Contacts of the helix formed by residues 114 - 134 (chain C) in PDB entry 3UX9
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 ALA 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASN* 1.3 85.4 + - - +
115C ASP* 1.3 66.9 + - - +
117C ILE* 3.4 7.7 + - - +
118C LEU* 3.2 23.6 + - - +
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Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 5.3 2.7 - - - +
113C ASN 4.2 5.1 - - - +
114C ALA* 1.3 79.2 - - - +
116C SER* 1.3 64.6 + - - +
118C LEU* 3.2 14.7 + - - +
119C ALA* 3.2 19.8 + - - +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 3.2 39.9 + - - -
56C VAL* 4.5 15.7 - - - -
113C ASN* 3.5 23.0 + - - -
114C ALA 3.2 0.4 - - - -
115C ASP* 1.3 79.0 - - - +
117C ILE* 1.3 63.2 + - - +
118C LEU 3.0 1.2 + - - -
119C ALA* 3.0 13.2 + - - +
120C VAL* 3.2 17.7 + - - +
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 3.8 37.2 - - - +
56C VAL* 4.3 12.1 - - + -
59C GLU* 3.6 27.8 - - + +
113C ASN* 3.0 24.7 + - - +
114C ALA* 3.4 7.4 + - - +
116C SER* 1.3 76.0 - - - +
118C LEU* 1.3 58.6 + - - +
120C VAL* 3.6 9.0 + - - +
121C LYS* 3.1 34.3 + - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ALA 3.2 12.6 + - - +
115C ASP* 3.2 17.0 - - - +
117C ILE* 1.3 75.7 - - - +
119C ALA* 1.3 60.9 + - - +
120C VAL 3.1 1.1 - - - -
121C LYS* 3.1 11.7 + - + +
122C LYS* 2.8 62.0 + - + +
125C ARG* 5.1 9.6 - - - +
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C PRO* 3.6 28.1 - - + +
42C GLU* 4.1 13.2 - - + +
115C ASP 3.2 8.7 + - - +
116C SER 3.0 8.8 + - - +
118C LEU* 1.3 79.2 - - - +
120C VAL* 1.3 57.9 + - - +
122C LYS* 3.7 11.9 - - - +
123C TYR* 3.0 28.9 + - - +
126C ARG* 4.3 3.6 + - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 6.3 0.7 - - + -
39C PRO* 4.7 7.0 - - + -
42C GLU* 5.7 3.8 - - + -
43C PHE* 4.4 24.7 - - + -
56C VAL* 4.7 11.7 - - + +
59C GLU* 4.3 11.7 - - + +
60C LEU* 4.1 23.8 - - + +
63C GLN* 4.4 0.4 - - + -
116C SER 3.2 15.2 + - - +
117C ILE* 3.8 9.4 - - - +
118C LEU 3.1 0.6 - - - -
119C ALA* 1.3 74.8 - - + +
121C LYS* 1.3 63.6 + - - +
123C TYR* 3.5 5.9 + - + +
124C PHE* 3.0 54.2 + - + -
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Residues in contact with LYS 121 (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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59C GLU* 3.6 25.3 + - + +
63C GLN* 3.7 28.4 - - - +
117C ILE* 3.1 25.1 + - - +
118C LEU* 3.1 12.4 + - + +
120C VAL* 1.3 73.7 - - - +
122C LYS* 1.3 66.4 + - - +
124C PHE* 3.1 6.1 + - - +
125C ARG* 3.0 46.9 + - - +
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 2.8 54.4 + - + +
119C ALA* 3.7 7.2 - - - +
121C LYS* 1.3 71.3 - - - +
123C TYR* 1.3 64.6 + - - +
125C ARG* 2.8 33.9 + - - +
126C ARG* 3.0 36.5 + - - +
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Residues in contact with TYR 123 (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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36C PHE* 3.6 24.5 - - + -
37C GLY 4.0 0.7 - - - -
38C PHE* 3.3 49.1 - + + -
39C PRO* 4.1 9.0 - - + -
119C ALA 3.0 16.7 + - - +
120C VAL* 3.5 4.7 - - + +
122C LYS* 1.3 77.8 - - - +
124C PHE* 1.3 92.4 + + - +
126C ARG* 3.2 21.2 + - - +
127C ILE* 3.2 38.8 + - + +
147C GLU* 2.9 23.6 + - - +
148C ILE* 4.5 2.0 - - + +
151C SER* 2.7 28.4 + - - -
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Residues in contact with PHE 124 (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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60C LEU* 3.8 16.2 - - + -
63C GLN* 3.4 43.7 - - + +
64C ILE* 3.6 40.4 - - + -
67C LEU* 4.5 11.9 - - + -
120C VAL* 3.0 35.9 + - + +
121C LYS 3.1 8.9 + - - +
123C TYR* 1.3 96.5 - + - +
125C ARG* 1.3 63.7 + - + +
127C ILE* 3.4 15.1 + - + +
128C THR* 3.3 25.8 + - - +
148C ILE* 4.0 17.7 - - + -
151C SER* 6.1 0.2 - - - -
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 5.1 8.9 - - - +
121C LYS* 3.0 42.1 + - - +
