Contacts of the helix formed by residues 904 - 920 (chain B) in PDB entry 5NC5
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 VAL 904 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B VAL 2.9 21.5 + - - +
902B MET 2.7 5.6 + - - +
903B LEU* 1.3 74.6 - - - +
905B VAL* 1.3 71.7 + - + +
906B PRO* 3.4 1.1 - - - -
907B LEU* 3.2 24.7 + - + +
935B ILE 5.4 0.2 - - - +
938B SER* 3.9 29.7 + - - +
939B ALA* 4.1 21.1 - - + -
942B ALA* 4.5 6.3 - - + -
1018B ALA* 4.1 26.2 - - + -
1022B VAL* 4.2 12.6 - - + -
1025B PHE* 4.0 9.1 - - + -
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Residues in contact with VAL 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B MET* 6.2 0.9 - - - -
902B MET* 3.0 19.3 - - + +
904B VAL* 1.3 84.3 - - + +
906B PRO* 1.3 74.3 - - + +
907B LEU 3.1 1.4 + - - -
908B GLY* 3.3 9.0 + - - -
909B VAL* 3.6 13.6 + - + +
935B ILE* 4.0 33.1 - - + +
938B SER* 5.0 3.2 + - - -
939B ALA* 6.2 0.7 - - + -
1111B D10 5.9 1.8 - - + -
1116B D10 4.0 35.0 - - + -
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Residues in contact with PRO 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B TYR* 3.7 8.5 - - + +
548B ILE* 5.0 4.0 - - + -
549B VAL* 3.6 34.3 - - + -
552B MET* 3.9 18.1 - - + +
902B MET 4.6 0.2 - - - +
903B LEU 3.1 16.4 - - - +
904B VAL 3.5 0.9 - - - -
905B VAL* 1.3 96.9 - - + +
907B LEU* 1.3 68.0 + - + +
908B GLY 3.2 0.2 - - - -
909B VAL* 3.7 10.1 - - + -
910B ILE* 3.0 28.8 + - - +
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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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545B TYR* 3.9 31.4 - - + -
548B ILE* 4.7 13.2 - - + -
903B LEU 4.5 0.9 - - - +
904B VAL* 3.3 26.5 - - + +
905B VAL 3.1 1.2 + - - -
906B PRO* 1.3 80.0 - - + +
908B GLY* 1.3 50.5 + - - +
910B ILE* 3.1 12.9 - - - +
1013B THR* 2.5 32.9 + - - -
1014B ALA* 3.5 9.8 + - - -
1017B LEU* 3.8 19.9 - - + +
1018B ALA* 3.6 31.0 - - - +
1021B PHE* 3.9 22.7 - - + -
1025B PHE* 4.5 2.2 - - + -
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Residues in contact with GLY 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B VAL 4.1 1.2 + - - -
905B VAL 3.3 6.5 + - - -
906B PRO 3.2 0.4 - - - -
907B LEU* 1.3 78.9 - - - +
909B VAL* 1.3 65.0 + - - +
910B ILE 3.3 0.4 + - - -
911B GLY 3.5 0.9 + - - -
912B ALA* 3.3 6.1 + - - +
934B THR* 4.0 13.4 - - - +
935B ILE* 5.9 0.9 - - - -
938B SER* 4.9 3.4 + - - -
1010B GLY* 3.0 29.5 - - - -
1014B ALA* 3.6 23.5 - - - +
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Residues in contact with VAL 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B MET* 3.8 15.0 - - + -
556B PHE* 5.0 5.2 - - + -
905B VAL* 3.6 18.6 - - + +
906B PRO* 3.3 10.2 + - + +
908B GLY* 1.3 75.1 - - - +
910B ILE* 1.3 59.2 + - - +
912B ALA* 3.1 1.9 + - - +
913B LEU* 2.8 51.5 + - + +
931B LEU* 4.2 28.7 - - + -
935B ILE* 3.8 27.4 - - + -
1111B D10 5.3 4.7 - - + -
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Residues in contact with ILE 910 (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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548B ILE* 3.8 26.5 - - + +
551B GLY* 3.9 2.7 - - - -
552B MET* 3.6 37.2 - - + +
555B LEU* 3.8 17.5 - - + -
906B PRO 3.0 13.9 + - - +
907B LEU* 3.1 26.0 - - - +
909B VAL* 1.3 77.7 - - - +
911B GLY* 1.3 58.2 + - - +
913B LEU* 3.4 4.4 + - - +
914B LEU* 2.9 44.9 + - + +
1013B THR* 3.9 7.4 - - + +
1017B LEU* 4.8 6.7 - - + -
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Residues in contact with GLY 911 (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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908B GLY 3.5 0.2 + - - -
909B VAL 3.3 0.2 - - - -
910B ILE* 1.3 75.7 - - - +
912B ALA* 1.3 60.9 + - - +
914B LEU* 3.7 8.0 - - - +
915B ALA* 3.0 28.6 + - - +
1009B GLY* 3.4 13.5 - - - -
1013B THR* 3.2 41.6 + - - -
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Residues in contact with ALA 912 (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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908B GLY 3.3 11.1 + - - +
