Contacts of the helix formed by residues 129 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A HIS* 3.4 36.0 - - + +
83A ASP* 2.7 30.4 - - - +
86A GLY* 3.7 14.3 - - - +
123A THR* 6.1 0.5 - - - -
126A LEU* 3.7 24.3 - - + +
127A PRO 3.2 3.7 - - - +
128A GLU* 1.3 84.2 - - - +
130A VAL* 1.3 64.6 + - - +
131A LYS 3.2 4.2 + - - -
132A ILE* 3.3 37.9 + - + +
133A ALA* 3.6 5.5 + - - +
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Residues in contact with VAL 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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127A PRO 4.1 11.4 - - - +
128A GLU* 3.1 12.4 + - - +
129A GLU* 1.3 72.3 - - - +
131A LYS* 1.3 68.8 + - + +
132A ILE 3.4 0.2 - - - -
133A ALA* 3.4 9.7 + - + +
134A GLU* 2.8 31.2 + - - +
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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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86A GLY 3.2 25.4 - - - +
87A LYS* 4.1 7.0 - - - +
88A PHE* 3.6 36.9 - - + -
91A LEU* 3.5 6.3 - - + +
129A GLU 3.2 1.2 - - - -
130A VAL* 1.3 83.7 - - + +
132A ILE* 1.3 60.1 + - - +
134A GLU* 3.6 4.9 - - - +
135A ALA* 2.8 32.6 + - - +
5C ASP 4.5 8.7 + - - -
7C ASP* 2.5 47.2 + - - +
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Residues in contact with ILE 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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74A MET* 4.4 12.1 - - + -
85A VAL* 4.7 1.1 - - + -
86A GLY* 3.8 24.5 - - - +
91A LEU* 3.5 15.0 - - + +
119A LEU* 4.1 23.5 - - + +
122A TRP* 3.9 51.4 - - + +
123A THR* 4.2 5.2 - - + +
126A LEU* 5.0 1.3 - - + +
129A GLU* 3.3 30.2 + - + +
131A LYS* 1.3 79.0 - - - +
133A ALA* 1.3 58.1 + - - +
135A ALA* 3.3 2.4 + - - +
136A TYR* 2.9 28.2 + - - +
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Residues in contact with ALA 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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123A THR* 3.8 24.1 - - + +
127A PRO* 5.7 4.3 - - + +
129A GLU 3.6 5.3 + - - +
130A VAL* 3.4 15.8 + - + +
131A LYS 3.3 0.4 - - - -
132A ILE* 1.3 79.4 - - - +
134A GLU* 1.3 63.0 + - - +
136A TYR* 3.5 1.9 + - - +
137A GLN* 3.1 23.9 + - - +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.7 22.7 - - + -
130A VAL* 2.8 22.3 + - - +
131A LYS* 3.2 7.6 + - - +
133A ALA* 1.3 74.3 - - - +
135A ALA* 1.3 62.8 + - - +
137A GLN* 3.6 2.2 + - - +
138A MET* 3.0 24.3 + - + +
10C LEU* 3.6 21.2 - - + +
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Residues in contact with ALA 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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88A PHE* 4.7 1.2 - - + -
91A LEU* 4.0 23.1 - - + -
95A ILE* 4.2 19.3 - - + -
119A LEU* 5.3 4.9 - - + -
131A LYS 2.8 17.2 + - - +
132A ILE 3.5 4.5 - - - +
134A GLU* 1.3 77.2 - - - +
136A TYR* 1.3 61.0 + - - +
138A MET* 3.4 4.6 + - - +
139A LEU* 3.1 30.6 + - + +
10C LEU* 4.4 14.6 - - + -
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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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116A LEU* 3.8 12.3 + - + -
119A LEU* 3.7 26.1 - - + +
120A TYR* 3.6 44.5 - + + +
123A THR* 3.8 23.6 - - + -
132A ILE 2.9 16.5 + - - +
133A ALA 3.9 1.8 - - - +
134A GLU 3.3 0.2 - - - -
135A ALA* 1.3 77.0 - - - +
137A GLN* 1.3 59.1 + - + +
139A LEU* 3.2 8.8 + - + +
140A LYS* 2.9 53.6 + - - +
145A VAL* 3.7 33.6 - - + +
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Residues in contact with GLN 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 ALA 3.1 15.7 + - - +
134A GLU* 4.7 2.0 - - - +
136A TYR* 1.3 74.2 - - + +
138A MET* 1.3 55.8 + - - +
140A LYS* 3.8 28.0 - - + +
141A LYS* 2.6 59.2 + - + +
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Residues in contact with MET 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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95A ILE* 3.9 19.3 - - + -
134A GLU 3.0 19.9 + - - +
135A ALA 3.5 3.4 - - - +
137A GLN* 1.3 76.6 - - - +
139A LEU* 1.3 75.9 + - + +
141A LYS* 3.3 7.2 + - + +
142A GLN* 3.0 60.8 + - + +
10C LEU* 4.0 13.7 - - + -
11C LEU 3.4 20.0 - - - +
12C GLU* 3.2 38.6 - - + +
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Residues in contact with LEU 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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95A ILE* 4.4 17.0 - - + -
98A VAL* 4.1 25.8 - - + -
99A SER* 5.1 0.2 - - - -
116A LEU* 4.1 7.9 - - + -
119A LEU* 3.7 30.1 - - + -
135A ALA* 3.1 17.8 + - + +
136A TYR* 3.2 8.7 + - + +
138A MET* 1.3 86.5 - - + +
140A LYS* 1.3 59.5 + - - +
142A GLN* 3.4 18.1 + - - +
143A GLY 3.3 3.3 + - - -
144A ILE* 2.9 46.7 + - + +
145A VAL* 3.2 14.8 + - + -
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Residues in contact with LYS 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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120A TYR* 6.3 0.6 - - - -
136A TYR* 2.9 44.1 + - - +
137A GLN* 3.6 28.4 - - + +
138A MET 3.2 0.2 - - - -
139A LEU* 1.3 73.5 - - - +
141A LYS* 1.3 66.3 + - - +
143A GLY* 3.1 11.4 + - - -
145A VAL* 3.3 34.3 - - + +
146A LYS* 4.7 15.7 - - + +
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Residues in contact with LYS 141 (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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137A GLN* 2.6 41.3 + - + +
138A MET* 3.7 7.0 - - + +
140A LYS* 1.3 74.7 - - - +
142A GLN* 1.3 58.9 + - + +
143A GLY 3.2 1.0 + - - -
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Residues in contact with GLN 142 (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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95A ILE* 5.8 0.2 - - - +
99A SER* 5.1 2.5 + - - -
101A LYS* 5.4 8.6 - - - +
138A MET* 3.0 55.1 + - + +
139A LEU* 3.4 7.5 + - - +
140A LYS 3.2 0.2 - - - -
141A LYS* 1.3 76.3 - - + +
143A GLY* 1.3 59.5 + - - +
144A ILE* 3.5 28.0 + - + +
12C GLU* 4.4 18.0 + - - +
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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