Contacts of the helix formed by residues 113 - 132 (chain A) in PDB entry 2OZO
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 GLY 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 3.5 17.4 + - - -
38A GLN* 5.7 0.2 - - - -
111A GLN* 3.3 3.2 + - - -
112A PRO* 1.3 73.2 - - - +
114A VAL* 1.3 61.5 + - - -
115A PHE 3.3 3.6 - - - -
116A ASP* 2.8 15.4 + - - -
117A CYS* 3.1 34.4 + - - -
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Residues in contact with VAL 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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113A GLY* 1.3 72.0 - - - -
115A PHE* 1.3 64.7 + - + +
117A CYS* 3.8 5.9 - - + +
118A LEU* 2.8 28.1 + - + +
238A TYR* 3.6 34.3 - - + +
241A LEU* 5.5 11.8 - - + +
242A LYS* 5.1 16.6 - - + -
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Residues in contact with PHE 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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38A GLN* 4.0 19.3 - - + +
39A CYS 3.7 13.2 - - - -
40A LEU* 3.8 14.8 - - - -
42A SER 3.5 25.6 - - - -
43A LEU* 3.4 39.6 - - + +
44A GLY 4.5 3.8 - - - +
113A GLY 3.3 0.4 - - - -
114A VAL* 1.3 81.7 - - + +
116A ASP* 1.3 60.5 + - - +
118A LEU* 3.7 8.1 - - + +
119A ARG* 2.9 33.4 + - - +
227A THR* 3.8 22.7 - - + -
229A PHE* 3.9 20.2 - + - -
238A TYR* 4.0 17.9 - + - -
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Residues in contact with ASP 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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2A PRO* 4.7 2.3 - - - +
3A ASP* 4.5 5.9 - - - +
38A GLN* 3.3 31.1 + - - +
112A PRO* 4.0 15.9 - - + +
113A GLY* 2.8 31.3 + - - +
114A VAL 3.3 0.2 - - - -
115A PHE* 1.3 73.4 - - - +
117A CYS* 1.3 65.3 + - - +
119A ARG* 3.2 35.0 + - - +
120A ASP* 3.1 32.5 + - - +
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Residues in contact with CYS 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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112A PRO* 5.4 7.6 - - - -
113A GLY 3.1 26.7 + - - +
114A VAL* 3.8 7.2 - - + +
116A ASP* 1.3 77.1 - - - +
118A LEU* 1.3 65.5 + - - +
120A ASP* 3.4 6.4 + - - +
121A ALA* 3.1 23.2 + - - +
241A LEU* 5.5 8.7 - - + -
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Residues in contact with LEU 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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43A LEU* 4.5 19.7 - - + -
114A VAL* 2.8 22.1 + - + +
115A PHE* 3.7 6.3 - - + +
117A CYS* 1.3 78.1 - - - +
119A ARG* 1.3 63.1 + - - +
121A ALA* 3.3 5.9 + - + +
122A MET* 3.1 38.5 + - + +
229A PHE* 4.5 1.6 - - + -
234A GLN* 3.7 24.2 - - + +
237A GLU* 3.6 37.7 - - + +
238A TYR* 3.7 22.2 - - + -
241A LEU* 4.9 14.1 - - + +
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Residues in contact with ARG 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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2A PRO* 2.9 46.3 + - - +
3A ASP* 3.7 19.8 + - - +
38A GLN* 5.2 2.0 - - - +
43A LEU* 6.3 1.3 - - + -
115A PHE* 2.9 19.9 + - - +
116A ASP* 3.2 43.9 + - - +
117A CYS 3.2 0.2 - - - -
118A LEU* 1.3 78.1 - - - +
120A ASP* 1.3 72.9 + - - +
122A MET* 3.4 14.1 + - + +
123A VAL* 3.2 29.0 + - + +
150A GLU* 2.8 36.3 - - + +
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Residues in contact with ASP 120 (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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2A PRO* 5.4 3.8 - - - +
116A ASP* 3.1 20.6 + - - +
117A CYS* 4.0 6.4 - - - +
119A ARG* 1.3 89.5 + - - +
121A ALA* 1.3 65.3 + - - +
123A VAL* 3.0 8.8 + - - +
124A ARG* 2.8 32.3 + - + +
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Residues in contact with ALA 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 CYS 3.1 12.5 + - - +
118A LEU* 3.5 13.7 - - + +
120A ASP* 1.3 78.3 - - - +
122A MET* 1.3 65.0 + - + +
124A ARG* 3.4 6.9 - - - +
125A ASP* 2.9 27.4 + - - +
241A LEU* 5.6 6.7 - - + -
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Residues in contact with MET 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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43A LEU* 5.7 1.6 - - + -
118A LEU* 3.1 31.7 + - + +
119A ARG* 3.8 13.5 - - + +
