Contacts of the helix formed by residues 1017 - 1028 (chain A) in PDB entry 6A5T
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 THR1017 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A ASP 5.4 0.9 - - - +
999A LEU* 4.4 14.1 + - + +
1001A VAL* 3.9 27.8 - - + -
1013A GLN* 3.5 13.3 + - - +
1014A GLN* 4.3 3.4 + - - -
1015A ASN 3.7 0.4 - - - -
1016A ALA* 1.3 78.4 - - + +
1018A SER* 1.3 58.5 + - - +
1019A LEU 3.4 2.2 - - - +
1020A PHE* 4.0 16.6 - - + +
1021A GLN* 2.9 48.4 + - - +
1055A PHE* 4.3 13.2 - - + -
204E SER* 5.9 0.2 - - - +
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Residues in contact with SER1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943A PHE* 4.2 24.7 - - - -
1014A GLN* 3.2 21.8 + - - +
1015A ASN* 4.1 5.0 + - - -
1016A ALA 3.1 4.2 + - - -
1017A THR* 1.3 76.7 - - - +
1019A LEU* 1.3 59.2 + - - +
1021A GLN* 3.2 8.8 + - - +
1022A CYS* 2.8 35.0 + - - -
1025A ARG* 4.8 0.3 + - - -
204E SER 4.3 7.0 - - - -
206E ARG* 5.0 8.4 + - - +
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Residues in contact with LEU1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884A ILE* 3.9 22.0 - - + +
943A PHE* 5.4 0.7 - - + -
944A LEU* 3.6 31.6 - - + -
948A VAL* 5.8 0.2 - - + -
949A PHE* 3.6 26.2 - - + -
956A TRP* 5.2 3.4 - - + -
958A LEU* 4.1 21.5 - - + +
1016A ALA 4.4 0.2 + - - -
1017A THR 3.4 0.2 - - - -
1018A SER* 1.3 78.2 - - - +
1020A PHE* 1.3 58.2 + - - +
1022A CYS* 3.1 7.5 + - + +
1023A LEU* 3.0 24.3 + - - +
202E GLU 4.7 0.9 - - - +
203E THR* 4.3 19.5 - - - +
204E SER* 3.9 23.8 + - - +
205E GLY* 4.1 8.4 - - - +
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Residues in contact with PHE1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A LEU* 5.8 2.2 - - + -
958A LEU* 5.0 6.4 - - + +
959A PRO* 3.5 35.7 - - + -
960A VAL* 4.4 15.7 - - + -
962A LEU* 5.3 1.8 - - + -
999A LEU* 3.4 32.3 - - + -
1017A THR* 3.7 16.1 + - + +
1018A SER 3.3 0.4 - - - -
1019A LEU* 1.3 75.8 - - - +
1021A GLN* 1.3 66.8 + - - +
1023A LEU* 3.2 16.7 + - + +
1024A VAL* 3.0 44.7 + - + +
1051A ILE* 4.6 15.3 - - + -
1055A PHE* 3.8 29.2 - + + -
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Residues in contact with GLN1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996A CYS* 3.2 46.1 + - - +
999A LEU* 5.0 9.4 - - + +
1014A GLN* 3.0 35.0 + - - +
1017A THR* 2.9 40.0 + - - +
1018A SER* 3.2 4.9 + - - +
1020A PHE* 1.3 75.7 - - - +
1022A CYS* 1.3 62.6 + - - +
1024A VAL* 3.3 5.2 + - - +
1025A ARG* 3.0 54.9 + - - +
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Residues in contact with CYS1022 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884A ILE* 5.2 3.8 - - + +
886A THR* 5.3 2.4 + - - +
937A LEU* 5.8 0.7 - - - +
940A ASP* 3.1 43.8 - - + +
943A PHE* 4.2 17.3 - - - -
944A LEU* 4.3 22.4 - - + -
1018A SER* 2.8 26.6 + - - -
1019A LEU* 3.1 11.4 + - + +
1021A GLN* 1.3 77.2 - - - +
1023A LEU* 1.3 57.4 - - - +
1025A ARG* 3.6 2.7 + - - +
1026A ALA* 2.8 31.1 + - - +
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Residues in contact with LEU1023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A GLN* 3.1 27.8 - - + +
