Contacts of the helix formed by residues 898 - 909 (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 LEU 898 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359B MET* 3.9 11.7 - - + +
360B LEU* 3.9 28.5 - - + +
361B PRO* 4.1 10.1 - - + -
365B LEU* 3.9 28.3 - - + -
840B VAL* 3.8 13.6 - - + +
895B SER 5.2 0.4 + - - -
896B LEU* 3.0 1.2 - - - +
897B ARG* 1.3 106.3 - - + +
899B PHE* 1.3 63.4 + - - +
900B PRO* 3.6 2.2 - - - -
901B LEU* 3.9 12.9 - - + +
902B PHE* 3.2 59.0 + - + -
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Residues in contact with PHE 899 (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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405B LEU* 4.0 13.0 - - + -
840B VAL* 3.7 18.1 - - + +
843B ILE* 3.8 16.6 - - + -
844B SER* 4.7 6.7 - - - -
847B LEU* 3.7 26.9 - - + -
870B ALA* 3.8 8.5 - - + -
871B VAL* 3.7 24.0 - - + -
874B SER* 3.3 25.8 - - - -
875B LEU* 5.1 3.8 - - + -
896B LEU* 2.9 40.0 + - + +
898B LEU* 1.3 76.1 - - - +
900B PRO* 1.3 67.4 - - + +
902B PHE* 3.6 0.7 + - - -
903B VAL* 3.1 44.9 + - + +
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Residues in contact with PRO 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.6 26.2 - - + -
871B VAL* 3.7 22.4 - - + -
875B LEU* 4.1 8.3 - - + -
890B LEU* 5.4 0.2 - - + -
896B LEU 3.6 7.6 - - - +
897B ARG 4.4 2.7 - - - +
898B LEU 3.9 0.7 - - - -
899B PHE* 1.3 95.2 - - + +
901B LEU* 1.3 56.1 + - - +
903B VAL* 3.4 0.3 + - - +
904B LEU* 2.9 32.2 + - - +
1080B TYR* 4.6 2.0 - - + +
1083B PHE* 3.4 12.6 - - + -
1084B LEU* 4.1 16.8 - - + -
1087B ILE* 3.9 18.2 - - + -
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Residues in contact with LEU 901 (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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359B MET* 4.4 20.0 - - - -
360B LEU* 4.4 20.4 - - + -
897B ARG 5.3 0.2 - - - +
898B LEU* 3.6 15.2 + - + +
899B PHE 3.3 0.2 - - - -
900B PRO* 1.3 82.4 - - - +
902B PHE* 1.3 62.8 + - + +
904B LEU* 3.7 2.2 - - - +
905B ALA* 3.0 28.1 + - - +
943B HIS* 4.0 22.2 - - + +
1070B ILE* 3.5 30.5 - - + +
1071B GLU* 3.9 25.6 - - + +
1080B TYR* 3.8 27.2 + - + +
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Residues in contact with PHE 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.5 6.5 - - + -
365B LEU* 3.8 29.2 - - + -
840B VAL* 3.8 22.0 - - + -
841B GLN* 4.1 2.0 - - + -
844B SER* 3.6 20.0 - - - +
898B LEU* 3.2 38.9 + - + +
899B PHE* 4.3 2.5 - - - +
901B LEU* 1.3 83.1 - - + +
903B VAL* 1.3 60.9 + - - +
905B ALA* 3.3 5.7 + - - +
906B LEU* 2.8 31.6 + - - +
939B MET* 3.8 26.2 - - + -
942B THR* 4.2 3.5 - - + +
943B HIS* 3.8 39.5 - + + -
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Residues in contact with VAL 903 (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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844B SER* 5.3 1.6 - - - +
847B LEU* 4.8 8.1 - - + -
867B LEU* 4.1 30.3 - - + +
871B VAL* 3.4 29.2 - - + -
899B PHE* 3.1 39.0 + - + +
900B PRO 3.8 2.2 - - - +
902B PHE* 1.3 73.2 - - + +
904B LEU* 1.3 56.1 + - - +
906B LEU* 3.0 16.0 - - + +
907B LEU* 2.7 45.7 + - + +
1083B PHE* 4.4 5.6 - - + -
