Contacts of the helix formed by residues 137 - 149 (chain A) in PDB entry 1GZQ
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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP 3.8 9.0 + - - -
123A PHE* 4.3 11.5 - - - -
134A SER 2.6 16.0 + - - -
136A GLU* 1.3 81.0 - - - +
138A GLY* 1.3 60.0 + - - +
140A ARG* 3.4 12.3 + - - +
141A ALA* 2.9 34.9 + - - -
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Residues in contact with GLY 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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134A SER 3.8 1.9 + - - +
135A PRO* 3.3 11.1 + - - +
136A GLU 3.3 4.2 + - - -
137A GLY* 1.3 81.9 - - - +
139A SER* 1.3 63.0 + - - -
141A ALA* 3.9 1.2 - - - +
142A GLN* 3.5 24.7 + - - +
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Residues in contact with SER 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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138A GLY* 1.3 70.3 - - - -
140A ARG* 1.3 74.1 + - - +
142A GLN* 3.1 15.4 + - - +
143A LYS* 2.8 26.5 + - - +
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Residues in contact with ARG 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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88A PHE* 3.5 32.5 + - + +
89A GLN* 2.5 34.5 + - - +
90A MET* 3.6 27.5 - - - +
91A LYS* 4.9 4.4 - - - +
118A LEU* 4.0 20.8 - - - +
123A PHE* 3.8 19.3 - - + -
137A GLY 3.4 9.0 - - - +
139A SER* 1.3 85.5 + - - +
141A ALA* 1.3 53.5 + - - +
143A LYS* 3.1 5.1 + - - +
144A PHE* 2.8 35.3 + - - +
1284A D12 6.4 0.2 - - - -
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Residues in contact with ALA 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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123A PHE* 3.2 42.4 - - + +
124A LEU* 5.4 0.2 - - + -
133A PRO* 3.7 14.9 - - + +
134A SER 4.0 2.0 - - - +
137A GLY* 2.9 31.9 + - - +
138A GLY 3.9 1.3 - - - +
140A ARG* 1.3 72.9 - - - +
142A GLN* 1.3 58.0 + - - +
144A PHE* 3.9 0.7 - - - +
145A CYS* 3.0 33.8 + - - +
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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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133A PRO* 3.9 21.8 - - + -
138A GLY 3.5 17.7 + - - +
139A SER* 3.1 15.3 + - - +
141A ALA* 1.3 76.9 - - - +
143A LYS* 1.3 58.2 + - - +
145A CYS* 4.0 0.5 - - - +
146A ALA* 2.9 33.1 + - - +
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Residues in contact with LYS 143 (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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87A ASP* 2.7 44.0 + - - +
88A PHE* 3.9 25.6 - - + -
139A SER* 2.8 18.1 + - - +
140A ARG* 3.5 5.2 - - - +
142A GLN* 1.3 76.2 - - - +
144A PHE* 1.3 60.6 + - - +
146A ALA* 3.7 4.9 - - - +
147A LEU* 2.8 36.6 + - + +
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Residues in contact with PHE 144 (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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77A PHE* 5.8 2.5 - + - -
88A PHE* 3.7 14.9 - + + -
123A PHE* 3.8 14.6 - + + -
124A LEU* 3.6 31.6 - - + -
140A ARG 2.8 19.8 + - - +
141A ALA 3.9 0.2 - - - +
143A LYS* 1.3 69.9 - - - +
145A CYS* 1.3 61.3 + - - +
147A LEU* 3.0 4.0 + - - +
148A ILE* 2.7 58.7 + - + +
1280A PII 4.0 29.4 - - + -
1284A D12 3.5 46.0 - - + -
1285A TWT 4.1 24.5 - - + -
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Residues in contact with CYS 145 (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 LEU* 4.3 8.7 - - - -
131A CYS* 2.0 66.2 - - + +
132A VAL 3.9 1.8 - - - -
133A PRO* 3.5 28.5 - - + -
141A ALA 3.0 15.4 + - - +
142A GLN 4.0 0.4 - - - +
144A PHE* 1.3 76.0 - - - +
146A ALA* 1.3 65.0 + - - +
147A LEU 3.1 0.7 + - - -
148A ILE* 3.4 0.6 - - - +
149A ILE* 3.2 31.7 + - - +
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Residues in contact with ALA 146 (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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142A GLN 2.9 21.0 + - - +
143A LYS* 3.7 6.5 - - - +
145A CYS* 1.3 75.9 - - - +
147A LEU* 1.3 59.2 + - - +
149A ILE* 3.1 27.8 - - - +
150A GLN* 3.8 10.4 - - - +
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Residues in contact with LEU 147 (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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84A PHE* 3.7 27.8 - - + -
88A PHE* 4.0 23.8 - - + -
143A LYS* 2.8 23.2 + - + +
144A PHE* 3.3 4.0 - - + +
146A ALA* 1.3 75.2 - - - +
148A ILE* 1.3 68.1 + - - +
150A GLN* 3.0 35.9 + - - +
151A TYR* 3.4 31.1 - - + +
1284A D12 4.2 13.0 - - + -
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Residues in contact with ILE 148 (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 CYS* 3.9 10.8 - - - -
144A PHE* 2.7 41.4 + - + +
145A CYS* 3.4 17.3 - - - +
147A LEU* 1.3 74.5 - - - +
149A ILE* 1.3 70.4 + - + +
151A TYR* 3.0 28.7 + - + +
154A ILE* 3.8 25.1 - - + -
155A MET* 3.9 5.2 - - - +
1280A PII 4.0 39.5 - - + -
1284A D12 4.1 21.3 - - + +
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Residues in contact with ILE 149 (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 SER* 6.0 0.2 - - - -
131A CYS* 3.9 22.0 - - + +
145A CYS 3.2 13.7 - - - +
146A ALA* 3.1 30.1 - - - +
148A ILE* 1.3 78.8 - - + +
150A GLN* 1.3 62.7 + - + +
151A TYR 3.1 3.2 + - - -
152A GLN* 4.8 4.9 + - - +
155A MET* 3.7 36.5 - - + +
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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