122C LYS* 2.8 33.9 + - - +
124C PHE* 1.3 67.9 - - - +
126C ARG* 1.3 66.2 + - - +
127C ILE 3.0 1.8 - - - -
128C THR* 2.9 10.9 + - - +
129C LEU* 2.8 35.9 + - + +
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Residues in contact with ARG 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 6.1 2.7 - - + -
36C PHE* 2.8 50.5 + - + +
37C GLY* 3.2 20.0 + - - -
39C PRO* 5.2 1.8 - - - +
119C ALA* 4.3 5.7 + - - +
122C LYS* 3.0 42.4 + - - +
123C TYR* 3.3 26.0 - - - +
125C ARG* 1.3 75.2 - - + +
127C ILE* 1.3 57.9 + - - +
129C LEU* 3.4 14.9 - - + +
130C TYR* 2.9 29.6 + - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 3.9 22.7 - - + -
67C LEU* 4.4 11.2 - - + -
123C TYR* 3.2 44.3 + - + +
124C PHE* 3.5 17.9 - - + +
125C ARG 3.0 0.4 - - - -
126C ARG* 1.3 77.8 - - - +
128C THR* 1.3 58.9 + - - +
130C TYR* 3.1 5.4 - - - +
131C LEU* 2.9 31.6 + - + +
144C VAL* 4.1 30.7 - - + -
147C GLU* 4.5 7.6 - - + -
148C ILE* 4.0 18.2 - - + -
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Residues in contact with THR 128 (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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67C LEU* 4.3 21.3 - - + -
124C PHE* 3.3 14.1 + - + +
125C ARG* 2.9 16.2 + - - +
127C ILE* 1.3 70.5 - - - +
129C LEU* 1.3 60.6 + - - +
131C LEU* 2.9 10.9 + - + +
132C THR* 2.7 42.1 + - - -
136C TYR* 4.3 10.3 + - - +
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Residues in contact with LEU 129 (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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125C ARG* 2.8 26.3 + - + +
126C ARG* 3.4 16.6 - - + +
128C THR* 1.3 82.0 + - - +
130C TYR* 1.3 63.7 + - - +
132C THR* 3.1 10.4 + - - +
133C GLU* 2.8 33.9 + - + +
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Residues in contact with TYR 130 (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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32C ASP* 2.7 32.6 + - - +
34C HIS* 3.9 22.7 - + + -
36C PHE* 3.5 24.2 - + + -
126C ARG 2.9 14.7 + - - +
127C ILE 3.1 8.5 - - - +
129C LEU* 1.3 73.8 - - - +
131C LEU* 1.3 69.0 + - - +
133C GLU* 3.0 19.5 + - + +
134C LYS* 3.0 49.2 + - + +
140C ALA* 3.7 37.3 - - + -
143C VAL* 3.6 19.9 - - + +
144C VAL* 4.1 9.9 - - + -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 4.4 10.1 - - + -
127C ILE* 2.9 24.5 + - + +
128C THR* 2.9 11.2 + - - +
130C TYR* 1.3 76.1 - - + +
132C THR* 1.3 59.2 + - - +
134C LYS* 3.4 2.0 + - - -
135C LYS 3.1 2.3 + - - -
136C TYR* 2.7 69.8 + - + +
140C ALA* 4.0 26.7 - - + +
141C TRP* 4.1 29.4 - - + -
144C VAL* 4.0 25.8 - - + -
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Residues in contact with THR 132 (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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128C THR* 2.7 20.9 + - - -
129C LEU* 3.4 11.0 - - - +
131C LEU* 1.3 74.6 - - - +
133C GLU* 1.3 66.2 + - - +
135C LYS* 2.9 20.4 + - - +
136C TYR* 3.8 20.5 + - + -
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Residues in contact with GLU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 2.8 26.0 + - + +
130C TYR* 3.4 20.3 + - + +
132C THR* 1.3 73.5 - - - +
134C LYS* 1.3 62.4 + - + +
135C LYS* 3.4 17.1 + - - +
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Residues in contact with LYS 134 (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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31C MET 3.7 15.8 + - - -
32C ASP* 3.5 27.5 + - - +
130C TYR* 3.0 54.9 + - + +
131C LEU 4.1 1.1 - - - +
132C THR 3.1 0.4 - - - -
133C GLU* 1.3 80.7 - - + +
135C LYS* 1.3 72.0 + - - +
136C TYR 3.1 1.3 + - - -
137C SER* 3.2 19.1 + - - +
140C ALA* 3.7 20.4 - - + -
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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
------------------------------------------------------------
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