Contacts of the helix formed by residues 121 - 139 (chain J) in PDB entry 7C97
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 SER 121 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J ASN 4.4 0.2 + - - -
120J GLY* 1.3 78.1 - - - +
122J ALA* 1.3 67.6 + - - +
123J SER* 3.1 15.9 + - - -
124J GLU* 3.1 6.7 + - - +
125J ALA* 3.0 16.3 + - - +
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J SER* 1.3 73.8 - - - +
123J SER* 1.3 63.6 + - - +
125J ALA* 3.7 15.6 + - - +
126J ASP* 3.7 11.1 + - - +
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Residues in contact with SER 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J SER* 4.0 12.9 - - - -
122J ALA* 1.3 81.1 - - - +
124J GLU* 1.3 77.3 + - - +
126J ASP* 3.4 13.0 + - - +
127J ALA* 3.7 5.5 + - - +
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Residues in contact with GLU 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J THR* 3.2 36.7 + - + +
120J GLY* 5.3 0.3 - - - -
121J SER* 3.1 10.0 + - - +
123J SER* 1.3 87.3 + - - +
125J ALA* 1.3 60.7 + - - +
126J ASP 3.2 0.4 - - - -
127J ALA* 2.9 28.7 + - + +
128J ALA* 3.0 15.2 + - - +
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Residues in contact with ALA 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J THR 3.8 14.5 + - - +
117J ILE* 4.4 15.5 - - - +
120J GLY 4.5 1.3 - - - +
121J SER 3.0 16.4 + - - +
122J ALA* 3.8 13.7 - - - +
123J SER 3.2 0.2 - - - -
124J GLU* 1.3 78.1 - - - +
126J ASP* 1.3 57.0 + - - +
128J ALA* 3.6 1.9 + - - +
129J ARG* 3.0 45.2 + - - +
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Residues in contact with ASP 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA 3.7 6.7 + - - +
123J SER 3.4 10.4 + - - +
124J GLU 3.2 0.6 - - - -
125J ALA* 1.3 76.3 - - - +
127J ALA* 1.3 65.7 + - - +
129J ARG* 3.3 17.1 + - - +
130J LYS* 3.5 31.2 + - - +
131J GLN* 4.8 0.5 + - - +
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Residues in contact with ALA 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J SER 3.7 2.5 + - - +
124J GLU* 2.9 25.9 + - + +
126J ASP* 1.3 81.1 - - - +
128J ALA* 1.3 60.0 + - - +
131J GLN* 2.7 46.6 + - - +
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Residues in contact with ALA 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J LEU* 3.5 33.1 - - + +
116J THR* 4.3 7.2 - - - +
117J ILE* 3.3 33.4 - - + +
124J GLU 3.0 11.7 + - - +
125J ALA 4.3 0.2 - - - +
127J ALA* 1.3 76.3 - - - +
129J ARG* 1.3 62.7 + - - +
131J GLN* 4.6 1.3 - - - -
132J LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 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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117J ILE* 3.6 19.5 + - - +
125J ALA* 3.0 57.8 + - - +
126J ASP* 3.7 12.4 - - - +
127J ALA 3.2 1.2 - - - -
128J ALA* 1.3 80.4 - - - +
130J LYS* 1.3 78.0 + - - +
132J LEU* 3.7 0.2 - - - +
133J ARG* 3.2 13.3 + - - +
171J LEU* 2.4 39.0 + - - +
172J GLY* 3.3 14.8 + - - -
173J ILE* 3.0 49.1 - - + +
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Residues in contact with LYS 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 ASP* 3.5 23.5 + - - +
129J ARG* 1.3 86.8 - - - +
131J GLN* 1.3 68.4 + - + +
132J LEU 3.1 1.8 - - - -
133J ARG* 3.0 26.7 + - + +
134J GLU* 3.4 18.8 + - + +
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Residues in contact with GLN 131 (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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113J LEU* 5.4 5.0 - - + +
126J ASP 5.4 0.4 - - - +
127J ALA* 2.7 37.8 + - - +
128J ALA* 4.6 2.3 - - - +
129J ARG 3.5 0.2 - - - -
130J LYS* 1.3 79.2 - - + +
132J LEU* 1.3 60.3 + - - +
134J GLU* 4.2 4.6 + - - +
135J GLU* 3.5 23.7 + - - +
