Contacts of the helix formed by residues 129 - 142 (chain B) in PDB entry 3G2V
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B HIS* 3.5 33.7 - - + +
83B ASP* 2.8 31.5 - - - +
86B GLY* 3.9 11.5 - - - +
123B THR* 5.9 1.0 - - - -
126B LEU* 3.1 30.1 + - + +
127B PRO* 4.2 2.1 - - - +
128B GLU* 1.3 78.6 - - + +
130B VAL* 1.3 63.2 + - - +
131B LYS* 3.3 3.6 - - - -
132B ILE* 3.2 40.8 + - + +
133B ALA* 3.7 4.5 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PRO 3.9 16.8 - - - +
128B GLU* 3.3 11.9 + - - +
129B GLU* 1.3 68.7 - - - +
131B LYS* 1.3 71.6 + - + +
133B ALA* 3.2 10.1 + - - +
134B GLU* 3.0 27.6 + - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLY 3.3 25.8 - - - +
87B LYS* 4.1 7.8 - - - +
88B PHE* 3.5 38.1 - - + -
91B LEU* 3.5 6.0 - - + +
129B GLU 3.3 0.8 - - - -
130B VAL* 1.3 82.7 - - + +
132B ILE* 1.3 60.1 + - - +
134B GLU* 3.9 5.1 - - - +
135B ALA* 3.0 29.3 + - - +
6D SEP 5.7 2.6 + - - -
7D ASP* 2.8 41.3 + - - +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B MET* 4.5 9.0 - - + -
85B VAL* 4.5 1.6 - - + +
86B GLY* 3.6 27.6 - - - +
91B LEU* 3.8 13.9 - - + -
119B LEU* 4.0 39.7 - - + +
122B TRP* 4.1 32.8 - - + +
123B THR* 4.1 6.1 - - + +
129B GLU* 3.2 34.4 + - + +
131B LYS* 1.3 78.5 - - - +
133B ALA* 1.3 57.0 + - - +
135B ALA* 3.3 3.6 + - - +
136B TYR* 3.0 26.2 + - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR* 3.8 24.9 - - + +
127B PRO* 5.9 3.8 - - + +
129B GLU 3.7 5.1 + - - +
130B VAL* 3.2 13.1 + - - +
132B ILE* 1.3 76.7 - - - +
134B GLU* 1.3 60.6 + - - +
136B TYR* 3.2 2.8 + - - +
137B GLN* 2.9 30.7 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 3.8 16.6 - - + -
130B VAL* 3.0 16.0 + - - +
131B LYS* 3.9 8.3 - - - +
133B ALA* 1.3 75.7 - - - +
135B ALA* 1.3 62.8 + - - +
137B GLN* 3.4 7.8 + - + +
138B MET* 3.1 23.0 + - + +
10D LEU* 3.9 23.7 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PHE* 4.8 0.4 - - - -
91B LEU* 3.9 21.5 - - + -
95B ILE* 4.2 18.5 - - + +
119B LEU* 5.4 4.5 - - + -
131B LYS 3.0 18.6 + - - +
132B ILE 3.6 5.4 - - - +
133B ALA 3.2 0.2 - - - -
134B GLU* 1.3 76.1 - - - +
136B TYR* 1.3 61.1 + - - +
138B MET* 3.4 4.9 + - - +
139B LEU* 3.2 29.6 + - + +
10D LEU* 4.2 17.0 - - + -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.8 21.7 + - + -
119B LEU* 3.9 26.2 - - + +
120B TYR* 3.6 36.5 - + + +
123B THR* 3.9 18.2 - - + -
132B ILE 3.0 16.1 + - - +
133B ALA 3.6 4.0 - - - +
135B ALA* 1.3 75.5 - - - +
137B GLN* 1.3 61.5 + - - +
139B LEU* 3.3 9.4 + - + +
140B LYS* 3.0 39.9 + - - +
145B VAL* 3.2 43.0 - - + +
146B LYS* 4.3 11.6 - - - +
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ALA 2.9 16.1 + - - +
134B GLU* 3.8 7.9 - - + +
136B TYR* 1.3 79.1 - - - +
138B MET* 1.3 52.9 + - - +
140B LYS* 3.4 19.4 + - - +
141B LYS* 2.7 49.3 + - + +
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Residues in contact with MET 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.6 9.2 - - + -
134B GLU* 3.1 16.9 + - + +
135B ALA 3.6 4.7 - - - +
136B TYR 3.2 0.2 - - - -
137B GLN* 1.3 77.3 - - - +
139B LEU* 1.3 82.1 + - + +
141B LYS* 3.1 9.0 + - + +
142B GLN* 2.9 66.3 + - + +
10D LEU* 4.2 20.6 - - + -
11D LEU 3.4 26.2 - - - +
12D GLU* 3.9 18.8 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.4 18.4 - - + -
98B VAL* 3.9 18.8 - - + -
116B LEU* 3.9 16.4 - - + -
119B LEU* 3.8 28.3 - - + -
135B ALA 3.2 16.0 + - - +
136B TYR* 3.6 9.4 - - + +
138B MET* 1.3 93.8 - - + +
140B LYS* 1.3 55.5 + - - +
142B GLN* 3.4 2.8 + - - -
143B GLY 3.0 6.2 + - - -
144B ILE* 2.8 58.8 + - + +
145B VAL* 3.7 11.9 - - + -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 3.0 33.1 + - - +
137B GLN* 3.6 23.3 + - - +
139B LEU* 1.3 73.2 - - - +
141B LYS* 1.3 65.6 + - - +
143B GLY* 3.1 12.8 + - - -
145B VAL* 3.7 35.1 - - + +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLN* 2.7 35.8 + - + +
138B MET* 3.1 13.9 + - + +
140B LYS* 1.3 74.2 - - - +
142B GLN* 1.3 62.9 + - + +
143B GLY* 3.4 0.9 + - - -
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER* 4.6 1.7 + - - -
101B LYS* 3.9 23.6 + - - +
138B MET* 2.9 45.1 + - + +
139B LEU 3.4 4.0 + - - +
140B LYS 3.3 0.2 - - - -
141B LYS* 1.3 79.9 - - + +
143B GLY* 1.3 60.5 + - - +
144B ILE* 3.3 24.9 + - + +
12D GLU* 2.6 31.5 + - - +
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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