Contacts of the helix formed by residues 126 - 137 (chain A) in PDB entry 1GTA
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 LEU 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.0 28.0 - - + -
122A PHE* 3.0 29.5 + - + +
123A LEU* 4.0 23.1 - - + +
125A LYS* 1.3 76.7 - - - +
127A PRO* 1.3 67.7 - - + +
129A MET* 3.1 10.1 + - - -
130A LEU* 2.9 56.1 + - + +
162A VAL* 4.0 23.1 - - + -
169A CYS* 4.2 12.8 - - + -
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Residues in contact with PRO 127 (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 LEU 3.2 20.0 - - - +
124A SER* 3.9 7.9 - - - +
125A LYS 3.5 4.7 - - - -
126A LEU* 1.3 90.0 - - + +
128A GLU* 1.3 55.8 + - - +
130A LEU* 4.1 3.8 - - + -
131A LYS* 2.9 30.1 + - - +
169A CYS* 6.1 1.3 - - + +
173A PHE* 3.6 24.9 - - + -
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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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124A SER 5.4 0.6 + - - +
125A LYS* 2.9 17.6 + - - +
127A PRO* 1.3 76.7 - - - +
129A MET* 1.3 68.9 + - - +
131A LYS* 3.1 41.2 + - - +
132A MET* 3.5 18.7 + - - +
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Residues in contact with MET 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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98A ALA 5.9 0.4 - - - +
101A ASP* 3.9 33.0 - - + +
102A ILE* 3.8 31.9 - - + -
122A PHE* 5.0 9.0 - - + -
125A LYS* 3.8 19.7 - - + +
126A LEU* 3.1 21.5 + - - +
128A GLU* 1.3 85.2 - - - +
130A LEU* 1.3 64.1 + - - +
132A MET* 3.2 34.2 + - + +
133A PHE* 3.6 14.6 - - + -
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Residues in contact with LEU 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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102A ILE* 3.9 17.0 - - + -
126A LEU* 2.9 52.5 + - + +
127A PRO* 3.6 5.2 - - + +
129A MET* 1.3 75.3 - - - +
131A LYS* 1.3 61.9 + - - +
133A PHE* 3.2 8.0 + - + -
134A GLU* 3.0 20.8 + - - +
155A LEU* 5.6 0.4 - - + -
159A LEU* 4.4 17.7 - - + -
162A VAL* 5.1 3.8 - - + -
169A CYS* 3.9 14.8 - - + +
170A LEU* 4.2 10.1 - - + -
173A PHE* 3.7 31.4 - - + -
176A LEU* 3.7 14.2 - - + +
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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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127A PRO 2.9 19.7 + - - +
128A GLU* 3.1 43.2 + - - +
129A MET 3.4 0.2 - - - -
130A LEU* 1.3 69.7 - - - +
132A MET* 1.4 69.0 + - - +
134A GLU* 3.1 4.6 + - + +
135A ASP* 2.9 55.2 + - - +
173A PHE* 3.7 17.2 - - + -
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Residues in contact with MET 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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98A ALA* 4.8 19.7 - - + +
101A ASP* 6.0 1.8 - - - +
128A GLU* 3.5 18.1 + - - +
129A MET* 3.2 30.0 + - + +
131A LYS* 1.4 86.8 - - - +
133A PHE* 1.3 60.6 + - + +
135A ASP* 3.6 7.6 + - - +
136A ARG* 3.1 25.5 + - - +
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Residues in contact with PHE 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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95A LEU* 4.4 10.8 - - + -
98A ALA* 3.6 36.1 - - + -
99A VAL* 3.6 28.7 - - + -
102A ILE* 3.7 28.7 - - + -
129A MET* 3.6 15.9 - - + -
130A LEU* 3.2 8.1 + - + +
132A MET* 1.3 78.7 - - + +
134A GLU* 1.3 66.8 + - - +
136A ARG* 3.0 17.5 + - + +
137A LEU* 3.0 17.0 + - - +
143A LEU* 4.1 26.0 - - + -
155A LEU* 4.2 16.4 - - + -
176A LEU* 3.9 20.0 - - + -
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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
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130A LEU 3.0 13.0 + - - +
131A LYS* 3.5 10.1 - - + +
133A PHE* 1.3 75.4 - - - +
135A ASP* 1.3 68.1 + - - +
137A LEU* 3.3 9.9 + - - +
138A CYS* 3.3 21.1 + - - -
172A ALA 5.1 1.1 - - - +
173A PHE* 3.5 27.7 - - + +
174A PRO* 3.3 14.4 - - - +
175A LYS* 2.8 37.9 + - - +
176A LEU* 3.0 36.6 + - + +
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Residues in contact with ASP 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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131A LYS* 2.9 41.7 + - - +
132A MET* 3.8 6.1 - - - +
134A GLU* 1.3 82.6 - - - +
136A ARG* 1.3 60.2 + - - +
138A CYS* 3.3 23.9 + - - +
139A HIS* 4.7 0.5 + - - -
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Residues in contact with ARG 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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91A GLU* 2.9 29.4 + - - -
94A MET* 5.9 1.4 - - - -
95A LEU* 3.8 20.9 - - + +
132A MET 3.1 15.2 + - - +
133A PHE* 3.0 16.2 + - + +
135A ASP* 1.3 75.3 - - - +
137A LEU* 1.3 61.8 + - - +
138A CYS 3.2 1.0 + - - -
139A HIS 4.0 1.7 + - - -
140A LYS* 3.4 50.9 + - - +
143A LEU* 2.8 40.4 + - + +
144A ASN* 2.9 29.1 + - - +
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Residues in contact with LEU 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 PHE 3.0 11.7 + - - +
134A GLU 3.3 5.1 + - - +
135A ASP 3.2 0.4 - - - -
136A ARG* 1.3 73.8 - - - +
138A CYS* 1.3 64.3 + - - +
139A HIS 3.1 3.6 - - - -
140A LYS* 3.2 25.5 - - + +
141A THR 4.1 7.4 - - - +
142A TYR 3.7 32.5 - - - +
143A LEU* 3.8 20.9 - - + +
155A LEU* 5.1 0.2 - - + -
175A LYS* 3.8 22.3 + - + +
176A LEU* 3.9 23.8 - - + -
179A PHE* 3.8 34.3 - - + -
182A ARG* 5.3 1.6 - - - +
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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