Contacts of the helix formed by residues 126 - 140 (chain G) in PDB entry 1G3I
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 126 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1G THR 3.2 4.8 + - - -
2G THR* 3.1 26.1 + - - +
125G SER* 1.3 81.4 + - - +
127G GLY* 1.3 64.9 + - - +
128G ASN 3.7 0.4 - - - -
129G TYR* 3.4 25.0 + - - +
130G ALA 3.2 15.1 + - - -
156G ALA* 3.6 1.8 - - - +
160G CYS* 4.0 10.7 - - - -
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Residues in contact with GLY 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 4.5 2.5 - - - -
122G ALA* 3.7 21.2 - - - +
123G ILE 4.2 11.9 - - - -
124G GLY 3.3 12.8 + - - -
125G SER 3.1 7.1 + - - -
126G GLY* 1.3 72.4 - - - +
128G ASN* 1.3 69.3 + - - +
129G TYR 2.8 2.4 + - - -
130G ALA* 2.9 6.1 + - - +
131G LEU* 2.7 21.5 + - - +
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Residues in contact with ASN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G SER 5.0 7.1 + - - -
126G GLY 3.7 0.4 - - - -
127G GLY* 1.3 72.3 - - - +
129G TYR* 1.3 55.4 + - + +
131G LEU* 3.4 17.4 - - - +
132G SER* 2.7 39.7 + - - -
25H THR* 3.5 26.0 + - - +
26H VAL 5.6 1.0 + - - -
129M TYR* 3.2 40.9 + - + -
159M ILE* 4.3 11.9 - - + +
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Residues in contact with TYR 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G SER 4.7 6.5 - - - -
126G GLY* 3.5 25.4 - - - +
127G GLY 2.8 1.6 + - - -
128G ASN* 1.3 82.0 - - + +
130G ALA* 1.3 63.8 + - - +
131G LEU 2.8 0.2 + - - -
132G SER* 2.9 10.5 + - - -
133G ALA* 2.9 13.4 + - - +
156G ALA* 3.7 17.9 - - + -
159G ILE* 3.5 27.8 - - + -
160G CYS* 4.4 9.0 - - + -
128M ASN* 3.5 24.5 + - + -
129M TYR* 3.4 31.9 + + - -
132M SER* 3.6 25.7 - - - +
25R THR* 3.4 21.9 - - + +
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Residues in contact with ALA 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 3.7 26.5 - - + -
4G VAL* 4.0 25.5 - - + +
126G GLY 3.2 0.8 + - - -
127G GLY* 2.9 9.6 + - - +
129G TYR* 1.3 76.7 - - - +
131G LEU* 1.3 56.7 + - - +
133G ALA* 4.3 0.7 - - - -
134G ALA* 2.9 30.0 + - - +
152G SER* 3.3 24.0 - - - +
153G LEU 4.6 0.2 - - - +
156G ALA* 3.5 6.8 - - + +
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Residues in contact with LEU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 4.8 0.7 - - - -
120G ILE* 3.9 25.4 - - + +
121G LEU* 5.5 0.2 - - - -
122G ALA* 4.1 17.4 - - + +
127G GLY 2.7 17.1 + - - +
128G ASN* 3.4 18.8 - - - +
129G TYR 2.8 0.4 + - - -
130G ALA* 1.3 70.1 - - - +
132G SER* 1.3 59.9 + - - +
134G ALA* 2.8 6.6 + - - +
135G ARG* 2.6 90.0 + - + +
26H VAL 5.6 1.8 - - - +
159M ILE* 3.8 14.6 - - + -
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Residues in contact with SER 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ASN 2.7 25.7 + - - -
129G TYR 3.4 3.6 - - - -
131G LEU* 1.3 73.6 - - - +
133G ALA* 1.3 63.2 + - - +
135G ARG* 3.5 4.1 + - - +
136G ALA* 2.9 23.8 + - - +
129M TYR* 3.6 36.6 - - - +
132M SER* 4.0 4.7 - - - -
133M ALA* 4.3 3.0 - - - -
155M ILE* 3.6 21.5 - - - +
159M ILE* 3.5 17.0 - - - +
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Residues in contact with ALA 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G TYR 2.9 10.8 + - - +