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Residues in contact with LEU 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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110J TRP* 3.9 32.8 - - + +
113J LEU* 3.3 27.5 - - + +
114J MET* 5.6 8.5 - - + -
117J ILE* 4.9 8.7 - - + -
128J ALA 3.0 20.3 + - - +
129J ARG 3.7 0.2 - - - +
130J LYS 3.1 0.4 - - - -
131J GLN* 1.3 78.8 - - - +
133J ARG* 1.3 63.3 + - - +
134J GLU 3.3 0.2 - - - -
135J GLU* 3.0 21.0 + - - +
136J LEU* 3.0 45.3 + - + +
168J LEU* 6.2 1.8 - - + -
173J ILE* 3.9 24.7 - - + -
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Residues in contact with ARG 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 ARG* 3.2 13.8 + - - +
130J LYS* 3.0 24.5 + - + +
132J LEU* 1.3 77.5 - - - +
134J GLU* 1.3 57.9 + - + +
136J LEU* 2.7 40.9 + - + +
137J LEU* 3.3 29.7 + - + +
173J ILE* 3.9 19.1 - - + +
174J GLU 2.7 29.3 + - - +
175J PHE* 3.3 7.8 - - + +
176J SER* 2.9 42.4 + - - +
178J PRO* 4.5 4.8 + - - +
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Residues in contact with GLU 134 (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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130J LYS* 3.4 14.1 + - + +
131J GLN* 4.6 5.2 - - - +
132J LEU 3.3 0.6 - - - -
133J ARG* 1.3 81.8 + - + +
135J GLU* 1.3 59.9 + - + +
137J LEU* 3.0 42.7 - - - +
138J ALA* 3.4 11.8 + - - +
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Residues in contact with GLU 135 (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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109J ASP* 5.2 4.5 - - - +
110J TRP* 3.0 40.3 + - + -
113J LEU* 4.7 7.1 - - - +
131J GLN* 3.5 21.3 - - - +
132J LEU* 3.0 15.1 + - - +
134J GLU* 1.3 78.1 - - + +
136J LEU* 1.3 62.4 + - - +
138J ALA* 3.3 18.4 + - - +
139J ILE* 3.9 12.7 + - + +
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Residues in contact with LEU 136 (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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110J TRP* 3.4 35.4 - - + -
132J LEU* 3.0 48.2 - - + +
133J ARG* 2.7 35.4 + - + +
135J GLU* 1.3 72.9 - - - +
137J LEU* 1.3 55.7 + - - +
139J ILE* 4.3 3.1 + - - +
140J ALA 4.1 2.6 + - - -
165J LEU* 6.5 0.7 - - + -
168J LEU* 5.0 14.4 - - + -
173J ILE* 4.4 12.3 - - + -
175J PHE* 4.3 22.4 - - + -
183J LEU* 3.6 21.8 - - - +
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Residues in contact with LEU 137 (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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133J ARG* 3.6 25.6 - - + +
134J GLU* 3.0 55.4 - - - +
136J LEU* 1.3 74.9 - - + +
138J ALA* 1.3 63.4 + - - +
139J ILE 3.4 1.6 - - - -
140J ALA* 3.0 22.1 - - - +
141J PRO* 3.1 8.8 - - - +
175J PHE* 5.4 3.1 - - + -
178J PRO* 3.8 30.1 - - + +
179J GLY* 3.3 23.1 - - - +
183J LEU* 4.9 0.2 - - - -
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Residues in contact with ALA 138 (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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134J GLU 3.4 17.3 + - - +
135J GLU* 3.3 12.6 + - - +
137J LEU* 1.3 78.9 - - - +
139J ILE* 1.3 63.4 + - + +
140J ALA 3.1 0.2 - - - -
141J PRO* 3.4 12.6 - - - +
142J VAL* 4.1 4.5 - - - +
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Residues in contact with ILE 139 (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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105J ARG* 4.3 18.6 - - - +
110J TRP* 4.5 19.5 - - + -
135J GLU* 3.9 14.0 + - + +
136J LEU 4.3 3.1 + - - +
137J LEU 3.4 0.2 - - - -
138J ALA* 1.3 78.1 - - + +
140J ALA* 1.3 64.0 + - - +
142J VAL* 3.0 53.5 - - + +
143J PHE* 3.0 12.2 - - + -
149J PHE* 3.5 34.5 - - + -
183J LEU* 4.7 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