Contacts of the helix formed by residues 129 - 140 (chain I) in PDB entry 1GD2
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 VAL 129 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124I GLN 4.8 1.2 + - - -
125I LEU* 4.1 31.8 - - + +
130I ARG* 1.3 66.0 + - - +
131I GLN 3.4 1.9 - - - +
132I LEU* 3.8 17.9 - - + +
133I GLU* 3.3 26.6 + - + +
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Residues in contact with ARG 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H GLN* 4.5 11.8 + - - +
124I GLN 4.0 11.9 - - - +
125I LEU 3.7 16.5 + - - +
126I ARG 5.0 5.4 - - - +
129I VAL* 1.3 80.2 - - - +
131I GLN* 1.3 60.1 + - + +
133I GLU* 4.6 1.7 - - - +
134I GLU* 3.5 24.1 + - - +
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Residues in contact with GLN 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H GLN* 4.3 16.4 - - - +
129I VAL* 4.4 0.8 - - - +
130I ARG* 1.3 78.0 - - + +
132I LEU* 1.3 58.3 + - - +
134I GLU* 4.2 4.7 - - - +
135I GLU* 3.2 25.2 + - - +
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Residues in contact with LEU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I VAL* 3.8 17.6 - - + -
130I ARG 3.3 0.4 - - - -
131I GLN* 1.3 79.3 - - - +
133I GLU* 1.3 62.2 + - - +
134I GLU 3.3 0.4 - - - -
135I GLU* 3.7 4.3 + - - +
136I LEU* 3.3 23.2 + - - +
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Residues in contact with GLU 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I VAL 3.3 16.5 + - - +
130I ARG* 4.6 2.7 - - - +
132I LEU* 1.3 78.5 - - - +
134I GLU* 1.3 61.3 + - - +
136I LEU* 3.7 5.6 + - - +
137I ARG* 3.4 22.2 + - - +
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Residues in contact with GLU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H GLN* 5.5 4.7 - - - +
130I ARG 3.5 18.6 + - - +
131I GLN* 4.6 4.3 - - - +
132I LEU 3.3 0.4 - - - -
133I GLU* 1.3 77.9 - - - +
135I GLU* 1.3 59.2 + - - +
136I LEU 3.3 0.4 - - - -
137I ARG* 4.0 5.9 - - - +
138I ILE* 3.2 26.5 + - - +
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Residues in contact with GLU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I GLN 3.2 20.5 + - - +
132I LEU* 3.7 5.8 + - - +
134I GLU* 1.3 77.4 - - - +
136I LEU* 1.3 61.5 + - - +
137I ARG 3.4 0.2 - - - -
138I ILE* 3.6 6.8 + - - +
139I LEU* 3.3 23.4 + - - +
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Residues in contact with LEU 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I LEU 3.3 18.6 + - - +
133I GLU* 3.9 7.6 - - - +
134I GLU 3.3 0.2 - - - -
135I GLU* 1.3 78.7 - - - +
137I ARG* 1.3 57.1 + - - +
139I LEU* 3.5 3.7 + - - +
140I LYS* 2.8 33.5 + - - +
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Residues in contact with ARG 137 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133I GLU 3.4 15.0 + - - +
134I GLU* 3.7 6.5 + - - +
136I LEU* 1.3 76.8 - - - +
138I ILE* 1.3 62.6 + - - +
139I LEU 3.2 0.8 + - - -
140I LYS* 3.8 17.6 + - - +
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Residues in contact with ILE 138 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134I GLU 3.2 19.5 + - - +
135I GLU* 3.9 8.3 - - - +
136I LEU 3.3 0.4 - - - -
137I ARG* 1.3 76.5 - - - +
139I LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I GLU 3.3 17.6 + - - +
136I LEU* 3.9 5.4 - - - +
137I ARG 3.2 0.2 - - - -
138I ILE* 1.3 79.8 - - - +
140I LYS* 1.3 62.0 + - + +
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Residues in contact with LYS 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I LEU 2.8 20.4 + - - +
137I ARG* 3.8 13.9 + - - -
138I ILE 5.2 0.2 - - - -
139I LEU* 1.3 81.2 - - - +
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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