 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902B PHE* 4.2 3.1 - - + +
905B ALA* 3.5 22.5 - - + +
906B LEU* 3.5 53.7 - - + +
909B GLN* 3.6 21.3 + - + +
938B LEU* 2.8 28.8 + - - +
939B MET* 4.2 7.4 - - + -
941B THR* 1.3 75.8 - - - +
943B HIS* 1.3 60.6 + - + +
944B PRO* 3.4 6.6 - - - +
1068B ASN* 5.1 1.4 - - - +
1070B ILE* 4.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 3.8 31.1 - - + +
901B LEU* 4.0 26.4 - - + +
902B PHE* 3.8 32.9 - + + -
905B ALA* 4.4 5.4 - - + -
939B MET* 2.8 27.3 + - + +
940B LEU* 4.0 2.1 - - - +
942B THR* 1.3 76.6 - - + +
944B PRO* 1.3 72.6 + - - +
945B SER* 3.7 4.1 + - - -
970B ILE* 6.0 1.3 - - + -
971B LEU 5.2 1.1 - - - -
973B LEU* 3.5 32.5 + - + +
1070B ILE* 4.3 10.5 - - + +
1071B GLU* 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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