Contacts of the helix formed by residues 1017 - 1032 (chain A) in PDB entry 4C48
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 LEU1017 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A ILE* 5.5 12.6 - - + -
907A LEU* 3.5 42.8 - - + +
910A ILE* 6.0 5.4 - - + -
1013A THR* 3.0 27.9 + - + +
1015A THR 3.1 0.4 - - - -
1016A VAL* 1.3 86.4 - - + +
1018A ALA* 1.3 61.4 + - - +
1019A ILE 3.4 0.9 - - - -
1020A PHE* 3.4 11.4 + - - +
1021A PHE* 2.9 43.9 - - + -
29C LEU* 4.6 10.1 - - + -
33C PHE* 5.7 2.0 - - + -
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Residues in contact with ALA1018 (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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904A VAL* 4.9 5.2 - - + -
907A LEU* 3.7 23.8 - - + -
938A SER* 5.2 5.2 - - - +
941A ASN* 6.2 2.9 - - + -
942A ALA* 6.2 0.2 - - + -
1013A THR 3.7 2.0 + - - +
1014A ALA* 3.0 31.2 - - - +
1015A THR 3.4 2.0 + - - -
1017A LEU* 1.3 75.3 - - - +
1019A ILE* 1.3 60.8 + - + +
1020A PHE 3.1 2.5 - - - -
1022A VAL* 3.0 44.2 + - + +
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Residues in contact with ILE1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 2.3 52.1 + - + +
531A VAL* 4.5 0.2 - - - +
941A ASN* 6.2 1.1 - - + -
945A ILE* 5.1 11.8 - - + +
968A VAL* 4.2 0.9 - - - +
972A LEU* 4.0 15.5 - - + -
975A ILE* 4.0 34.3 - - + -
976A LEU* 5.3 4.3 - - + -
1015A THR* 3.2 20.2 - - - +
1016A VAL 3.8 7.4 - - - +
1018A ALA* 1.3 77.8 - - + +
1020A PHE* 1.3 59.7 + - + +
1023A PRO* 3.3 19.1 - - - +
26C ILE* 3.5 30.7 - - + -
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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
----------------------------------------------------------
527A TYR* 3.4 39.7 - + - -
530A SER* 4.8 3.1 - - - -
531A VAL* 4.2 6.5 - - + +
534A ILE* 3.6 35.7 - - + +
1016A VAL 3.3 27.6 - - - -
1017A LEU 3.4 8.2 + - - +
1018A ALA 3.1 0.6 - - - -
1019A ILE* 1.3 79.8 - - + +
1021A PHE* 1.3 68.7 + - + +
1022A VAL 3.6 0.2 - - - -
1023A PRO* 3.4 13.1 - - - +
1024A VAL* 3.8 12.4 - - - +
26C ILE* 3.8 26.7 - - + -
29C LEU* 3.6 21.8 - - + -
30C GLY* 3.9 13.7 - - - -
33C PHE* 3.4 20.6 - + + -
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Residues in contact with PHE1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A TYR* 4.0 32.8 - + - -
544A LEU* 4.2 14.1 - - + -
545A TYR* 4.3 19.5 - + + -
548A ILE* 5.5 4.7 - - + -
907A LEU* 3.5 15.3 - - + -
1017A LEU* 2.9 50.3 - - + -
1018A ALA 3.4 2.0 + - - -
1020A PHE* 1.3 80.6 - - + +
1022A VAL* 1.3 65.7 + - - +
1024A VAL* 2.9 31.8 + - + +
1025A PHE* 3.2 31.0 + + + -
33C PHE* 4.0 28.7 - + - -
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Residues in contact with VAL1022 (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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900A SER 5.8 1.1 - - - +
904A VAL* 3.5 15.7 - - + -
942A ALA* 3.5 30.3 - - + +
945A ILE* 3.6 25.8 - - + -
946A VAL* 3.6 28.5 - - + -
1018A ALA* 3.0 25.3 + - + +
1019A ILE* 5.1 0.9 - - - +
1021A PHE* 1.3 75.2 - - - +
1023A PRO* 1.3 71.0 - - + +
1025A PHE* 3.0 19.8 + - - +
1026A PHE* 3.0 11.3 + - - +
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Residues in contact with PRO1023 (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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531A VAL* 4.1 18.4 - - + -
534A ILE* 6.2 0.2 - - + -
535A LEU* 3.9 12.6 - - + -
945A ILE* 5.1 5.4 - - + -
964A THR* 3.8 23.8 - - + -
968A VAL* 4.4 12.3 - - + -
1019A ILE* 3.3 25.6 - - - +
1020A PHE 3.4 12.1 - - - +
1022A VAL* 1.3 97.2 - - + +
1024A VAL* 1.3 56.6 + - - +
1026A PHE* 3.3 5.5 + - + +
1027A VAL* 3.0 31.9 + - - +
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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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534A ILE* 3.7 33.9 - - + +
535A LEU* 4.0 8.1 - - + -
538A THR* 4.7 11.0 - - - +
541A TYR* 4.4 17.3 - - + -
542A LEU* 5.2 8.1 - - + +
1020A PHE 3.8 9.4 - - - +
1021A PHE* 2.9 21.8 + - + +
1023A PRO* 1.3 73.8 - - + +
1025A PHE* 1.3 80.6 + - + +
1027A VAL* 3.1 13.0 - - + +
1028A VAL* 2.8 35.8 + - + +