909B VAL 3.1 7.7 + - - +
911B GLY* 1.3 75.2 - - - +
913B LEU* 1.3 66.5 + - - +
915B ALA* 3.2 2.6 + - - +
916B ALA* 3.0 24.8 + - - +
927B PHE* 3.9 5.9 - - + -
931B LEU* 3.6 26.0 - - + -
934B THR* 5.7 1.3 - - + +
1006B GLY* 3.2 34.2 - - - +
1009B GLY* 4.5 0.2 - - - -
1010B GLY* 3.5 2.4 - - - +
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Residues in contact with LEU 913 (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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552B MET* 3.7 30.7 - - + +
555B LEU* 4.0 14.8 - - + +
556B PHE* 3.8 36.1 - - + +
559B LEU* 4.1 14.4 - - + -
909B VAL* 2.8 39.2 + - + +
910B ILE* 3.7 4.3 - - - +
912B ALA* 1.3 76.6 - - - +
914B LEU* 1.3 56.4 + - - +
916B ALA* 3.8 1.0 - - - +
917B THR* 2.7 38.7 + - - +
923B ASN* 5.8 0.4 - - - +
927B PHE* 3.9 23.1 - - + -
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Residues in contact with LEU 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B LEU* 3.2 38.1 - - + -
910B ILE* 2.9 35.8 + - + +
911B GLY* 3.7 10.3 - - - +
913B LEU* 1.3 76.5 - - - +
915B ALA* 1.3 63.9 + - - +
917B THR* 3.8 3.8 - - - -
918B PHE* 3.0 28.4 + - - +
1013B THR* 5.0 5.6 - - + -
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Residues in contact with ALA 915 (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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911B GLY 3.0 18.7 + - - +
912B ALA 3.2 3.3 + - - +
914B LEU* 1.3 77.1 - - - +
916B ALA* 1.3 61.5 + - - +
918B PHE* 3.7 9.5 + - - -
919B ARG* 3.3 24.4 + - - +
1005B THR* 3.6 32.6 + - - +
1009B GLY* 3.9 9.2 - - - +
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Residues in contact with ALA 916 (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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559B LEU* 4.1 15.3 - - + -
912B ALA 3.0 15.8 + - - +
913B LEU 3.8 2.0 - - - +
915B ALA* 1.3 76.6 - - - +
917B THR* 1.3 64.4 + - - +
919B ARG* 3.2 2.0 + - - -
920B GLY 3.1 4.7 + - - -
921B LEU* 3.0 40.7 + - + -
922B THR 5.1 0.4 - - - +
927B PHE* 3.9 23.6 - - + -
1005B THR* 4.2 10.3 + - - +
1006B GLY* 5.5 0.4 - - - -
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Residues in contact with THR 917 (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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555B LEU* 3.8 32.2 + - + +
558B ARG* 5.7 9.6 - - + -
559B LEU* 4.1 22.4 - - + +
913B LEU* 2.7 28.5 + - - +
914B LEU* 3.9 3.4 - - - -
916B ALA* 1.3 71.9 - - - +
918B PHE* 1.3 61.1 + - - +
920B GLY* 3.4 11.5 + - - -
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Residues in contact with PHE 918 (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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914B LEU 3.0 16.3 + - - +
915B ALA* 3.9 11.2 - - - -
917B THR* 1.3 76.5 - - - +
919B ARG* 1.3 71.8 + - + +
920B GLY* 3.2 3.3 + - - -
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Residues in contact with ARG 919 (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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915B ALA 3.3 14.0 + - - +
916B ALA 3.2 4.4 + - - +
918B PHE* 1.3 89.9 - - + +
920B GLY* 1.3 60.8 + - - +
921B LEU* 3.3 40.5 - - + +
990B VAL* 3.1 21.4 + - - +
991B ILE* 4.9 3.4 + - - +
992B SER 4.6 3.4 + - - -
993B THR* 6.3 0.4 - - - +
1001B ASN* 3.1 31.1 - - - +
1005B THR* 3.7 19.4 - - - +
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Residues in contact with GLY 920 (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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916B ALA 3.1 4.2 + - - -
917B THR 3.4 8.0 + - - -
918B PHE 3.2 5.7 + - - -
919B ARG* 1.3 78.4 - - - +
921B LEU* 1.3 67.8 + - - +
922B THR* 4.7 4.0 - - - +
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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
------------------------------------------------------------
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