Contacts of the helix formed by residues 1050 - 1059 (chain C) in PDB entry 3DLS
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 THR1050 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1030C ILE* 4.5 19.1 - - + -
1041C ILE* 5.0 1.6 - - - -
1049C VAL* 1.3 82.4 - - - +
1051C LEU* 1.3 65.3 + - - +
1052C GLU* 3.7 15.1 + - + +
1053C ILE* 3.1 37.4 + - + +
1054C ALA 2.9 24.1 + - - -
1077C PHE* 4.8 4.0 - - + -
1148C GLY 5.6 1.4 + - - -
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Residues in contact with LEU1051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C ILE* 3.6 47.4 - - + +
1050C THR* 1.3 74.8 + - - +
1052C GLU* 1.3 59.9 + - - +
1054C ALA* 4.3 3.8 - - + -
1055C ILE* 3.1 41.4 + - + +
1147C PHE 4.4 1.6 - - - +
1148C GLY 5.7 3.4 - - - +
1150C ALA 3.4 25.4 - - - +
1151C ALA* 4.3 11.7 - - + -
1152C TYR* 3.7 28.5 - - + +
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Residues in contact with GLU1052 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028C LYS* 2.7 41.6 + - - +
1030C ILE* 4.3 11.4 - - + +
1050C THR* 3.2 14.9 + - + +
1051C LEU* 1.3 78.9 - - - +
1053C ILE* 1.3 56.0 + - - +
1056C LEU* 3.1 36.3 + - + +
1079C LEU* 3.9 21.2 - - + +
1146C ASP* 4.0 1.7 + - - -
1147C PHE* 3.4 38.4 + - + +
1148C GLY* 3.7 20.7 + - - -
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Residues in contact with ILE1053 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030C ILE* 3.8 22.7 - - + -
1046C LEU* 4.0 4.7 - - + -
1049C VAL* 3.7 23.6 - - + -
1050C THR* 3.1 27.3 + - + +
1052C GLU* 1.3 77.6 - - - +
1054C ALA* 1.3 56.7 + - - +
1056C LEU* 3.8 3.2 - - - +
1057C SER* 2.7 38.8 + - - -
1070C ILE* 3.8 32.3 - - + +
1077C PHE* 3.6 38.4 - - + -
1079C LEU* 4.5 13.9 - - + -
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Residues in contact with ALA1054 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C ILE* 4.3 8.7 - - + -
1043C ASP* 3.6 20.9 - - - +
1046C LEU* 3.9 11.7 - - - -
1049C VAL* 3.8 13.4 - - + +
1050C THR 2.9 16.3 + - - +
1051C LEU* 4.0 12.1 - - + +
1053C ILE* 1.3 79.2 - - - +
1055C ILE* 1.3 61.4 + - - +
1057C SER* 3.5 6.8 + - - -
1058C ARG* 3.2 24.7 - - - +
1152C TYR* 4.7 4.0 - - + +
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Residues in contact with ILE1055 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051C LEU* 3.1 26.6 + - + +
1052C GLU* 4.4 1.3 - - - +
1054C ALA* 1.3 77.7 - - - +
1056C LEU* 1.3 58.9 + - - +
1058C ARG* 3.0 20.1 + - - +
1059C VAL* 3.1 22.0 + - + +
1124C ILE* 3.8 27.4 - - + -
1147C PHE* 3.6 28.9 - - + -
1150C ALA* 3.6 36.8 - - + +
1151C ALA* 4.2 4.0 - - - +
1152C TYR* 3.6 30.5 - - + +
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Residues in contact with LEU1056 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052C GLU* 3.1 32.6 + - + +
1053C ILE* 4.1 3.8 - - - +
1054C ALA 3.4 0.2 - - - -
1055C ILE* 1.3 76.8 - - - +
1057C SER* 1.3 61.0 + - - +
1058C ARG 3.4 0.3 + - - -
1059C VAL* 4.0 22.0 - - + +
1064C ILE* 4.3 0.4 - - + -
1065C ILE* 3.9 33.7 - - + +
1067C VAL* 3.3 28.9 - - + +
1070C ILE* 5.8 0.9 - - + -
1079C LEU* 3.9 32.1 - - + -
1081C MET* 5.0 2.5 - - - -
1146C ASP 5.8 1.3 - - - +
1147C PHE* 3.9 35.9 - - + +
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Residues in contact with SER1057 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043C ASP* 5.4 0.7 - - - -
1046C LEU* 3.2 36.1 - - - +
1053C ILE 2.7 22.0 + - - -
1054C ALA 3.6 6.7 - - - -
1055C ILE 3.3 0.2 - - - -
1056C LEU* 1.3 76.2 - - - +
1058C ARG* 1.3 61.4 + - - +
1059C VAL 5.1 0.6 - - - +
1067C VAL* 5.1 2.9 - - - -
1070C ILE* 3.3 14.1 - - - +
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Residues in contact with ARG1058 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043C ASP* 3.6 23.5 + - - +
1054C ALA 3.2 19.3 - - - +
1055C ILE* 3.0 7.9 + - - +
1057C SER* 1.3 82.1 - - - +
1059C VAL* 1.3 68.5 + - + +
1060C GLU* 3.5 4.9 + - - +
1118C TYR* 4.4 2.1 + - - -
1122C LYS* 4.4 24.2 + - + +
1124C ILE* 4.5 7.1 - - - +
1152C TYR* 3.0 44.7 + - - -
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Residues in contact with VAL1059 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055C ILE* 3.1 24.4 + - + +
1056C LEU* 4.0 21.4 - - + +
1057C SER 5.1 0.3 - - - -
1058C ARG* 1.3 78.9 - - + +
1060C GLU* 1.3 61.2 + - - +
1061C HIS 4.2 0.2 - - - -
1064C ILE* 3.7 31.5 - - + +
1065C ILE 5.3 2.8 - - - +
1118C TYR* 3.4 21.5 - - + +
1119C LEU* 3.9 13.9 - - + -
1122C LYS* 4.9 4.5 - - + -
1124C ILE* 3.8 26.2 - - + -
1147C PHE* 4.9 0.9 - - + -
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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