Contacts of the helix formed by residues 113 - 132 (chain C) in PDB entry 4WLU
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 LEU 113 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET* 5.6 4.0 - - + -
102C VAL* 3.4 34.5 - - + +
103C PRO 3.6 15.9 - - - +
104C ARG* 3.6 22.2 - - + +
108C MET* 3.3 24.5 - - + -
109C THR 4.3 0.4 - - - +
110C ARG* 3.3 15.7 - - - +
111C ASP 3.0 0.8 - - - -
112C ASP* 1.3 75.3 - - - +
114C PHE* 1.3 64.5 + - - +
115C ASN 3.2 2.5 + - - -
116C THR* 3.3 7.3 + - - -
117C ASN* 3.1 32.6 + - - +
142C ASN* 3.9 12.8 - - + +
143C PRO* 4.5 1.8 - - - -
402C NAD 3.6 20.2 - - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 3.0 20.4 + - - +
112C ASP 3.3 1.2 - - - -
113C LEU* 1.3 76.7 - - - +
115C ASN* 1.3 73.6 + - - +
118C ALA* 2.8 52.0 + - + +
143C PRO* 4.0 17.9 - - + +
146C SER* 3.6 31.9 - - - -
147C THR* 5.9 0.7 - - + -
150C ILE* 4.1 10.5 - - + -
329C LYS* 3.6 58.6 - - + +
330C GLY* 4.2 0.2 - - - -
333C PHE* 3.7 24.7 - + + -
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 3.6 28.7 - - - +
108A MET* 4.1 1.5 - - + +
109A THR* 4.1 13.9 - - - +
112A ASP* 2.8 38.0 + - - +
112C ASP 4.7 1.6 + - - -
113C LEU 3.3 0.8 - - - -
114C PHE* 1.3 96.4 - - - +
116C THR* 1.3 60.8 + - - +
118C ALA* 4.6 1.7 - - - +
119C THR* 4.3 11.8 + - - -
329C LYS* 5.8 0.2 - - - -
333C PHE* 5.8 1.9 - - - -
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 3.8 6.0 + - + +
106A PRO* 2.8 28.8 + - + +
107A GLY* 4.4 0.4 - - - -
108A MET* 3.1 25.6 + - - +
102C VAL* 3.7 24.9 - - + -
113C LEU* 3.3 7.6 + - - -
114C PHE 3.2 0.4 - - - -
115C ASN* 1.3 78.6 - - - +
117C ASN* 1.3 70.5 + - - +
118C ALA 3.4 0.6 + - - -
119C THR* 3.6 6.2 + - - -
120C ILE* 3.4 38.4 + - + +
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Residues in contact with ASN 117 (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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101C GLY* 3.2 11.4 - - - -
102C VAL* 2.9 30.6 + - - +
113C LEU* 3.1 16.6 + - - +
114C PHE 4.6 0.2 - - - +
116C THR* 1.3 83.4 - - - +
118C ALA* 1.3 60.2 + - - +
120C ILE* 3.7 4.5 - - + -
121C VAL* 2.8 35.6 + - + +
141C ALA* 4.5 8.0 - - + +
142C ASN 2.8 32.3 + - - +
143C PRO* 5.0 0.4 - - + -
147C THR* 4.9 2.0 - - + -
402C NAD 3.0 24.7 + - - -
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 2.8 38.7 + - + +
115C ASN* 5.1 1.6 - - - -
117C ASN* 1.3 76.6 - - - +
119C THR* 1.3 57.7 + - - +
121C VAL* 3.9 1.8 - - - +
122C ALA* 2.9 31.2 + - - +
143C PRO* 5.9 0.2 - - - +
147C THR* 5.2 3.1 - - - +
150C ILE* 3.7 28.6 - - + +
333C PHE* 3.5 20.0 - - + -
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Residues in contact with THR 119 (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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107A GLY* 6.1 1.1 - - - -
115C ASN 4.3 9.1 + - - -
116C THR 3.6 9.2 + - - -
117C ASN 3.3 0.2 - - - -
118C ALA* 1.3 75.1 - - - +
120C ILE* 1.3 66.5 + - + +
122C ALA* 3.9 2.0 - - - +
123C THR* 2.7 42.6 + - - +
333C PHE* 3.5 22.2 - - - -
337C LEU* 5.9 0.2 - - - +
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Residues in contact with ILE 120 (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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100C ALA* 3.9 21.1 - - + +
101C GLY* 3.9 6.7 - - - -
102C VAL* 5.1 0.9 - - + -
116C THR* 3.4 36.7 + - + +
117C ASN* 3.2 17.1 + - - +
119C THR* 1.3 81.4 - - + +
121C VAL* 1.3 58.4 + - - +
123C THR* 3.7 3.3 - - - -
124C LEU* 3.0 54.6 + - + +
402C NAD 3.6 40.4 - - + +
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Residues in contact with VAL 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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98C ILE* 5.0 7.0 - - + -
100C ALA 4.8 3.1 - - - +
117C ASN 2.8 23.6 + - - +
118C ALA* 4.0 2.5 - - - +
120C ILE* 1.3 73.1 - - + +
122C ALA* 1.3 51.9 + - - +
124C LEU* 4.8 3.8 - - - -
125C THR* 2.7 47.4 + - + +
139C VAL* 4.6 7.2 - - + -
141C ALA* 3.7 29.6 - - + -
147C THR* 3.8 28.0 - - + +
150C ILE* 4.3 7.4 - - + -
151C THR* 3.4 26.0 - - - +
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Residues in contact with ALA 122 (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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118C ALA 2.9 19.2 + - - +
119C THR* 3.9 4.0 - - - +
121C VAL* 1.3 76.4 - - - +
123C THR* 1.3 62.6 + - - +
125C THR* 3.4 6.3 + - - -
126C ALA* 3.0 26.5 + - - +