120A ASP 3.2 0.2 - - - -
121A ALA* 1.3 77.4 - - + +
123A VAL* 1.3 63.9 + - - +
125A ASP* 3.5 3.9 - - - +
126A TYR* 2.7 25.5 + - - +
153A ILE* 3.9 36.6 - - + -
233A TRP* 4.6 15.0 - - + +
234A GLN* 4.1 35.2 - - + +
237A GLU* 3.9 31.4 - - + -
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Residues in contact with VAL 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 ARG* 3.2 18.6 - - + +
120A ASP* 3.0 9.3 + - - +
122A MET* 1.3 75.5 - - - +
124A ARG* 1.3 58.7 + - - +
126A TYR* 2.9 18.5 + - - +
127A VAL* 3.0 21.9 + - + +
142A ILE* 4.3 18.2 - - + -
146A ALA* 4.3 17.7 - - + +
149A VAL* 3.7 22.4 - - + -
150A GLU* 4.0 23.3 - - + -
153A ILE* 3.7 19.5 - - + +
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Residues in contact with ARG 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 ASP* 2.8 26.4 + - - +
121A ALA* 3.4 8.3 - - - +
123A VAL* 1.3 73.2 - - - +
125A ASP* 1.3 60.4 + - + +
126A TYR 3.0 5.0 + - - -
127A VAL* 3.3 2.1 + - - +
128A ARG* 3.1 30.3 + - - +
138A LEU* 3.9 21.1 - - + +
139A GLU* 4.7 13.9 - - - +
142A ILE* 3.5 39.0 - - + +
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Residues in contact with ASP 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 ALA 2.9 19.5 + - - +
122A MET* 3.5 3.8 - - - +
124A ARG* 1.3 76.5 - - + +
126A TYR* 1.3 56.4 + - - +
127A VAL 3.6 0.2 - - - -
128A ARG* 4.2 14.2 - - - +
129A GLN* 2.8 32.7 + - - +
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Residues in contact with TYR 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 MET 2.7 18.7 + - - +
123A VAL* 2.9 12.3 + - - +
125A ASP* 1.3 79.1 - - - +
127A VAL* 1.3 56.9 + - - +
129A GLN* 3.6 7.4 - - - +
130A THR* 2.4 68.8 + - + +
131A TRP* 4.2 9.0 - + - -
149A VAL* 3.5 20.6 - - + -
152A LEU* 3.4 37.3 - - + +
153A ILE* 3.5 23.3 - - + -
156A THR* 4.3 15.7 - - + +
233A TRP* 3.6 25.1 - + + -
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Residues in contact with VAL 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 VAL* 3.0 15.9 + - + +
124A ARG 4.1 0.4 - - - +
126A TYR* 1.3 73.3 - - + +
128A ARG* 1.3 69.3 + - - +
131A TRP* 2.8 47.0 + - + +
132A LYS 3.6 0.5 + - - -
133A LEU* 4.1 7.8 + - + -
138A LEU* 3.5 20.0 - - + -
141A ALA* 3.8 21.8 - - + -
142A ILE* 4.1 19.3 - - + +
149A VAL* 4.2 25.6 - - + -
315A PHE* 4.5 4.3 - - + -
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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 ARG* 3.1 21.8 + - - +
125A ASP* 4.2 12.8 - - - +
127A VAL* 1.3 78.3 - - - +
129A GLN* 1.3 56.7 + - + +
132A LYS* 2.7 40.8 + - + +
133A LEU 3.8 9.0 - - - +
134A GLU* 2.5 46.6 + - - -
138A LEU* 3.3 28.8 - - + +
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Residues in contact with GLN 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 ASP 2.8 21.6 + - - +
126A TYR* 3.6 14.1 + - - +
127A VAL 3.0 0.4 - - - -
128A ARG* 1.3 87.2 - - + +
130A THR* 1.3 66.0 + - - +
131A TRP 3.2 1.2 + - - -
132A LYS* 3.5 21.6 + - - +
161A MET* 5.9 2.4 - - - +
233A TRP* 4.8 15.2 - - - -
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Residues in contact with THR 130 (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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126A TYR* 2.4 58.3 + - + +
129A GLN* 1.3 77.2 + - - +
131A TRP* 1.3 91.9 + - + +
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Residues in contact with TRP 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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126A TYR* 4.2 13.5 - + - -
127A VAL* 2.8 28.4 + - + +
130A THR* 1.3 106.9 + - + +
132A LYS* 1.3 70.9 + - - +
133A LEU* 2.8 15.7 + - + +
149A VAL* 5.1 5.6 - - + -
152A LEU* 4.7 11.7 - - + -
313A SER* 3.9 22.7 - - - -
315A PHE* 2.9 75.3 + + + -
316A GLU* 4.9 2.4 - - - +
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Residues in contact with LYS 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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128A ARG* 2.7 25.2 + - + +
129A GLN* 3.5 17.7 + - - +
131A TRP* 1.3 78.2 - - - +
133A LEU* 1.3 61.2 + - - +
134A GLU* 4.1 2.1 + - - +
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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