Contacts of the helix formed by residues 114 - 129 (chain f) in PDB entry 5T0J
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 ASN 114 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65f ASN* 3.5 7.3 - - - +
69f LYS* 3.3 50.8 - - + +
112f MET* 3.2 35.4 - - - +
113f LEU* 1.3 99.8 - - - +
115f ASP* 1.3 72.5 + - - +
117f GLU 4.3 0.2 - - - -
118f LEU* 3.3 25.3 + - - +
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Residues in contact with ASP 115 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65f ASN* 2.4 38.2 + - - +
100f PHE* 3.8 10.1 - - + -
109f LEU* 3.3 44.5 - - + +
110f ALA 3.8 13.0 - - - +
112f MET* 4.5 5.9 + - + +
114f ASN* 1.3 82.9 - - - +
116f MET* 1.3 74.7 + - + +
118f LEU* 3.5 1.4 + - - +
119f VAL* 3.2 31.9 + - + +
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Residues in contact with MET 116 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109f LEU* 4.7 1.1 - - + -
111f LEU* 3.7 22.2 - - + -
112f MET* 3.2 34.9 + - + +
114f ASN 3.6 0.2 - - - -
115f ASP* 1.3 88.7 - - + +
117f GLU* 1.3 58.3 + - - +
119f VAL* 3.3 11.2 - - + +
120f GLU* 3.0 33.4 + - - +
139f LEU* 4.6 13.0 - - + -
141f ARG* 3.8 45.8 - - + +
143f GLY* 4.8 3.1 - - - -
144f VAL* 4.1 23.1 - - + -
147f GLU* 4.7 5.0 - - - +
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Residues in contact with GLU 117 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72f LEU* 3.5 43.5 - - + +
112f MET 3.2 4.7 + - - +
113f LEU* 2.9 44.6 - - - +
114f ASN 4.1 0.4 + - - -
115f ASP 3.4 0.4 - - - -
116f MET* 1.3 79.6 - - - +
118f LEU* 1.3 58.0 + - - +
120f GLU* 4.1 8.4 - - - +
121f ASP* 3.1 30.9 + - + +
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Residues in contact with LEU 118 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64f GLU* 3.7 24.0 - - - +
65f ASN* 3.3 28.7 - - + +
68f ALA* 3.7 32.5 - - + +
69f LYS* 6.1 0.2 - - + -
72f LEU* 6.2 0.4 - - - +
75f THR* 4.4 14.0 - - + +
96f VAL* 6.3 3.8 - - + -
114f ASN 3.3 18.2 + - - +
115f ASP 4.0 1.8 - - - +
116f MET 3.3 0.6 - - - -
117f GLU* 1.3 79.3 - - - +
119f VAL* 1.3 73.9 + - + +
121f ASP* 3.6 4.3 + - - +
122f ILE* 3.4 27.0 + - + +
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Residues in contact with VAL 119 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96f VAL* 5.8 3.6 - - + -
115f ASP* 3.2 21.5 + - + +
116f MET* 3.3 20.4 - - + +
118f LEU* 1.3 88.3 - - + +
120f GLU* 1.3 60.4 + - - +
122f ILE* 3.3 11.5 - - + +
123f PHE* 3.2 25.8 + - - +
135f MET* 4.4 30.7 - - + -
139f LEU* 6.1 3.6 - - + -
144f VAL* 4.2 22.0 - - + -
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Residues in contact with GLU 120 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116f MET* 3.0 19.9 + - - +
117f GLU* 4.1 9.1 - - - +
119f VAL* 1.3 79.1 - - + +
121f ASP* 1.3 66.0 + - - +
122f ILE 3.2 0.2 - - - -
123f PHE* 3.0 19.5 + - + +
124f THR* 3.3 13.1 + - - +
144f VAL* 5.7 2.5 - - + -
147f GLU* 3.0 47.1 - - + +
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Residues in contact with ASP 121 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72f LEU 4.2 10.4 - - - +
73f TYR 4.1 2.8 - - - +
75f THR* 3.7 12.2 - - + -
76f SER* 3.0 49.4 + - - +
117f GLU* 3.1 22.1 + - + +
118f LEU* 3.6 5.6 + - - +
119f VAL 3.5 0.2 - - - -