150C ILE* 3.9 12.7 - - + +
154C VAL* 4.0 10.0 - - + +
333C PHE* 3.9 17.7 - - + -
337C LEU* 3.9 16.6 - - + -
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 6.4 1.6 - - + -
86C LEU* 5.8 4.5 - - + -
119C THR* 2.7 32.2 + - - +
120C ILE* 3.7 4.9 - - - -
122C ALA* 1.3 78.6 - - - +
124C LEU* 1.3 68.3 + - + +
126C ALA* 3.4 7.4 + - - +
127C ALA* 3.2 19.8 + - - +
402C NAD 6.4 0.2 - - - -
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.9 22.9 - - + +
56C TYR* 3.8 28.7 - - + +
86C LEU* 3.9 13.9 - - + -
98C ILE* 3.9 17.9 - - + -
100C ALA* 3.4 33.2 - - + -
120C ILE* 3.0 30.4 + - + +
121C VAL 4.2 1.6 - - - +
123C THR* 1.3 82.2 - - + +
125C THR* 1.3 57.9 + - - +
127C ALA* 3.2 8.9 + - - +
128C CYS* 3.0 30.1 + - - -
402C NAD 4.1 9.9 - - + +
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Residues in contact with THR 125 (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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98C ILE* 3.8 24.2 - - + -
121C VAL* 2.7 30.9 + - + +
122C ALA* 3.4 8.0 + - - -
124C LEU* 1.3 73.0 - - - +
126C ALA* 1.3 59.3 + - - +
128C CYS* 4.1 6.3 - - - -
129C ALA* 2.9 23.9 + - - +
137C ILE* 4.5 2.5 - - + -
139C VAL* 5.0 0.2 - - + -
151C THR* 3.5 42.8 - - + +
154C VAL* 3.8 13.7 - - - +
155C PHE* 3.2 13.9 - - - -
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Residues in contact with ALA 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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122C ALA 3.0 20.5 + - - +
123C THR* 3.6 6.5 - - - +
124C LEU 3.3 0.2 - - - -
125C THR* 1.3 75.8 + - - +
127C ALA* 1.3 63.3 + - - +
129C ALA* 3.3 3.3 + - - +
130C GLN* 3.1 34.5 + - - +
154C VAL* 3.4 17.3 - - + -
158C HIS* 3.7 16.3 + - + +
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Residues in contact with ALA 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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86C LEU* 3.5 31.0 - - + -
90C LEU* 3.4 13.9 - - + +
123C THR 3.2 6.9 + - - +
124C LEU 3.2 10.9 + - - +
126C ALA* 1.3 76.3 - - - +
128C CYS* 1.3 58.9 + - - +
130C GLN* 4.5 4.9 - - - +
131C HIS* 2.9 43.4 + - + -
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Residues in contact with CYS 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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30C LEU* 4.2 5.2 - - - -
90C LEU* 4.0 14.1 - - - -
96C VAL* 3.7 31.0 - - - -
98C ILE* 4.6 4.3 - - - -
124C LEU 3.0 17.2 + - - -
125C THR* 3.5 14.1 - - - +
126C ALA 3.3 0.2 - - - -
127C ALA* 1.3 74.5 - - - +
129C ALA* 1.3 60.9 + - - +
132C CYS* 2.9 43.9 + - - -
137C ILE* 4.0 15.0 - - + -
155C PHE* 3.9 14.6 - - + -
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Residues in contact with ALA 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 THR 2.9 14.7 + - - +
126C ALA* 3.5 8.7 - - - +
128C CYS* 1.3 75.8 - - - +
130C GLN* 1.3 61.5 + - - +
133C PRO* 3.3 21.2 - - - +
154C VAL 4.7 0.2 - - - +
155C PHE* 3.7 23.0 - - + -
158C HIS* 3.7 33.0 - - + +
160C VAL* 3.8 15.6 - - + +
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Residues in contact with GLN 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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126C ALA* 3.1 20.5 + - - +
127C ALA* 4.5 2.4 - - - -
128C CYS 3.2 0.2 - - - -
129C ALA* 1.3 80.4 - - - +
131C HIS* 1.3 87.4 + - + +
132C CYS 3.8 0.2 - - - -
133C PRO* 4.0 6.1 - - - +
158C HIS* 3.3 30.9 + - + -
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Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PRO* 3.6 45.9 - - + +
90C LEU* 4.0 17.0 - - + -
91C LYS* 4.1 29.1 + - + +
92C GLY 4.5 2.1 + - - -
127C ALA* 2.9 31.9 + - + +
130C GLN* 1.3 103.0 + - + +
132C CYS* 1.3 63.0 + - - +
133C PRO* 3.6 4.1 - - - +
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Residues in contact with CYS 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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90C LEU* 3.4 33.9 - - - +
92C GLY 4.9 0.9 - - - +
93C CYS* 4.3 10.1 - - + +
96C VAL* 3.8 28.0 - - - -
128C CYS* 2.9 26.2 + - - +
131C HIS* 1.3 79.9 - - - +
133C PRO* 1.4 66.9 - - - +
134C GLU* 3.1 4.0 - - - -
135C ALA* 3.1 22.1 + - + +
137C ILE* 4.8 2.9 - - - +
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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
------------------------------------------------------------
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