Contacts of the helix formed by residues 120 - 136 (chain C) in PDB entry 4X2Q
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 VAL 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C LYS* 5.0 0.2 - - - +
116C GLN* 3.0 28.5 + - + +
119C TYR* 1.3 85.5 - - + +
121C ASP* 1.3 64.3 + - - +
122C LEU 3.5 0.4 - - - -
123C GLN* 3.4 3.3 + - - +
124C GLY* 2.9 27.9 + - - -
173C LEU* 5.1 4.0 - - + +
296C PHE* 3.9 31.2 - - + -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 3.8 24.0 - - + +
112C LYS* 2.7 40.7 + - - +
116C GLN 3.2 3.0 + - - -
117C ALA* 3.6 16.2 - - + +
120C VAL* 1.3 81.8 - - - +
122C LEU* 1.3 61.6 + - + +
124C GLY* 3.3 1.6 + - - -
125C VAL* 2.9 32.6 + - + +
170C PHE* 3.6 26.2 - - - +
171C PRO* 5.6 0.2 - - - +
172C LEU* 6.1 0.9 - - + -
173C LEU* 3.6 17.5 - - + +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.9 20.6 - - + -
99C ARG* 3.7 35.4 - - + +
102C LEU* 3.7 20.9 - - + +
103C ALA* 3.6 24.7 - - + +
106C GLU* 5.1 3.6 - - + -
117C ALA 3.1 23.1 + - - +
118C PHE* 4.2 6.7 - - - +
121C ASP* 1.3 78.7 - - + +
123C GLN* 1.3 67.1 + - - +
125C VAL* 3.5 4.2 - - - +
126C ILE* 2.8 32.4 + - + +
172C LEU* 3.7 26.7 - - + -
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Residues in contact with GLN 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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99C ARG* 3.5 28.9 - - - +
118C PHE 3.9 1.6 + - - -
119C TYR* 3.4 35.1 + - - +
120C VAL 3.4 2.9 + - - +
122C LEU* 1.3 76.4 - - - +
124C GLY* 1.3 53.8 + - - +
126C ILE* 3.3 4.3 + - - +
127C LYS* 2.8 69.5 + - + +
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Residues in contact with GLY 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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120C VAL 2.9 14.5 + - - -
121C ASP 3.5 4.3 - - - -
123C GLN* 1.3 76.9 + - - +
125C VAL* 1.3 61.5 + - - +
127C LYS* 3.2 7.3 + - - +
128C THR* 2.9 31.6 + - - +
173C LEU* 3.9 15.3 - - - -
177C TRP* 6.2 0.2 - - - -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 4.0 18.6 - - + -
121C ASP 2.9 25.2 + - - +
122C LEU* 3.1 14.3 + - + +
124C GLY* 1.3 70.4 - - - +
126C ILE* 1.3 62.9 + - - +
128C THR* 3.2 14.6 + - - -
129C PHE* 3.3 39.5 + - + -
172C LEU* 3.9 33.0 - - + -
173C LEU* 3.8 21.9 - - - +
176C ALA* 3.8 13.0 - - + -
204C MET* 5.5 0.4 - - - -
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Residues in contact with ILE 126 (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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92C ALA* 4.3 9.8 - - + +
95C VAL* 3.7 23.1 - - + +
96C GLU* 3.9 24.2 - - - +
99C ARG* 3.8 43.1 - - + +
122C LEU 2.8 24.6 + - - +
123C GLN* 3.7 3.1 - - - +
125C VAL* 1.3 69.9 - - - +
127C LYS* 1.3 65.1 + - + +
129C PHE* 3.3 8.8 + - - +
130C ARG* 3.2 52.0 + - + +
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Residues in contact with LYS 127 (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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80A ASP* 5.7 2.2 + - - -
82A SER* 5.0 15.5 - - - +
123C GLN* 2.8 59.0 + - + +
124C GLY* 3.4 8.3 - - - +
126C ILE* 1.3 74.1 - - + +
128C THR* 1.3 59.1 + - + +
130C ARG* 3.4 6.6 + - - +
131C TYR* 3.0 27.8 + - - +
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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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124C GLY* 2.9 20.0 + - - +
125C VAL 3.2 9.9 + - - -
127C LYS* 1.3 74.8 - - + +
129C PHE* 1.3 61.8 + - - +
131C TYR* 3.2 7.0 + - - +
132C TYR* 2.9 47.4 + - + -
176C ALA* 3.8 23.3 + - - +
177C TRP* 3.3 33.7 - - + +
180C ALA* 4.7 0.9 - - - -
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Residues in contact with PHE 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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88C LEU* 3.8 32.1 - - + +
91C LEU* 3.8 20.9 - - + -
