Contacts of the helix formed by residues 918 - 930 (chain I) in PDB entry 2VKZ
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 THR 918 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1682C LYS* 5.4 4.3 - - + +
917I MET* 1.3 76.0 - - - +
919I TYR* 1.3 65.8 + - - +
920I GLU* 3.6 4.9 + - - +
921I GLU* 2.8 48.1 + - - +
922I VAL* 3.1 14.0 + - - +
990I ALA 4.0 2.7 - - - -
991I ARG 3.5 26.0 + - - +
992I GLU 4.2 5.4 - - - +
993I GLN 3.3 25.1 - - - +
994I PHE* 4.1 12.1 - - + +
995I LEU* 4.3 2.9 - - - -
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Residues in contact with TYR 919 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918I THR* 1.3 74.6 - - - +
920I GLU* 1.3 60.8 + - - +
923I ALA 3.1 17.2 + - - -
950I PHE* 3.5 21.1 - + - -
953I ARG* 5.3 2.0 - - + -
954I VAL* 3.9 20.4 - - + -
957I ARG* 4.0 4.1 - - + +
958I PHE* 3.5 35.2 - + - -
984I PHE* 3.3 20.6 - - + -
990I ALA* 3.4 12.7 + - + +
993I GLN* 3.8 11.2 - - - -
994I PHE 3.5 20.2 - - - -
995I LEU* 3.5 24.9 - - + -
996I ASN* 2.8 26.0 + - - +
999I ASP* 2.5 32.8 + - + -
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Residues in contact with GLU 920 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918I THR* 3.0 7.6 + - - +
919I TYR* 1.3 77.6 - - - +
921I GLU* 1.3 64.8 + - + +
922I VAL 2.9 1.2 + - - -
923I ALA* 2.9 4.5 + - - +
924I LYS* 2.9 60.8 + - + +
980I ILE* 5.1 1.5 - - + +
981I GLU* 4.6 5.9 - - - +
984I PHE* 3.3 30.9 - - + +
990I ALA 3.6 1.2 + - - -
991I ARG* 3.1 49.4 + - - +
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Residues in contact with GLU 921 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907I VAL* 3.4 29.1 - - + +
912I ARG* 2.7 33.0 + - - -
916I THR 4.7 0.2 - - - +
917I MET* 3.5 17.1 - - + +
918I THR* 2.8 41.9 + - - +
920I GLU* 1.3 78.5 - - + +
922I VAL* 1.3 56.7 + - - +
924I LYS* 3.9 6.8 - - - +
925I ARG* 2.9 29.5 + - - +
994I PHE* 5.3 0.2 - - - -
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Residues in contact with VAL 922 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904I PHE* 3.9 7.6 - - + -
914I LEU* 4.5 1.6 - - + -
917I MET* 3.7 33.9 - - + -
918I THR 3.1 13.6 + - - +
920I GLU 3.0 1.0 - - - -
921I GLU* 1.3 72.1 - - - +
923I ALA* 1.3 56.4 + - - +
925I ARG* 3.1 3.6 + - - +
926I LEU* 2.7 41.7 + - + +
950I PHE* 3.5 28.7 - - + -
995I LEU* 4.1 20.2 - - + -
1003I PHE* 3.8 28.0 - - + -
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Residues in contact with ALA 923 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919I TYR 3.1 11.2 + - - +
920I GLU 2.9 7.4 + - - +
922I VAL* 1.3 79.2 - - - +
924I LYS* 1.3 58.2 + - - +
926I LEU* 3.4 8.5 + - - +
927I VAL* 3.1 24.1 + - - +
947I THR* 5.6 2.1 - - - -
950I PHE* 3.8 9.8 - - + -
951I LEU* 3.8 28.0 - - + -
980I ILE* 3.5 18.6 - - + +
984I PHE* 3.9 11.0 - - + -
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Residues in contact with LYS 924 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920I GLU* 2.9 49.5 + - + +
921I GLU* 4.0 6.5 - - - +
923I ALA* 1.3 75.1 - - - +
