Contacts of the helix formed by residues 127 - 141 (chain A) in PDB entry 1GAJ
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TRP* 4.6 15.4 - - + -
125A PRO* 4.8 5.3 - - + +
126A LYS* 1.3 77.0 - - - +
128A GLU* 1.3 55.1 + - - +
129A GLU* 2.7 6.8 + - + +
130A MET* 2.7 57.0 + - + +
131A VAL* 3.0 9.1 + - - -
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Residues in contact with GLU 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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126A LYS 3.4 4.8 + - - -
127A GLU* 1.3 69.5 - - - +
129A GLU* 1.3 62.9 + - - +
131A VAL* 3.9 7.6 - - - +
132A GLU* 3.0 26.0 + - + +
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Residues in contact with GLU 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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127A GLU* 2.7 9.6 + - + +
128A GLU* 1.3 77.0 - - - +
130A MET* 1.3 69.2 + - + +
132A GLU* 3.3 8.2 + - - +
133A LYS* 3.3 18.5 + - - +
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Residues in contact with MET 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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104A LEU* 3.7 14.6 - - + -
107A GLU* 3.8 41.1 - - + +
125A PRO* 3.0 47.1 - - + +
127A GLU* 2.7 47.8 + - + +
129A GLU* 1.3 75.5 - - + +
131A VAL* 1.3 47.7 + - - -
133A LYS* 2.9 17.1 + - - +
134A ALA* 2.8 32.4 + - - +
169A MET* 4.1 2.8 - - - +
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Residues in contact with VAL 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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100A LEU* 4.0 15.7 - - + -
104A LEU* 4.1 13.0 - - + -
126A LYS* 3.6 31.4 - - + +
127A GLU 3.0 15.7 + - - +
128A GLU* 3.9 7.2 - - - +
130A MET* 1.3 77.1 - - - +
132A GLU* 1.3 61.7 + - - +
134A ALA* 3.1 7.5 + - - +
135A PHE* 2.9 49.8 + - + -
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Residues in contact with GLU 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 GLU* 3.0 20.1 + - + +
129A GLU* 3.5 9.2 - - - +
131A VAL* 1.3 75.9 - - - +
133A LYS* 1.3 59.4 + - - +
135A PHE* 3.4 10.4 + - - +
136A LYS* 2.9 57.9 + - - +
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Residues in contact with LYS 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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107A GLU* 2.8 40.6 + - - -
129A GLU 3.3 8.0 + - - +
130A MET* 2.9 12.6 + - - +
132A GLU* 1.3 80.1 - - - +
134A ALA* 1.3 64.1 + - - +
136A LYS* 3.1 9.7 + - + +
137A ILE* 2.9 39.9 + - + +
168A LEU 5.1 0.2 - - - +
169A MET* 3.1 26.5 + - - +
171A ASN* 4.5 22.2 - - - +
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Residues in contact with ALA 134 (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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100A LEU* 3.4 23.3 - - + -
103A LEU* 3.6 12.4 - - + +
104A LEU* 4.2 3.6 - - + -
130A MET 2.8 12.0 + - - +
131A VAL* 3.1 11.9 + - - +
133A LYS* 1.3 76.1 - - - +
135A PHE* 1.3 51.7 + - - +
137A ILE* 3.2 3.6 + - - +
138A LEU* 2.7 40.0 + - - +
169A MET* 3.7 24.8 - - + -
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Residues in contact with PHE 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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100A LEU* 4.0 9.2 - - + -
131A VAL* 2.9 45.5 + - + +
132A GLU* 3.7 11.9 - - - +
134A ALA* 1.3 73.5 - - - +
136A LYS* 1.3 57.8 + - - +
138A LEU* 3.6 10.9 - - + +
139A GLU* 2.7 36.6 + - - +
144A SER* 4.7 13.7 + - - -
147A TYR* 3.6 50.3 - + + -
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Residues in contact with LYS 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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132A GLU* 2.9 45.7 + - - +
133A LYS* 3.1 13.2 + - + +
135A PHE* 1.3 76.0 - - - +
137A ILE* 1.3 58.8 + - + +
139A GLU* 3.2 21.1 - - - +
140A PHE* 3.0 25.3 + - - +
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Residues in contact with ILE 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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103A LEU* 3.9 5.2 - - + -
133A LYS* 2.9 27.1 + - + +
134A ALA 3.5 5.4 - - - +
136A LYS* 1.3 74.2 - - + +
138A LEU* 1.3 68.0 + - - +
139A GLU 2.9 1.6 - - - -
140A PHE* 2.9 8.5 + - + +
141A LEU* 2.8 26.1 + - + +
165A GLY* 3.8 28.9 - - - +
168A LEU* 3.8 26.9 - - + +
169A MET* 3.7 45.5 - - + +
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Residues in contact with LEU 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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99A VAL* 3.6 26.7 - - + -
100A LEU* 4.1 18.8 - - + -
103A LEU* 4.0 19.1 - - + -
134A ALA 2.7 23.8 + - - +
135A PHE* 3.7 11.0 - - + +
137A ILE* 1.3 72.1 - - - +
139A GLU* 1.3 56.4 + - - +
141A LEU* 3.4 4.8 + - + +
142A LYS 2.9 7.1 + - - -
143A LEU* 2.7 49.5 + - + +
144A SER* 3.9 16.6 - - - +
147A TYR* 3.6 35.2 - - + -
162A VAL* 5.8 0.4 - - + -
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Residues in contact with GLU 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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135A PHE 2.7 18.1 + - - +
136A LYS* 3.2 21.8 - - - +
138A LEU* 1.3 74.8 - - - +
140A PHE* 1.3 60.4 + - - +
142A LYS* 2.7 28.4 + - - +
144A SER* 3.7 13.4 + - - +
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Residues in contact with PHE 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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136A LYS 3.0 13.1 + - - +
137A ILE* 2.9 11.0 + - + +
139A GLU* 1.3 76.7 - - - +
141A LEU* 1.3 84.4 + - + +
142A LYS* 3.2 7.8 + - - +
168A LEU* 4.9 7.0 - - + -
195A HIS* 3.8 16.8 + + - -
198A GLU* 3.1 48.2 - - + +
199A LEU* 3.9 28.0 - - + -
202A LYS* 3.0 38.4 - - - +
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Residues in contact with LEU 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 ILE* 2.8 27.8 + - + +
138A LEU* 3.9 5.8 - - + +
140A PHE* 1.3 94.1 - - + +
142A LYS* 1.3 70.5 + - - +
143A LEU* 3.7 27.1 - - + +
161A LEU* 3.4 42.0 - - + +
162A VAL* 5.1 0.4 - - - -
164A ILE* 4.7 4.5 - - + -
165A GLY* 3.7 23.6 - - - +
168A LEU* 4.5 8.3 - - + -
195A HIS* 3.4 30.6 + - + -
199A LEU* 5.5 0.4 - - + -
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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