Contacts of the helix formed by residues 126 - 139 (chain C) in PDB entry 3HW4
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 GLU 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C THR* 4.3 1.2 + - - -
125C ARG* 1.3 81.0 - - + +
127C VAL* 1.3 64.8 + - - +
128C HIS* 4.5 6.8 - - + +
129C THR* 3.3 23.2 + - - +
130C TYR* 3.1 20.8 + - - +
153C GLU* 4.0 9.9 - - - +
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Residues in contact with VAL 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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123C THR* 4.0 2.2 - - + -
125C ARG 3.7 0.2 + - - -
126C GLU* 1.3 69.8 - - - +
128C HIS* 1.3 63.7 + - + +
130C TYR* 4.0 0.3 - - - +
131C TYR* 2.8 31.9 + - - +
147C ILE* 3.8 28.4 - - + +
148C PHE 4.1 0.4 - - - -
149C SER* 3.6 24.9 - - - +
153C GLU* 3.2 51.6 + - + +
154C GLU* 3.9 6.1 - - - +
155C MET* 3.8 27.1 - - + -
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Residues in contact with HIS 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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126C GLU* 3.3 8.4 - - + +
127C VAL* 1.3 80.3 - - + +
129C THR* 1.3 69.3 + - - +
131C TYR* 3.5 2.5 - - - +
132C LEU* 3.1 56.6 + - + +
155C MET* 3.5 31.5 - - + +
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Residues in contact with THR 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* 4.4 13.5 - - - +
126C GLU* 3.3 28.0 + - - +
128C HIS* 1.3 81.7 - - - +
130C TYR* 1.3 64.4 + - - +
132C LEU* 3.2 13.3 + - - +
133C GLU* 3.0 40.4 + - + +
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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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121C GLY* 3.8 22.6 - - - -
122C VAL 4.1 13.9 + - - -
123C THR* 3.5 24.2 - - + +
125C ARG* 3.4 14.3 - - - +
126C GLU 3.1 9.0 + - - +
127C VAL 4.0 2.2 - - - +
128C HIS 3.4 0.2 - - - -
129C THR* 1.3 77.9 - - - +
131C TYR* 1.3 63.9 + - - +
133C GLU* 3.1 14.7 + - + +
134C LYS* 3.0 46.8 + - - +
147C ILE* 3.8 20.2 - - + -
195C GLU* 3.4 30.7 - - + -
196C ARG 5.4 0.2 - - - -
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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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127C VAL 2.8 23.4 + - - +
128C HIS* 3.5 1.8 - - - +
130C TYR* 1.3 73.5 - - - +
132C LEU* 1.3 70.2 + - + +
134C LYS* 3.3 3.5 + - - +
135C ALA* 2.9 38.5 + - + +
145C ILE* 3.5 34.5 - - + +
147C ILE* 3.6 16.8 - - + +
155C MET* 3.5 35.4 - - + -
156C ALA 3.9 2.2 - - - -
157C THR* 2.9 45.4 + - - +
158C LYS 4.7 0.2 + - - -
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Residues in contact with LEU 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 HIS* 3.1 47.1 + - + +
129C THR* 3.2 10.5 + - + +
131C TYR* 1.3 88.2 - - + +
133C GLU* 1.3 66.3 + - + +
135C ALA* 3.9 6.6 - - + +
136C ASN* 3.1 24.9 + - - +
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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
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125C ARG* 2.7 45.1 + - - -
129C THR* 3.0 27.0 + - + +
130C TYR* 3.1 17.6 + - + +
132C LEU* 1.3 76.7 - - + +
134C LYS* 1.3 58.9 - - - +
136C ASN* 3.3 5.6 + - - +
137C LYS* 3.0 26.7 + - - +
196C ARG 4.0 0.3 - - - +
197C GLY* 3.1 28.9 - - - +
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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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41C HIS* 5.7 1.8 + - - -
119C GLU* 4.1 37.6 + - + +
120C ILE 4.5 14.6 + - - -
121C GLY* 5.0 1.5 - - - -
130C TYR* 3.0 42.5 + - - +
131C TYR* 3.6 7.4 - - - +
133C GLU* 1.3 74.1 - - - +
135C ALA* 1.3 64.3 + - - +
137C LYS* 3.2 17.5 + - + +
138C ILE* 3.1 30.7 + - + +
145C ILE* 4.1 23.6 - - + -
147C ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 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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131C TYR* 2.9 28.2 + - + +
132C LEU* 3.9 10.5 - - + +
134C LYS* 1.3 77.2 - - - +
136C ASN* 1.3 57.2 + - - +
139C LYS* 3.0 27.7 + - - +
140C SER* 3.2 13.7 + - - +
145C ILE* 3.6 18.3 - - + +
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Residues in contact with ASN 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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132C LEU 3.1 17.7 + - - +
133C GLU* 3.6 6.1 - - - +
134C LYS 3.2 0.2 - - - -
135C ALA* 1.3 73.6 - - - +
137C LYS* 1.3 66.1 + - - +
139C LYS* 3.3 35.3 + - - +
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Residues in contact with LYS 137 (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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24C TYR* 5.7 2.8 + - - -
104C LYS* 5.6 0.9 - - - +
105C PHE* 3.5 54.9 - - + +
119C GLU* 5.9 0.9 - - - -
133C GLU 3.0 13.8 + - - +
134C LYS* 3.2 22.2 + - + +
136C ASN* 1.3 80.1 - - - +
138C ILE* 1.3 69.3 + - + +
139C LYS* 3.6 10.4 + - - +
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Residues in contact with ILE 138 (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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104C LYS* 3.5 18.1 + - - +
105C PHE* 4.5 15.5 - - + +
119C GLU* 3.6 37.7 - - + +
134C LYS* 3.1 19.1 + - + +
135C ALA* 4.3 0.2 - - - -
137C LYS* 1.3 89.6 - - + +
139C LYS* 1.3 73.4 + - - +
140C SER* 2.9 36.4 - - - +
143C THR* 4.0 15.3 - - + +
145C ILE* 3.8 30.1 - - + -
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Residues in contact with LYS 139 (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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104C LYS* 3.1 34.1 + - + +
135C ALA 3.0 12.0 + - - +
136C ASN* 3.3 37.2 + - - +
137C LYS* 4.3 8.8 + - - +
138C ILE* 1.3 81.3 - - - +
140C SER* 1.3 60.4 + - - +
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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
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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