92C ALA* 4.0 9.9 - - + -
95C VAL* 4.5 9.6 - - + -
125C VAL* 3.3 34.7 + - + -
126C ILE* 3.3 7.7 + - - +
128C THR* 1.3 81.5 + - - +
130C ARG* 1.3 56.9 + - - +
132C TYR* 3.5 1.0 + - - +
133C ALA* 2.9 29.0 + - - +
175C PHE* 4.9 1.1 - + - -
176C ALA* 3.9 18.4 - - + -
179C ILE* 4.4 9.0 - - + -
180C ALA* 3.7 35.4 - - + -
204C MET* 3.7 32.8 - - + -
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Residues in contact with ARG 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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86A ARG* 3.2 48.9 - - - +
89A ASP* 5.5 0.4 - - - -
138A LYS* 4.8 0.9 + - - -
89C ASP* 3.2 25.5 + - - +
92C ALA* 3.5 14.6 + - + +
93C ASP* 2.9 43.9 + - - +
96C GLU* 4.7 12.1 + - - +
126C ILE* 3.2 32.1 + - + +
127C LYS* 3.6 8.5 - - - +
129C PHE* 1.3 73.4 - - - +
131C TYR* 1.3 65.3 + - - +
133C ALA* 3.4 8.5 - - - +
134C GLY* 3.2 17.2 + - - -
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Residues in contact with TYR 131 (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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137A ASP* 3.2 44.1 + - - -
138A LYS* 3.1 35.1 + - + +
140A HIS* 4.4 9.4 + - - -
127C LYS 3.0 14.9 + - - +
128C THR* 3.2 13.2 + - - +
130C ARG* 1.3 76.7 - - - +
132C TYR* 1.3 84.8 + + - +
134C GLY 3.0 14.7 + - - -
135C TRP* 3.2 33.8 + + - -
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Residues in contact with TYR 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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88C LEU* 3.7 10.4 - - + +
128C THR* 2.9 36.4 + - + +
129C PHE 4.4 0.9 - - - +
131C TYR* 1.3 96.4 - + - +
133C ALA* 1.3 63.5 + - - +
134C GLY 3.2 0.2 - - - -
135C TRP* 3.7 13.2 - + - +
136C ALA* 3.3 17.3 + - - +
177C TRP* 5.9 4.3 - + - -
180C ALA* 3.7 33.4 - - + +
181C PRO* 3.8 38.6 - - + +
184C CYS* 3.4 21.3 - - + -
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Residues in contact with ALA 133 (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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85C GLY* 3.2 44.9 - - - +
88C LEU* 3.8 3.5 - - + +
89C ASP* 3.7 22.2 - - + +
129C PHE 2.9 19.5 + - - +
130C ARG* 3.4 8.5 - - - +
132C TYR* 1.3 77.4 - - - +
134C GLY* 1.3 61.6 + - - +
136C ALA* 3.8 5.0 + - - +
137C ASP* 4.6 4.0 - - - +
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Residues in contact with GLY 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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134A GLY* 3.8 15.9 - - - -
138A LYS* 3.7 16.4 - - - -
130C ARG 3.2 5.5 + - - -
131C TYR 3.0 10.2 + - - -
133C ALA* 1.3 81.5 - - - +
135C TRP* 1.3 58.9 + - - +
137C ASP* 3.6 2.8 - - - +
138C LYS* 2.7 31.0 + - - +
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Residues in contact with TRP 135 (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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135A TRP* 4.7 15.3 - + - -
138A LYS* 3.3 26.2 - - + +
140A HIS* 3.9 28.7 - + - -
131C TYR* 3.2 44.3 + + - +
132C TYR* 3.4 12.3 + + - +
133C ALA 3.4 0.6 - - - -
134C GLY* 1.3 77.7 - - - +
136C ALA* 1.3 55.8 + - - +
138C LYS* 2.7 68.7 + - + +
139C ILE* 3.5 14.6 + - + +
140C HIS* 5.9 0.2 - + - -
184C CYS* 3.5 19.5 - - - -
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Residues in contact with ALA 136 (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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145B PRO* 5.0 2.3 - - - +
81C ALA* 3.3 31.5 - - - +
82C SER* 5.3 0.2 - - - -
84C ARG* 4.3 5.5 + - - +
85C GLY* 3.6 26.0 - - - +
132C TYR 3.3 8.4 + - - +
133C ALA 4.0 2.2 - - - +
134C GLY 3.5 1.2 - - - -
135C TRP* 1.3 76.5 - - - +
137C ASP* 1.3 58.2 + - - +
138C LYS 3.5 1.6 + - - -
139C ILE* 3.7 15.2 + - - +
184C CYS* 3.6 27.2 - - - +
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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