130G ALA* 3.5 7.0 - - - +
132G SER* 1.3 76.4 - - - +
134G ALA* 1.3 64.3 + - - +
136G ALA* 2.8 14.7 + - - +
137G LEU* 2.8 16.4 + - - +
152G SER* 3.5 19.7 - - - +
155G ILE* 3.6 33.4 - - + -
132M SER* 3.9 5.8 - - - +
136M ALA* 3.9 11.0 - - + -
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Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 4.5 3.6 - - + -
6G VAL* 4.0 7.4 - - + -
120G ILE* 3.9 23.3 - - + -
130G ALA 2.9 17.9 + - - +
131G LEU* 2.8 9.2 + - - +
133G ALA* 1.3 71.2 - - - +
135G ARG* 1.3 64.3 + - - +
137G LEU 2.9 2.9 + - - -
138G VAL* 2.7 29.1 + - - +
148G ILE* 3.7 15.5 - - + -
152G SER* 3.0 14.1 + - - +
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Residues in contact with ARG 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G GLU* 5.2 8.5 - - - +
118G ASP* 3.7 27.7 + - - -
120G ILE* 3.9 18.3 + - + +
131G LEU* 2.6 67.7 + - + +
132G SER* 3.7 6.7 - - - +
134G ALA* 1.3 71.4 - - - +
136G ALA* 1.3 61.8 + - - +
138G VAL* 3.9 0.7 - - - +
139G GLU* 3.0 44.5 + - - +
26H VAL 4.5 8.7 + - - -
27H MET 5.7 1.6 + - - -
155M ILE* 4.6 14.0 + - + +
158M ASP* 4.2 13.2 + - - +
159M ILE* 3.8 22.0 - - - +
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Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G SER 2.9 13.3 + - - +
133G ALA 2.8 11.0 + - - +
135G ARG* 1.3 77.2 - - - +
137G LEU* 1.3 58.3 + - - +
139G GLU* 5.0 1.6 - - - -
140G ASN* 3.0 39.1 + - - +
133M ALA* 4.1 12.6 - - + +
136M ALA* 3.9 11.7 - - + -
137M LEU* 3.6 24.2 - - + -
155M ILE* 4.7 9.1 - - + +
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ALA 2.8 7.8 + - - +
134G ALA 3.7 4.7 - - - +
136G ALA* 1.3 74.1 - - + +
138G VAL* 1.3 59.4 + - - +
141G THR* 2.6 38.9 - - + +
143G LEU* 4.2 13.0 - - + -
148G ILE* 3.5 24.2 - - + +
151G LYS* 3.7 29.8 - - + -
152G SER* 4.1 14.8 - - - +
155G ILE* 5.2 1.8 - - + -
136M ALA* 3.2 44.4 - - + +
137M LEU* 4.4 3.4 - - + +
140M ASN* 4.1 13.5 - - + +
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Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G VAL* 4.1 13.9 - - + -
8G ARG* 3.4 34.7 + - + +
118G ASP* 4.9 16.4 - - + +
120G ILE* 3.4 25.8 - - + -
134G ALA 2.7 24.5 + - - +
135G ARG 3.9 3.4 - - - +
137G LEU* 1.3 75.1 - - - +
139G GLU* 1.3 67.1 + - + +
140G ASN 3.6 0.2 + - - -
141G THR 3.7 2.9 - - - +
148G ILE* 3.2 22.4 - - + -
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Residues in contact with GLU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ASP* 5.2 9.0 - - + +
135G ARG* 3.0 37.7 + - - +
136G ALA* 4.0 2.4 - - - +
138G VAL* 1.3 81.7 - - + +
140G ASN* 1.3 70.0 + - - +
141G THR 3.7 0.8 + - - -
154M ARG* 6.0 1.7 - - - -
155M ILE* 4.0 20.3 - - - +
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Residues in contact with ASN 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ALA* 3.0 21.5 + - - +
139G GLU* 1.3 92.7 + - - +
141G THR* 1.3 65.4 + - + +
137M LEU* 3.9 29.4 - - + +
141M THR* 4.6 12.7 + - + +
143M LEU* 4.6 18.2 - - + +
151M LYS* 4.5 12.4 - - - +
155M ILE* 5.8 2.0 - - - +
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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