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Residues in contact with LEU 904 (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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900B PRO 2.9 19.0 + - - +
901B LEU 3.7 2.7 - - - +
903B VAL* 1.3 76.9 - - - +
905B ALA* 1.3 57.9 + - - +
907B LEU* 2.9 30.8 + - + +
908B LYS* 2.9 32.6 + - + +
1070B ILE* 3.6 23.1 - - + +
1078B LEU* 4.1 9.2 - - + +
1080B TYR* 3.4 46.4 - - + +
1083B PHE* 3.8 28.0 - - + -
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Residues in contact with ALA 905 (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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901B LEU 3.0 18.9 + - - +
902B PHE* 3.4 9.9 - - - +
904B LEU* 1.3 76.2 - - - +
906B LEU* 1.3 62.9 + - - +
908B LYS* 3.2 2.6 + - - +
909B GLN* 2.9 23.2 + - - +
942B THR* 3.5 29.3 - - + +
943B HIS* 4.4 8.3 - - + -
1070B ILE* 3.9 29.9 - - + +
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Residues in contact with LEU 906 (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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844B SER* 3.7 36.1 - - - +
847B LEU* 5.2 0.9 - - + -
848B ALA* 4.4 18.8 - - + -
867B LEU* 4.6 19.3 - - + -
902B PHE 2.8 13.5 + - - +
903B VAL* 3.0 21.5 - - + +
905B ALA* 1.3 77.6 - - - +
907B LEU* 1.3 59.2 + - - +
909B GLN* 3.2 29.0 + - - +
912B PHE* 3.7 24.9 - - + +
938B LEU* 4.9 6.5 - - + -
939B MET* 6.5 0.4 - - - -
942B THR* 3.5 29.8 - - + +
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Residues in contact with LEU 907 (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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864B ARG* 3.2 63.0 + - + +
867B LEU* 3.8 17.5 - - + -
868B VAL* 3.6 25.6 - - + -
903B VAL* 2.7 26.2 + - + +
904B LEU* 2.9 14.3 + - + +
906B LEU* 1.3 74.0 - - - +
908B LYS* 1.3 57.4 + - + +
912B PHE* 4.6 4.0 - - + -
913B GLN* 3.1 23.1 + - - -
1083B PHE* 3.8 22.9 - - + -
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Residues in contact with LYS 908 (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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904B LEU* 2.9 27.9 + - + +
905B ALA 3.2 3.6 + - - +
906B LEU 3.2 0.2 - - - -
907B LEU* 1.3 77.4 - - + +
909B GLN* 1.3 62.6 + - - +
913B GLN* 2.9 26.7 - - - +
1067B GLN 5.2 7.2 - - - +
1069B MET 4.2 1.0 + - - -
1070B ILE* 2.6 53.0 + - + +
1071B GLU 4.0 0.6 - - - -
1072B ASP 2.6 28.9 + - - -
1073B ARG* 4.7 0.6 - - - +
1074B THR* 6.1 1.0 - - - -
1077B ALA* 4.3 21.0 - - + +
1078B LEU 3.1 23.2 + - - -
1079B SER* 4.4 0.2 - - - +
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Residues in contact with GLN 909 (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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905B ALA 2.9 12.4 + - - +
906B LEU* 3.2 19.0 + - - +
908B LYS* 1.3 77.7 - - - +
910B LYS* 1.3 60.7 + - + +
911B SER* 2.9 37.0 + - - +
912B PHE* 3.3 15.8 + - - -
913B GLN* 2.7 35.0 + - - +
926B ALA* 4.7 3.0 + - + +
930B VAL* 3.9 16.2 - - - +
938B LEU* 4.4 3.4 - - - +
941B THR* 4.3 17.5 - - + +
942B THR* 3.6 27.2 + - + +
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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