925I ARG* 1.3 59.3 + - - +
927I VAL* 3.9 4.0 - - - +
928I GLU* 3.0 28.6 + - - +
980I ILE* 4.0 19.5 - - + -
981I GLU* 3.9 19.8 + - - -
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Residues in contact with ARG 925 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896I ASN* 4.5 0.2 + - - -
902I PRO* 3.8 14.6 - - - +
903I TRP 3.5 5.7 + - - -
904I PHE* 2.9 44.6 + - + +
906I THR* 3.1 43.8 + - - +
907I VAL* 5.6 2.9 - - + +
908I ASN 5.8 1.2 - - - +
917I MET* 4.2 6.1 - - + -
921I GLU 2.9 20.3 + - - +
922I VAL* 3.1 4.2 + - - +
924I LYS* 1.3 74.1 - - - +
926I LEU* 1.3 64.1 + - - +
928I GLU* 3.0 40.3 + - - +
929I LEU* 3.0 44.9 + - - +
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Residues in contact with LEU 926 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904I PHE* 3.5 25.1 - - + -
922I VAL* 2.7 27.8 + - + +
923I ALA* 3.5 6.5 - - - +
925I ARG* 1.3 73.3 - - - +
927I VAL* 1.3 62.4 + - - +
929I LEU* 3.3 1.7 + - - -
930I MET* 3.1 48.5 + - + +
946I PHE* 3.7 31.4 - - + -
947I THR* 3.3 34.5 - - + -
950I PHE* 4.1 23.1 - - + -
1003I PHE* 4.1 3.4 - - + -
1017I PHE* 4.2 1.6 - - + -
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Residues in contact with VAL 927 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923I ALA 3.1 16.4 + - - +
924I LYS* 3.9 5.2 - - - +
926I LEU* 1.3 79.6 - - + +
928I GLU* 1.3 65.8 + - - +
931I PHE* 2.9 30.0 + - + +
933I ARG* 3.4 29.2 - - - +
938I TRP* 3.8 22.0 - - + -
947I THR* 5.4 1.8 - - + +
973I LEU* 5.0 3.1 - - + -
976I PRO* 3.6 26.9 - - + -
977I ASP* 4.3 3.4 - - - +
980I ILE* 4.0 16.8 - - + -
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Residues in contact with GLU 928 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906I THR 5.2 0.2 - - - +
908I ASN* 5.8 2.3 + - - -
924I LYS 3.0 17.3 + - - +
925I ARG* 3.0 47.8 + - - +
927I VAL* 1.3 82.3 - - - +
929I LEU* 1.3 60.0 + - + +
931I PHE 4.2 6.4 - - - +
933I ARG* 6.5 0.4 - - - -
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Residues in contact with LEU 929 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902I PRO* 3.6 27.4 - - + -
904I PHE* 4.3 11.9 - - + -
925I ARG* 3.0 61.4 + - + +
926I LEU 4.2 1.3 - - - +
928I GLU* 1.3 80.0 - - + +
930I MET* 1.3 64.3 + - + +
931I PHE 5.2 0.4 - - - -
932I ILE* 6.0 0.9 - - - +
943I TRP* 4.4 2.9 - - - -
1016I PRO* 4.0 27.3 - - + +
1017I PHE* 4.3 15.5 - - + -
1042I ALA* 4.8 11.7 - - - +
1044I VAL* 5.8 6.3 - - + -
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Residues in contact with MET 930 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926I LEU* 3.1 25.7 + - + +
929I LEU* 1.3 83.6 - - + +
931I PHE* 1.3 63.7 + - - +
932I ILE* 3.5 3.1 + - - -
938I TRP* 3.6 14.6 - - + -
939I PHE* 3.1 30.1 + - - +
943I TRP* 3.6 52.4 - - + +
946I PHE* 4.5 9.2 - - + -
947I THR* 4.0 11.9 - - - -
1015I VAL* 3.7 20.6 - - + -
1016I PRO* 3.8 8.1 - - + -
1017I PHE* 3.6 28.5 - - + -
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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