Contacts of the helix formed by residues 112 - 126 (chain D) in PDB entry 3AG2
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 GLU 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D PRO 4.7 0.8 + - - +
109D HIS* 3.2 40.2 + - - +
110D THR 3.4 0.2 - - - -
111D PHE* 1.3 78.6 - - - +
113D GLU* 1.3 66.3 + - - +
114D GLU* 4.5 5.4 - - + +
115D TRP* 3.1 12.5 + - + +
116D VAL* 2.9 19.8 + - - +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE 3.5 3.2 + - - -
112D GLU* 1.3 72.1 - - - +
114D GLU* 1.3 59.1 + - - +
116D VAL* 3.3 7.5 + - - +
117D ALA* 2.9 30.5 + - + +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLU* 3.3 3.6 - - + +
113D GLU* 1.3 76.9 - - - +
115D TRP* 1.3 67.9 + - - +
117D ALA* 3.3 6.8 + - + +
118D LYS* 3.0 58.0 + - + +
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Residues in contact with TRP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.5 29.4 - - + -
129B LYS 3.2 29.2 - - - -
130B PRO* 3.7 19.3 - - + -
131B GLY* 3.6 9.3 - - - +
132B GLU 3.1 16.8 + - - -
109D HIS* 3.5 35.4 - + - +
110D THR* 3.2 40.6 - - + +
112D GLU* 3.1 16.1 + - + +
114D GLU* 1.3 79.5 - - - +
116D VAL* 1.3 56.6 + - - +
118D LYS* 3.2 8.3 + - + +
119D GLN* 2.8 52.3 + - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D THR 3.6 15.9 - - - +
111D PHE* 3.8 18.2 - - + +
112D GLU 2.9 19.2 + - - +
113D GLU* 3.7 7.0 - - - +
114D GLU 3.2 0.2 - - - -
115D TRP* 1.3 75.8 - - - +
117D ALA* 1.3 60.2 + - - +
119D GLN* 3.8 15.3 - - - +
120D THR* 2.7 44.1 + - - +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLU* 2.9 19.5 + - + +
114D GLU* 3.8 7.4 - - + +
116D VAL* 1.3 79.3 - - - +
118D LYS* 1.3 62.6 + - + +
120D THR* 3.5 6.3 + - - -
121D LYS* 3.1 21.8 + - - +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 4.0 30.0 - - + +
131B GLY* 3.9 13.5 - - - +
114D GLU* 3.0 51.8 + - + +
115D TRP* 3.7 5.2 - - + +
117D ALA* 1.3 75.7 - - + +
119D GLN* 1.3 60.4 + - - +
121D LYS* 3.3 6.6 + - - +
122D ARG* 3.0 27.0 + - - +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ASP* 4.6 17.7 + - - +
131B GLY* 3.6 22.5 - - - +
132B GLU 3.3 8.8 - - - +
133B LEU* 3.6 33.3 - - + +
134B ARG 4.8 0.3 + - - -
110D THR* 4.5 7.9 + - - +
115D TRP* 2.8 46.6 + - - +
116D VAL* 3.9 13.0 - - - +
118D LYS* 1.3 69.7 - - - +
120D THR* 1.3 60.9 + - - +
122D ARG* 3.2 2.3 + - - +
123D MET* 2.9 43.4 + - + +
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 2.7 34.7 + - - +
117D ALA* 3.7 7.1 - - - -
118D LYS 3.3 0.2 - - - -
119D GLN* 1.3 77.8 + - - +
121D LYS* 1.3 63.1 + - - +
123D MET* 3.2 12.0 + - - +
124D LEU* 3.0 30.0 + - + +
134D PHE* 4.2 12.8 - - + -
145D TRP* 3.9 27.4 - - + -
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA 3.1 14.7 + - - +
118D LYS* 3.7 9.0 - - - +
120D THR* 1.3 76.5 - - - +
122D ARG* 1.3 59.2 + - - +
124D LEU* 3.1 12.8 + - + +
125D ASP* 2.7 54.9 + - - +
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Residues in contact with ARG 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO 5.2 2.9 - - - -
131B GLY* 3.5 29.8 + - - +
132B GLU* 3.6 12.2 + - - +
133B LEU* 3.9 6.9 - - - +
137B GLU* 2.6 42.1 + - - -
141B ARG* 3.4 22.2 - - - +
191B LEU* 4.0 3.2 - - - +
193B TYR* 3.4 7.3 + - - -
118D LYS 3.0 16.4 + - - +
119D GLN 3.7 4.0 - - - +
121D LYS* 1.3 76.2 - - - +
123D MET* 1.4 58.2 + - + +
125D ASP* 3.1 13.3 + - + +
126D MET* 2.8 56.9 + - + +
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B FME 4.1 31.0 - - + -
2B ALA 4.6 0.2 - - - +
3B TYR* 4.1 19.5 - - + -
4B PRO* 4.8 6.3 - - + -
133B LEU* 4.6 5.4 - - + -
119D GLN* 2.9 41.0 + - + +
120D THR* 3.7 7.4 - - - +
122D ARG* 1.4 75.5 - - + +
124D LEU* 1.3 56.9 + - - +
126D MET* 3.3 5.8 + - + -
127D LYS 3.0 6.6 + - - -
128D VAL* 2.9 51.0 + - + +
134D PHE* 3.7 35.9 - - + -
135D SER* 4.4 0.9 - - - -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D THR* 3.0 30.2 + - + +
121D LYS* 3.4 11.9 - - + +
123D MET* 1.3 74.4 - - - +
125D ASP* 1.3 66.1 + - - +
127D LYS* 3.0 7.6 + - - +
134D PHE* 3.7 18.6 - - + -
135D SER* 3.6 19.7 - - - +
138D TRP* 3.6 57.7 - - + +
140D TYR* 2.5 35.5 + - + +
145D TRP* 4.2 5.4 - - + -
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Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LYS* 2.7 56.7 + - - +
122D ARG* 3.1 14.0 + - + +
124D LEU* 1.3 74.3 - - - +
126D MET* 1.3 59.8 + - - +
127D LYS* 3.1 11.9 + - - +
140D TYR* 5.4 3.0 - - - -
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Residues in contact with MET 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B FME 5.1 2.2 - - - -
133B LEU* 4.9 2.9 - - + -
189B PRO 5.5 0.9 - - - +
190B GLY* 5.0 10.7 - - - -
191B LEU* 3.8 43.3 + - + +
192B TYR* 5.5 2.4 + - - -
193B TYR* 4.0 14.4 - - - +
122D ARG* 2.8 69.9 + - + +
123D MET* 3.5 10.8 - - + +
125D ASP* 1.3 76.5 - - - +
127D LYS* 1.3 71.9 + - - +
128D VAL* 3.3 18.9 + - + -
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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