Contacts of the helix formed by residues 114 - 133 (chain J) 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 ASP 114 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115J LEU* 1.3 57.7 + - - +
116J ARG* 3.4 9.9 - - - +
117J SER* 3.3 19.8 + - - -
118J ARG* 2.6 50.5 + - - +
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ASP* 1.3 75.6 - - - +
116J ARG* 1.3 77.2 + - + +
117J SER 2.7 14.6 + - - -
118J ARG* 3.2 17.4 + - + -
119J ILE* 3.2 42.2 + - + +
92L GLU* 5.6 14.6 - - + +
95L LYS* 4.8 8.7 - - + +
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Residues in contact with ARG 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ASP 3.4 6.5 - - - +
115J LEU* 1.3 105.1 - - + +
117J SER* 1.3 62.0 + - - +
120J GLU* 3.7 16.5 - - - +
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Residues in contact with SER 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J ASP* 3.5 25.1 + - - -
115J LEU 2.7 1.0 + - - -
116J ARG* 1.3 85.3 + - - +
118J ARG* 1.3 62.7 + - - +
119J ILE 3.5 0.7 - - - -
120J GLU* 3.5 8.2 - - - +
121J VAL* 2.9 34.4 + - - +
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Residues in contact with ARG 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J ASP* 2.6 35.0 + - - +
115J LEU* 3.9 14.8 - - + +
117J SER* 1.3 71.8 - - - +
119J ILE* 1.3 64.6 + - - +
121J VAL* 2.9 18.9 + - - +
122J LEU* 3.3 12.0 + - + +
93L ILE 5.7 2.4 + - - -
95L LYS* 3.4 36.3 - - + +
98L ALA* 4.5 9.3 - - + +
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Residues in contact with ILE 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 3.2 32.0 + - + +
116J ARG* 5.9 0.2 - - - -
118J ARG* 1.3 78.7 - - - +
120J GLU* 1.3 59.7 + - - +
122J LEU* 2.6 38.9 + - + +
123J LYS* 3.2 20.4 + - + +
154K ASP* 6.1 0.9 - - - +
95L LYS* 3.4 33.4 - - - +
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Residues in contact with GLU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU 4.2 1.6 + - - -
116J ARG 3.7 21.5 - - - +
117J SER* 3.4 12.4 + - - +
118J ARG 3.2 0.4 - - - -
119J ILE* 1.3 81.1 - - - +
121J VAL* 1.3 60.9 + - + +
123J LYS* 3.9 25.6 + - - +
124J ARG* 3.5 19.8 + - - +
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Residues in contact with VAL 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J SER* 2.9 22.4 + - - +
118J ARG* 2.9 12.0 + - - +
120J GLU* 1.3 77.1 - - + +
122J LEU* 1.3 67.6 + - + +
124J ARG* 3.7 10.8 + - + +
125J LYS* 3.2 24.1 + - + +
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Residues in contact with LEU 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J ARG* 3.3 10.1 + - + +
119J ILE* 2.6 24.2 + - + +
121J VAL* 1.3 69.7 - - + +
123J LYS* 1.3 58.2 + - + +
125J LYS* 2.7 8.6 + - + +
126J VAL* 2.6 39.3 + - + +
95L LYS* 3.9 21.5 - - + -
97L GLU* 4.5 13.0 - - + +
98L ALA* 3.3 51.4 - - + +
101L LEU* 5.1 7.6 - - + -
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Residues in contact with LYS 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J ILE* 3.2 19.5 + - + +
120J GLU* 4.3 29.5 + - - +
122J LEU* 1.3 76.9 - - + +
124J ARG* 1.3 63.9 + - - +
126J VAL* 3.4 11.7 - - + -
127J ILE* 2.8 37.6 + - + +
153K ILE* 4.5 25.1 - - + +
154K ASP* 5.1 10.5 + - - +
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Residues in contact with ARG 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J GLU* 3.5 17.9 + - - +
121J VAL* 3.8 12.8 - - + +
122J LEU 3.2 0.6 - - - -
123J LYS* 1.3 77.9 - - - +
125J LYS* 1.3 62.9 + - + +
127J ILE* 3.7 16.4 - - - +
128J GLU* 3.4 18.6 - - - +