883A THR 3.9 9.4 - - - +
884A ILE* 3.7 38.5 - - + +
885A ASP 4.6 2.7 - - - +
958A LEU* 3.7 24.7 - - + -
960A VAL 5.4 1.3 - - - +
962A LEU* 4.2 15.3 - - + -
1019A LEU 3.0 12.0 + - - +
1020A PHE* 3.2 17.0 + - + +
1022A CYS* 1.3 77.4 - - - +
1024A VAL* 1.3 64.6 + - - +
1026A ALA* 2.9 13.6 + - + +
1027A ARG* 3.0 23.5 + - + +
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Residues in contact with VAL1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962A LEU* 3.9 24.2 - - + -
992A VAL* 4.9 13.7 - - + -
995A LEU* 4.5 20.6 - - + -
996A CYS* 5.4 7.0 - - - -
999A LEU* 5.5 0.9 - - + -
1020A PHE* 3.0 44.9 + - + +
1021A GLN* 3.9 6.3 - - - +
1023A LEU* 1.3 76.1 - - - +
1025A ARG* 1.3 63.2 + - + +
1027A ARG* 3.2 2.9 + - - +
1028A LEU* 3.0 38.9 + - + +
1051A ILE* 4.9 7.4 - - + -
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Residues in contact with ARG1025 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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933A GLU* 5.9 7.4 - - - +
936A GLN* 4.1 29.2 - - - +
937A LEU* 4.1 19.0 - - + +
940A ASP* 3.3 29.2 + - - +
992A VAL* 4.0 24.7 - - + -
996A CYS* 3.6 14.8 - - - -
1018A SER* 4.8 0.4 + - - +
1021A GLN* 3.0 61.2 + - - +
1022A CYS* 3.8 4.4 - - - +
1024A VAL* 1.3 79.8 - - + +
1026A ALA* 1.3 60.1 + - - +
1027A ARG 3.2 0.4 + - - -
1028A LEU 4.7 3.4 - - - +
1029A ALA* 3.8 20.8 + - - +
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Residues in contact with ALA1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884A ILE* 5.1 1.8 - - + -
885A ASP* 3.4 20.3 - - + +
886A THR* 3.5 31.0 - - + +
898A TYR* 3.3 18.2 + - - -
937A LEU* 4.9 1.8 - - - +
1022A CYS 2.8 21.6 + - - +
1023A LEU* 2.9 10.5 + - + +
1025A ARG* 1.3 78.0 - - - +
1027A ARG* 1.3 60.9 + - - +
1032A ARG* 3.2 14.6 + - - -
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Residues in contact with ARG1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A GLN* 4.8 5.6 + - - +
883A THR* 2.6 45.7 + - - +
885A ASP* 2.6 28.4 + - - -
961A ASN* 5.2 1.8 + - - -
962A LEU* 4.1 21.3 - - + +
963A ARG* 3.8 42.2 - - - +
966A ILE* 5.1 4.5 - - + -
1023A LEU* 3.0 22.2 + - + +
1024A VAL 3.9 3.8 - - - +
1026A ALA* 1.3 76.1 - - - +
1028A LEU* 1.3 65.2 + - + +
1029A ALA 2.6 18.6 + - - -
1032A ARG* 3.3 36.5 + - - +
1033A ILE* 5.2 0.3 + - - +
1037A PHE* 5.3 8.3 - - + -
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Residues in contact with LEU1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A GLU* 4.7 2.6 - - - +
962A LEU* 5.8 3.8 - - + -
966A ILE* 3.5 31.2 - - + -
988A ILE* 4.5 3.8 - - - +
992A VAL* 4.1 27.8 - - + +
1024A VAL* 3.0 27.9 + - + +
1025A ARG* 4.4 4.3 - - - -
1027A ARG* 1.3 76.2 - - + +
1029A ALA* 1.3 65.6 + - - +
1033A ILE* 4.1 26.1 - - + +
1037A PHE* 4.9 2.7 - - + -
1039A LEU* 5.7 3.1 - - + -
1044A PHE* 4.8 14.6 - - + -
1047A VAL* 4.6 11.2 - - + -
1048A LEU* 5.1 9.2 - - + -
1051A ILE* 4.6 20.2 - - + -
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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