120f GLU* 1.3 77.7 - - - +
122f ILE* 1.3 60.0 + - - +
124f THR* 3.7 18.5 + - - -
125f SER* 4.7 2.1 + - - -
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Residues in contact with ILE 122 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75f THR* 4.9 17.0 - - + +
76f SER* 5.0 7.0 - - - +
78f VAL* 6.2 2.2 - - + -
85f GLU* 5.6 6.3 - - - +
89f LEU* 3.8 41.3 - - + -
118f LEU* 3.4 18.4 + - + +
119f VAL* 3.3 17.7 - - - +
121f ASP* 1.3 75.2 - - - +
123f PHE* 1.3 69.4 + - - +
124f THR 3.1 3.1 + - - -
125f SER* 3.4 12.8 + - - +
126f CYS* 3.1 19.7 + - - -
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Residues in contact with PHE 123 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119f VAL 3.2 20.9 + - - +
120f GLU* 3.0 16.5 + - + +
122f ILE* 1.3 75.4 - - - +
124f THR* 1.3 58.7 + - - +
126f CYS* 3.6 7.0 - - + -
127f LYS* 2.8 49.7 + - + +
134f GLN* 3.6 39.0 - - + -
136f ALA* 5.7 1.1 - - + -
144f VAL* 6.3 4.0 - - + -
147f GLU 3.4 23.6 - - - -
148f LEU* 3.1 42.2 - - + -
150f GLU* 3.4 15.7 - - - -
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Residues in contact with THR 124 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76f SER* 6.0 1.3 - - - +
120f GLU* 3.3 11.9 + - - +
121f ASP* 3.7 15.8 + - - -
122f ILE 3.1 0.6 - - - -
123f PHE* 1.3 80.4 - - - +
125f SER* 1.3 66.7 + - - +
127f LYS* 3.2 22.3 + - - +
128f ASP* 3.0 36.8 + - - +
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Residues in contact with SER 125 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76f SER* 5.0 8.7 + - - -
80f TYR* 4.1 17.4 + - - -
121f ASP 4.7 1.8 + - - -
122f ILE* 3.4 16.7 + - - +
124f THR* 1.3 80.4 - - - +
126f CYS* 1.3 62.0 + - - +
128f ASP* 3.5 22.4 + - - +
129f VAL* 3.9 11.8 + - - +
130f VAL* 4.4 7.7 - - - +
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Residues in contact with CYS 126 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89f LEU* 3.6 25.4 - - - -
122f ILE* 3.1 25.8 + - - -
123f PHE* 3.2 10.7 + - + +
124f THR 3.0 0.6 - - - -
125f SER* 1.3 79.5 - - - +
127f LYS* 1.3 61.6 + - - +
128f ASP 3.2 1.3 + - - -
129f VAL 4.1 1.6 + - - -
130f VAL* 3.2 25.2 - - - +
131f VAL* 4.6 4.6 - - - +
132f GLN* 5.5 1.4 + - - -
134f GLN* 3.4 48.9 + - + +
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Residues in contact with LYS 127 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123f PHE* 2.8 40.8 + - + +
124f THR* 3.2 29.3 + - - +
126f CYS* 1.3 71.7 - - - +
128f ASP* 1.3 76.4 + - - +
147f GLU 5.5 0.9 - - - +
149f SER 5.7 0.2 - - - +
150f GLU* 3.2 39.4 - - + +
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Residues in contact with ASP 128 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124f THR* 3.0 35.1 + - - +
125f SER* 3.5 18.2 + - - +
126f CYS 3.2 0.8 - - - -
127f LYS* 1.3 94.0 + - - +
129f VAL* 1.3 67.1 + - + +
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Residues in contact with VAL 129 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125f SER* 3.9 7.0 + - - +
126f CYS 4.6 0.4 - - - -
127f LYS 3.8 0.6 - - - -
128f ASP* 1.3 86.8 - - + +
130f VAL* 1.3 92.7 + - + +
131f VAL 4.6 1.6 - - - +
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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