Contacts of the helix formed by residues 124 - 140 (chain A) in PDB entry 2AF0
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A THR* 3.6 2.8 - - - +
123A LYS* 1.3 79.1 - - - +
125A PRO* 1.3 67.3 - - - +
126A GLN* 3.4 16.1 + - - +
127A LYS* 3.4 33.9 + - - +
128A LEU* 3.0 30.1 + - - +
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Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS 3.9 7.0 - - - +
124A SER* 1.3 85.2 - - - +
126A GLN* 1.3 62.6 + - - +
128A LEU* 3.7 14.4 - - + +
129A SER* 3.2 23.4 + - - -
165A ALA 5.5 1.6 - - - +
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A SER* 3.3 9.5 + - - +
125A PRO* 1.3 82.0 - - - +
127A LYS* 1.3 62.4 + - + +
129A SER* 3.3 12.2 + - - -
130A SER* 3.4 11.3 + - - -
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS 5.6 0.2 + - - -
122A THR* 3.9 19.6 + - + +
123A LYS* 4.6 5.4 - - - +
124A SER* 3.4 34.3 - - - +
126A GLN* 1.3 77.2 - - + +
128A LEU* 1.3 56.7 + - - +
129A SER 3.4 0.2 - - - -
130A SER* 3.0 12.8 + - - +
131A LYS* 2.8 57.2 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.1 73.6 - - + +
122A THR* 3.9 21.5 - - + +
123A LYS 6.2 0.2 - - - -
124A SER 3.0 21.9 + - - +
125A PRO* 3.7 13.7 - - + +
126A GLN 3.2 0.4 - - - -
127A LYS* 1.3 75.5 - - - +
129A SER* 1.3 64.3 + - - +
131A LYS* 4.6 0.2 - - - -
132A ALA* 3.2 8.0 + - - +
165A ALA* 3.2 27.4 - - - +
166A THR* 3.9 14.1 - - - +
167A SER* 4.2 5.6 - - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO 3.2 14.0 + - - -
126A GLN* 3.3 8.9 + - - -
128A LEU* 1.3 75.9 - - - +
130A SER* 1.3 57.5 + - - +
132A ALA* 3.3 4.2 + - - +
133A ARG* 3.0 35.2 + - - +
162A ILE* 2.8 29.8 + - - +
163A GLN* 3.2 18.0 + - - -
165A ALA* 4.2 4.7 - - - +
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN 3.4 8.7 + - - -
127A LYS* 3.0 21.4 + - - +
129A SER* 1.3 76.5 - - - +
131A LYS* 1.3 68.2 + - - +
133A ARG* 3.3 12.7 + - - +
134A LYS* 3.1 22.9 + - - +
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASP* 3.2 27.1 - - - +
119A PHE* 3.7 20.6 - - + -
122A THR* 2.9 34.8 - - - +
127A LYS* 2.8 49.6 + - - +
130A SER* 1.3 80.0 + - - +
132A ALA* 1.3 57.3 + - - +
134A LYS* 3.3 6.0 + - - +
135A ILE* 2.9 38.1 + - + +
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PHE* 3.8 9.4 - - + -
128A LEU 3.2 17.7 + - - +
129A SER* 3.4 5.8 - - - +
130A SER 3.2 0.6 - - - -
131A LYS* 1.3 79.9 - - - +
133A ARG* 1.3 63.2 + - - +
135A ILE 3.5 0.2 + - - -
136A TYR* 3.0 24.3 + - - +
162A ILE* 4.4 15.9 - - + +
165A ALA* 3.9 15.7 - - + -
169A CYS* 4.7 1.8 - - - -
170A PHE* 3.6 24.8 - - + -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A SER* 3.0 20.5 + - - +
130A SER* 3.3 12.4 + - - +
132A ALA* 1.3 76.5 - - - +
134A LYS* 1.3 53.2 + - - +
136A TYR* 3.3 7.4 - - - +
137A THR* 2.8 41.9 + - - +
162A ILE* 3.6 32.6 - - + +
163A GLN* 5.3 4.9 - - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A SER 3.1 16.1 + - - +
131A LYS* 3.7 7.6 - - - +
133A ARG* 1.3 73.6 - - - +
135A ILE* 1.3 69.0 + - + +
137A THR* 3.1 21.8 + - - +
138A ASP* 2.9 60.7 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.8 22.2 - - + -
115A ALA* 3.8 29.4 - - + +
116A CYS* 4.5 1.6 - - - +
119A PHE* 3.7 31.4 - - + -
131A LYS* 2.9 25.3 + - + +
134A LYS* 1.3 76.5 - - + +
136A TYR* 1.3 56.8 + - - +
138A ASP* 3.3 1.0 + - - -
139A PHE* 2.9 42.1 + - + +
140A ILE* 3.8 0.8 + - + -
170A PHE* 3.2 40.4 - - + -
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA 3.0 18.6 + - - +
133A ARG 3.3 6.3 - - - +
135A ILE* 1.3 77.3 - - - +
137A THR* 1.3 63.9 + - - +
140A ILE* 3.0 38.1 + - + -
141A GLU* 3.0 60.2 + - + +
155A LYS* 3.5 22.4 - - - +
158A ILE* 3.6 21.5 - - + -
159A ALA* 3.7 29.3 - - + +
162A ILE* 3.6 17.5 - - + -
170A PHE* 4.5 1.1 - - - -
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Residues in contact with THR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ARG* 2.8 27.7 + - - +
134A LYS* 3.1 27.9 + - - +
136A TYR* 1.3 78.2 - - - +
138A ASP* 1.3 63.9 + - - +
141A GLU* 3.8 28.0 + - - +
144A ALA* 3.4 13.9 - - - +
145A PRO* 3.9 7.4 - - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 2.9 48.4 + - - +
135A ILE* 4.7 0.2 - - - -
137A THR* 1.3 80.2 - - - +
139A PHE* 1.3 87.2 + - + +
144A ALA* 3.3 6.3 - - - +
145A PRO* 3.8 10.9 - - - +
146A LYS* 3.0 33.7 + - + +
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU 3.8 11.7 - - - -
111A GLU* 3.8 27.1 - - + -
112A PHE* 3.5 44.6 - + + -
115A ALA* 4.2 19.1 - - + -
135A ILE* 2.9 23.6 + - + +
138A ASP* 1.3 96.4 - - + +
140A ILE* 1.3 61.6 + - + +
144A ALA* 4.2 0.9 - - - -
146A LYS* 3.4 37.9 - - + +
147A GLU* 3.4 6.0 - - - +
148A ILE* 2.9 34.5 + - + +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.4 37.0 - - + -
135A ILE 4.1 5.6 - - - +
136A TYR* 3.0 45.0 + - + +
139A PHE* 1.3 86.1 - - + +
141A GLU* 1.3 68.9 + - - +
147A GLU* 4.3 6.3 - - - +
148A ILE* 4.1 6.0 - - + +
150A ILE* 4.0 14.3 - - + +
155A LYS* 3.7 34.9 + - + -
158A ILE* 4.0 16.6 - - + -
170A PHE* 4.2 12.8 - - + -
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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