Contacts of the helix formed by residues 109 - 129 (chain A) in PDB entry 6ABP
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 ALA 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 1.3 70.3 - - - +
110A ALA* 1.3 56.4 + - - +
111A THR 3.5 2.5 - - - -
112A LYS* 4.0 18.4 - - + -
113A ILE* 2.9 36.7 + - + +
150A ARG* 4.8 0.2 - - - -
282A GLU* 3.4 34.0 - - + +
283A VAL 3.1 13.6 + - - +
284A THR* 4.0 17.0 - - + -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 4.3 2.2 - - + -
108A LEU* 3.0 18.7 + - + -
109A ALA* 1.3 67.6 - - - +
111A THR* 1.3 61.4 + - - +
114A GLY 2.9 24.3 + - - -
147A THR* 3.6 35.9 - - - +
150A ARG* 3.8 29.1 - - + +
151A ARG* 3.3 17.3 - - + +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 3.5 0.4 - - - -
110A ALA* 1.3 78.0 - - - +
112A LYS* 1.3 68.8 - - - +
114A GLY* 3.2 1.4 + - - -
115A GLU* 2.9 55.7 + - + +
150A ARG* 3.4 40.8 + - - +
154A GLY* 4.2 6.5 - - - -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 3.4 21.3 + - + +
110A ALA 3.4 0.4 - - - -
111A THR* 1.3 84.7 - - + +
113A ILE* 1.4 62.6 + - + +
115A GLU* 3.1 32.2 + - + +
116A ARG* 3.0 26.5 + - - +
282A GLU* 6.1 0.4 - - - +
284A THR* 6.2 1.8 - - + -
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Residues in contact with ILE 113 (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 LEU* 4.1 18.2 - - + -
109A ALA* 2.9 35.9 + - + +
110A ALA* 4.4 3.1 - - - +
112A LYS* 1.4 79.9 - - + +
114A GLY* 1.4 58.9 + - - +
116A ARG* 3.2 4.8 + - - +
117A GLN* 2.9 23.7 + - - +
151A ARG* 5.2 1.6 - - + -
231A ILE* 3.9 33.9 - - + -
252A LEU* 3.7 18.6 - - + +
254A PRO* 4.6 7.6 - - + -
283A VAL 4.6 3.6 - - - +
284A THR 4.7 4.5 - - - +
285A ASP 4.0 19.1 - - - +
286A VAL* 4.3 20.2 - - + -
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Residues in contact with GLY 114 (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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110A ALA 2.9 16.0 + - - -
111A THR 3.7 0.9 - - - -
113A ILE* 1.4 72.7 - - - +
115A GLU* 1.3 67.1 + - - +
117A GLN* 3.0 17.4 + - - +
118A GLY 3.0 10.9 + - - -
151A ARG* 3.2 30.0 - - - +
155A SER* 3.1 14.4 - - - -
231A ILE* 4.7 2.2 - - - -
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Residues in contact with GLU 115 (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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111A THR* 2.9 30.8 + - - +
112A LYS* 3.1 36.6 - - + +
114A GLY* 1.3 74.5 - - - +
116A ARG* 1.3 58.0 + - - +
118A GLY 3.2 1.9 + - - -
119A GLN* 2.9 46.1 + - - +
154A GLY* 3.4 24.7 - - - +
157A ASP* 5.2 6.6 - - - +
158A ALA* 3.4 8.0 - - + +
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Residues in contact with ARG 116 (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 LYS 3.0 18.6 + - - +
113A ILE* 3.6 7.6 - - - +
114A GLY 3.0 0.4 - - - -
115A GLU* 1.3 77.5 - - - +
117A GLN* 1.3 63.7 + - - +
119A GLN* 3.2 19.7 + - - +
120A GLU* 2.8 58.3 + - - +
252A LEU* 3.9 21.3 - - + -
286A VAL* 3.9 30.8 + - + +
287A VAL* 5.2 1.4 - - - +
288A LEU* 4.3 21.2 - - - +
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Residues in contact with GLN 117 (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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113A ILE 2.9 13.2 + - - +
114A GLY* 3.0 10.0 + - - +
116A ARG* 1.3 76.6 - - - +
118A GLY* 1.3 56.1 + - - +
120A GLU* 3.7 3.6 - - - +
121A LEU* 2.9 37.2 + - + +
151A ARG* 4.9 1.7 - - - +
152A THR* 5.5 0.2 - - - -
155A SER* 2.9 26.5 + - - +
201A ILE 5.2 0.2 - - - -
202A VAL* 3.6 14.0 - - - +
203A GLY 3.0 28.4 + - - +
209A VAL* 4.4 0.2 - - - +
229A ILE* 2.8 36.6 + - + +
230A GLY 4.3 0.6 - - - -
231A ILE* 3.8 18.4 - - + +
252A LEU* 3.5 14.9 - - + +
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Residues in contact with GLY 118 (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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114A GLY 3.0 11.1 + - - -
115A GLU 3.2 2.4 + - - -
117A GLN* 1.3 74.4 - - - +
119A GLN* 1.3 63.4 + - - +
121A LEU* 4.2 3.4 - - - -
122A TYR* 3.1 24.9 + - - +
155A SER* 3.4 28.8 + - - -
158A ALA* 4.1 6.7 - - - -
159A LEU* 3.5 14.8 - - - +
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Residues in contact with GLN 119 (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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115A GLU* 2.9 34.6 + - - +