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Residues in contact with PHE1025 (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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542A LEU* 5.0 4.5 - - + -
545A TYR* 3.5 36.3 - + + -
900A SER* 3.2 24.9 - - - +
903A LEU* 3.3 32.8 - - + -
904A VAL* 3.5 39.5 - - + -
907A LEU* 3.8 4.3 - - + -
1021A PHE* 3.3 37.7 - + + -
1022A VAL* 3.0 6.7 + - - +
1024A VAL* 1.3 93.1 - - + +
1026A PHE* 1.3 61.2 + - - +
1028A VAL* 3.3 5.6 - - - +
1029A VAL* 3.0 32.2 + - - +
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Residues in contact with PHE1026 (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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892A TYR* 6.5 0.2 - + - -
897A ILE* 5.8 7.2 - - + -
900A SER* 3.7 14.0 - - - -
945A ILE* 6.2 0.7 - - + -
946A VAL* 3.6 44.4 - - + -
949A ALA* 3.5 29.2 - - + -
950A LYS* 4.2 12.6 - - + -
953A MET* 4.4 13.5 - - + -
960A LEU* 4.7 14.4 - - + -
964A THR* 3.7 20.9 - - - -
1022A VAL 3.0 13.9 + - - +
1023A PRO* 3.8 4.7 - - + +
1025A PHE* 1.3 79.2 - - - +
1027A VAL* 1.3 62.9 + - + +
1029A VAL* 3.9 2.0 + - + +
1030A ARG* 3.6 38.1 + - + +
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Residues in contact with VAL1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A LEU* 3.6 28.9 - - + +
538A THR* 4.2 11.9 - - - +
960A LEU* 3.7 14.8 - - + -
961A ILE* 4.5 6.7 - - + -
964A THR* 3.9 19.1 - - - +
1023A PRO 3.0 20.8 + - - +
1024A VAL* 3.1 20.6 - - - +
1026A PHE* 1.3 74.4 - - + +
1028A VAL* 1.3 67.4 + - - +
1029A VAL 3.1 2.2 - - - -
1030A ARG 2.8 4.2 + - - -
1031A ARG* 2.4 57.5 + - + +
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Residues in contact with VAL1028 (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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538A THR* 3.9 20.2 - - + +
542A LEU* 4.7 27.1 - - + -
903A LEU* 5.4 3.1 - - + -
1024A VAL* 2.8 25.0 + - + +
1025A PHE* 3.3 13.7 - - + +
1027A VAL* 1.3 75.2 - - - +
1029A VAL* 1.3 69.1 + - + +
1030A ARG 3.4 0.3 + - - -
1031A ARG* 4.2 3.8 - - - +
1032A ARG* 3.4 47.5 - - + +
1033A PHE* 4.1 1.7 + - - +
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Residues in contact with VAL1029 (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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896A SER* 3.4 43.4 + - - +
897A ILE* 4.4 6.3 - - - +
899A PHE* 4.6 4.7 - - + -
900A SER* 3.8 25.4 - - - +
903A LEU* 4.6 7.6 - - + -
1025A PHE 3.0 26.9 + - - +
1026A PHE 4.3 3.1 - - - +
1028A VAL* 1.3 81.5 - - + +
1030A ARG* 1.3 67.8 + - + +
1033A PHE* 3.8 22.1 - - - +
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Residues in contact with ARG1030 (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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894A SER* 4.0 22.1 + - - -
895A TRP 5.6 2.7 + - - -
896A SER* 6.0 0.7 - - - -
897A ILE* 5.1 9.1 - - - +
950A LYS* 4.8 16.4 - - - +
953A MET* 5.0 17.6 - - - +
954A ASP* 5.7 2.8 + - - -
960A LEU* 3.4 29.2 - - + +
1026A PHE* 3.7 30.0 - - + +
1027A VAL 2.8 3.4 + - - +
1029A VAL* 1.3 87.6 - - + +
1031A ARG* 1.3 66.2 + - - +
1032A ARG 3.0 2.0 - - - -
1033A PHE 2.8 14.1 + - - -
1034A SER* 2.2 41.7 + - - +
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Residues in contact with ARG1031 (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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535A LEU 3.4 24.5 + - - -
536A ARG* 4.8 8.5 + - - +
538A THR* 4.0 25.1 - - - +
960A LEU* 3.6 19.3 - - + -
961A ILE* 3.9 23.0 - - - +
1027A VAL* 2.4 48.9 + - + +
1028A VAL* 4.6 2.2 - - - -
1030A ARG* 1.3 70.0 - - - +
1032A ARG* 1.3 57.5 + - + +
1034A SER* 4.2 2.1 + - - -
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Residues in contact with ARG1032 (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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542A LEU* 5.5 10.5 - - - +
1028A VAL* 3.4 34.3 + - + +
1030A ARG 2.8 3.6 + - - -
1031A ARG* 1.3 77.5 - - + +
1033A PHE* 1.3 77.7 + - + +
1034A SER 4.1 0.9 - - - -
41C LYS* 3.0 26.7 - - - +
42C LYS* 2.5 41.3 + - - +
45C PRO* 3.4 32.0 - - + +
46C GLY* 6.1 0.7 - - - -
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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