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Residues in contact with LYS 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J VAL* 3.2 22.1 + - + +
122J LEU* 2.7 14.7 + - + +
124J ARG* 1.3 77.0 - - + +
126J VAL* 1.3 66.6 + - - +
127J ILE 3.2 0.9 - - - -
128J GLU* 2.8 54.4 + - - +
129J LYS* 3.1 33.9 + - - +
101L LEU* 5.4 8.3 - - + -
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Residues in contact with VAL 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J LEU* 2.6 22.6 + - + +
123J LYS* 3.1 23.1 - - + +
125J LYS* 1.3 68.8 - - - +
127J ILE* 1.3 87.5 + - + +
129J LYS* 2.6 28.0 + - + +
130J VAL* 2.8 22.5 + - + -
153K ILE* 5.4 7.6 - - + +
156K THR* 4.6 7.2 - - + -
157K VAL* 4.0 26.9 - - + -
161K ILE* 4.3 8.1 - - + -
101L LEU* 5.7 7.0 - - + +
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Residues in contact with ILE 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS* 3.0 21.1 - - + +
124J ARG* 3.7 17.7 - - - +
126J VAL* 1.3 87.7 - - + +
128J GLU* 1.3 76.0 + - + +
130J VAL* 2.8 28.3 + - + +
131J GLN* 3.3 9.0 + - + +
153K ILE* 4.1 33.7 - - + -
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Residues in contact with GLU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J ARG* 3.4 26.1 - - - +
125J LYS* 2.8 48.2 + - - +
126J VAL 2.8 1.2 + - - -
127J ILE* 1.3 84.1 - - + +
129J LYS* 1.3 72.4 + - - +
130J VAL 2.7 1.9 + - - -
131J GLN* 2.7 41.4 + - - +
132J HIS* 3.3 4.9 + - - +
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Residues in contact with LYS 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J LYS* 3.1 40.3 + - - +
126J VAL* 2.6 22.7 + - + +
128J GLU* 1.3 78.8 + - - +
130J VAL* 1.3 48.0 + - - +
132J HIS* 3.4 14.5 + - - +
133J ILE* 2.7 41.2 + - + +
161K ILE* 5.0 8.3 - - + -
101L LEU* 3.7 33.0 - - + -
103L HIS* 5.5 8.1 - - + -
104L ASP* 3.8 32.3 + - - +
107L ILE* 4.6 10.1 - - + +
108L ARG* 5.6 1.2 - - - +
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Residues in contact with VAL 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J VAL* 2.8 22.0 + - + +
127J ILE* 2.9 26.0 - - + +
128J GLU 2.7 3.6 + - - -
129J LYS* 1.3 73.7 - - - +
131J GLN* 1.3 57.0 + - + +
133J ILE* 2.9 22.5 - - + +
134J GLN* 3.0 20.4 - - + +
192J ASP* 3.6 31.9 - - + +
153K ILE* 5.6 4.5 - - + -
156K THR* 4.6 8.3 - - + -
161K ILE* 4.2 20.2 - - + -
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Residues in contact with GLN 131 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127J ILE* 3.6 10.8 - - + +
128J GLU* 2.7 44.6 + - - +
130J VAL* 1.3 74.5 - - + +
132J HIS* 1.3 95.6 + - - +
134J GLN* 2.8 27.6 + - - +
135J LEU* 2.9 16.3 + - - +
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Residues in contact with HIS 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLU* 3.3 4.7 + - - +
129J LYS* 3.8 18.5 + - - +
131J GLN* 1.3 90.3 + - - +
133J ILE* 1.3 58.6 + - - +
134J GLN 2.9 9.7 + - - -
135J LEU* 3.2 33.4 + - + +
136J LEU* 3.3 13.0 + - - +
107L ILE* 3.9 25.4 - - + +
111L GLN* 5.3 7.6 + - - -
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Residues in contact with ILE 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J LYS 2.7 29.5 + - - +
130J VAL* 2.9 21.0 - - + +
132J HIS* 1.3 74.5 - - - +
134J GLN* 1.3 56.0 + - - +
135J LEU 3.8 0.2 - - - -
136J LEU* 4.6 8.1 - - + -
137J GLN* 3.3 18.5 - - - +
161K ILE* 3.2 47.1 - - + +
164K ASN* 4.3 9.1 + - - +
165K LEU* 3.3 30.3 - - + -
168K LEU* 5.2 6.3 - - + -
107L ILE* 3.7 19.7 - - + +
110L LEU* 6.0 0.2 - - + -
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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