116A ARG* 3.2 26.1 + - - +
118A GLY* 1.3 77.5 - - - +
120A GLU* 1.4 63.9 + - + +
122A TYR* 3.4 5.7 + - - +
123A LYS* 3.0 33.6 + - + +
158A ALA* 4.4 11.3 - - + +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 2.8 59.6 + - + +
117A GLN* 3.9 2.7 - - - +
119A GLN* 1.4 75.4 - - - +
121A LEU* 1.3 65.0 + - - +
123A LYS* 3.4 32.6 + - - +
124A GLU* 3.0 25.1 + - - +
229A ILE* 3.7 19.6 - - + +
249A TYR* 5.7 0.8 - - + -
252A LEU* 4.8 6.3 - - + -
288A LEU* 3.8 26.9 - - + +
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Residues in contact with LEU 121 (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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117A GLN* 2.9 31.2 + - + +
118A GLY* 3.6 7.6 - - - +
120A GLU* 1.3 71.7 - - - +
122A TYR* 1.3 58.7 + - - +
124A GLU* 3.3 2.6 + - - +
125A MET* 2.9 29.3 + - - +
155A SER* 4.3 1.6 - - - +
159A LEU* 4.2 16.4 - - + -
200A LEU* 4.1 19.0 - - + +
201A ILE 4.2 7.0 - - - +
202A VAL* 3.5 31.4 - - + -
227A ILE* 3.5 41.0 - - + +
229A ILE* 3.7 22.4 - - + +
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Residues in contact with TYR 122 (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 GLY 3.1 14.7 + - - +
119A GLN* 3.7 5.8 - - - +
120A GLU 3.3 0.2 - - - -
121A LEU* 1.3 79.4 - - - +
123A LYS* 1.3 63.4 - - - +
125A MET* 3.2 34.8 + - + +
126A GLN* 2.9 52.5 + - - +
132A VAL* 5.9 1.1 - - + +
159A LEU* 4.0 16.6 - - + +
162A ALA* 3.4 44.2 + - + -
163A GLY* 4.5 4.2 + - - -
164A PHE* 4.1 25.1 - + + -
200A LEU* 5.1 0.4 - - - -
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Residues in contact with LYS 123 (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 GLN* 3.0 20.7 + - - +
120A GLU* 3.7 33.5 + - - +
121A LEU 3.2 0.2 - - - -
122A TYR* 1.3 80.8 - - - +
124A GLU* 1.3 62.3 + - - +
126A GLN* 3.3 12.9 + - - +
127A LYS* 2.8 43.1 + - - +
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Residues in contact with GLU 124 (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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120A GLU 3.0 14.6 + - - +
121A LEU 4.0 2.5 - - - +
123A LYS* 1.3 80.7 - - - +
125A MET* 1.3 62.9 + - - +
127A LYS* 3.2 27.9 + - - +
128A ARG* 2.8 55.7 + - - +
227A ILE* 3.5 29.6 - - + -
249A TYR* 3.6 37.2 + - + -
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Residues in contact with MET 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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121A LEU 2.9 14.5 + - - +
122A TYR* 3.4 47.6 - - + +
124A GLU* 1.3 76.5 - - - +
126A GLN* 1.3 69.4 + - + +
128A ARG* 3.3 4.6 + - - +
129A GLY 3.2 15.9 + - - -
130A TRP* 3.5 42.7 + - + +
132A VAL* 4.6 13.0 - - + -
135A SER* 4.7 5.8 - - - -
164A PHE* 3.9 28.0 - - + -
200A LEU* 4.2 10.8 - - + -
227A ILE* 3.6 14.9 - - + +
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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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122A TYR* 2.9 52.5 + - + +
123A LYS* 3.6 12.6 - - - +
125A MET* 1.3 81.1 - - + +
127A LYS* 1.3 65.8 + - - +
129A GLY* 3.0 15.1 + - - +
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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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123A LYS* 2.8 40.2 + - - +
124A GLU* 3.3 31.6 - - - +
126A GLN* 1.3 76.5 - - - +
128A ARG* 1.3 61.4 + - + +
129A GLY 3.5 0.2 + - - -
249A TYR* 5.4 2.2 - - - +
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Residues in contact with ARG 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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124A GLU* 2.8 38.4 + - - +
125A MET 3.7 5.4 - - - +
126A GLN 3.2 0.4 - - - -
127A LYS* 1.3 77.0 - - + +
129A GLY* 1.3 60.4 + - - +
130A TRP* 3.6 24.3 + - + +
223A ALA 3.2 8.3 + - - -
224A ALA* 3.0 34.9 + - - +
226A ILE 3.1 22.0 + - - -
227A ILE* 3.3 26.3 - - - +
247A GLY* 6.1 0.6 - - - -
249A TYR* 3.8 20.4 - - - +
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Residues in contact with GLY 129 (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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125A MET 3.2 1.8 + - - -
126A GLN* 3.0 16.0 + - - -
127A LYS 3.3 0.6 + - - -
128A ARG* 1.3 77.4 - - - +
130A TRP* 1.3 66.1 + - - +
131A ASP* 3.5 1.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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