Contacts of the helix formed by residues 122 - 135 (chain D) in PDB entry 2HPC
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 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D LYS* 1.3 61.2 + - - +
124D ARG* 2.7 44.5 - - - +
125D LYS* 2.9 33.4 + - + +
126D VAL* 3.2 15.9 + - + +
95F LYS* 4.2 18.2 - - + +
97F GLU 3.4 13.7 - - - +
98F ALA* 3.3 45.5 - - + +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 1.3 74.5 - - - +
124D ARG* 1.3 73.0 + - - +
125D LYS 2.5 17.4 + - - -
126D VAL* 3.3 28.5 + - + +
127D ILE* 3.6 6.1 + - - +
154E ASP* 4.3 27.6 - - - +
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 2.7 33.1 - - - +
123D LYS* 1.3 92.0 - - - +
125D LYS* 1.3 59.1 + - + +
127D ILE* 3.6 16.4 - - - +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 3.1 22.4 - - + +
123D LYS 2.5 12.7 + - - -
124D ARG* 1.3 78.3 - - - +
126D VAL* 1.3 64.8 + - + +
127D ILE* 2.9 4.7 + - - +
128D GLU* 2.6 43.1 + - - +
129D LYS* 3.9 20.0 + - + +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 3.2 15.7 + - + +
123D LYS* 3.5 19.1 - - + +
125D LYS* 1.3 77.0 - - + +
127D ILE* 1.3 72.5 + - - +
129D LYS* 2.4 34.5 + - + -
130D VAL* 2.7 26.3 + - + -
154E ASP* 5.7 7.9 - - - +
156E THR* 6.0 5.6 - - + -
157E VAL* 4.4 26.9 - - + -
161E ILE* 5.6 3.1 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS 3.6 5.5 + - - +
124D ARG* 3.6 24.2 - - - +
125D LYS* 2.9 8.0 - - - +
126D VAL* 1.3 81.7 - - - +
128D GLU* 1.3 82.3 + - + +
130D VAL* 3.4 10.9 - - - +
131D GLN* 3.1 30.8 + - + +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS* 2.6 43.9 + - - +
126D VAL 2.5 4.4 + - - -
127D ILE* 1.3 84.6 - - + +
129D LYS* 1.3 78.9 + - - +
131D GLN* 2.7 26.0 + - + +
132D HIS* 2.6 38.7 + - + -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS* 4.2 21.4 - - + +
126D VAL* 2.4 30.9 + - + +
128D GLU* 1.3 88.0 + - - +
130D VAL* 1.3 65.2 + - - +
132D HIS* 4.0 10.0 - - - +
133D ILE* 3.1 31.4 + - + +
161E ILE* 5.0 8.7 - - + -
100F ILE 5.3 4.0 - - - +
103F HIS* 3.3 34.1 - - + +
104F ASP* 3.9 23.7 + - - -
107F ILE* 4.4 6.9 - - + +
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 2.7 42.8 + - + +
127D ILE* 3.4 9.2 - - - +
128D GLU 2.8 0.8 + - - -
129D LYS* 1.3 70.6 - - - +
131D GLN* 1.3 51.7 + - - +
133D ILE* 2.9 13.0 - - - +
134D GLN* 2.6 34.6 + - + +
192D ASP* 4.6 25.1 - - - +
156E THR* 5.5 4.7 - - + -
161E ILE* 4.8 17.2 - - + +
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Residues in contact with GLN 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 3.2 21.0 - - - +
128D GLU* 2.7 46.0 + - - +
130D VAL* 1.3 72.0 - - + +
132D HIS* 1.3 65.2 + - - +
133D ILE 2.7 5.4 - - - -
134D GLN* 2.5 53.5 + - - +
135D LEU* 2.6 20.2 + - - +
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Residues in contact with HIS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU* 2.6 36.3 + - + +
129D LYS* 4.0 6.1 - - - +
131D GLN* 1.3 82.2 + - - +
133D ILE* 1.3 58.1 + - - +
135D LEU* 3.6 25.2 - - + +
136D LEU* 3.4 16.8 + - - +
107F ILE* 3.1 31.3 - - + +
111F GLN* 5.0 9.3 + - + +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LYS* 3.1 23.6 + - + +
130D VAL* 2.9 11.9 - - - +
131D GLN 2.7 0.6 + - - -
132D HIS* 1.3 75.7 - - - +
134D GLN* 1.3 57.3 + - - +
135D LEU 2.8 4.3 - - - -
136D LEU* 2.7 25.8 + - + +
137D GLN* 3.1 14.8 + - + +
161E ILE* 3.5 38.8 - - + -
164E ASN* 4.2 22.7 - - - +
165E LEU* 4.2 16.2 - - + -
168E LEU* 4.4 11.0 - - + -
103F HIS* 5.9 3.1 - - + -
107F ILE* 4.2 23.1 - - + -
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Residues in contact with GLN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D VAL* 2.6 19.0 + - + +
131D GLN* 2.5 41.0 + - - +
133D ILE* 1.3 72.3 - - - +
135D LEU* 1.3 58.3 + - + +
137D GLN* 3.3 33.2 - - - +
138D LYS* 3.6 22.9 - - - +
192D ASP* 5.2 5.0 - - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLN 2.6 17.5 + - - +
132D HIS* 3.6 24.2 - - + +
134D GLN* 1.3 76.5 - - + +
136D LEU* 1.3 61.7 + - - +
138D LYS* 3.5 7.3 + - + +
139D ASN* 3.0 47.6 + - - +
111F GLN* 4.3 21.3 - - - +
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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