Contacts of the helix formed by residues 126 - 141 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1R THR 3.2 5.3 + - - -
2R THR* 3.3 26.3 + - - +
125R SER* 1.3 81.7 + - - +
127R GLY* 1.3 68.4 + - - +
128R ASN 3.8 0.2 - - - -
129R TYR* 3.2 29.9 + - - +
130R ALA 3.2 7.6 + - - -
156R ALA* 3.9 0.8 - - - +
160R CYS* 4.0 10.4 - - - -
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Residues in contact with GLY 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR* 4.2 2.6 - - - +
122R ALA* 4.1 16.8 - - - +
123R ILE* 4.2 14.4 - - - -
124R GLY 3.2 12.6 + - - -
125R SER 2.9 9.9 + - - -
126R GLY* 1.3 78.9 - - - +
128R ASN* 1.3 55.5 + - - -
129R TYR 2.5 15.3 + - - -
130R ALA* 2.7 12.1 + - - +
131R LEU 2.9 7.9 + - - -
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Residues in contact with ASN 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L TYR* 3.5 25.3 + - + -
159L ILE* 4.0 15.8 - - + +
25Q THR* 3.7 32.2 + - - +
26Q VAL 5.1 3.3 - - - +
27Q MET* 6.1 0.3 - - - -
122R ALA* 4.9 0.6 + - - +
124R GLY 5.7 1.0 + - - -
125R SER 4.9 5.7 + - - -
126R GLY 3.8 0.2 - - - -
127R GLY* 1.3 71.9 - - - +
129R TYR* 1.3 52.9 + - + +
131R LEU* 3.5 20.3 - - - +
132R SER* 2.7 40.9 + - - -
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Residues in contact with TYR 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G THR* 3.1 24.8 - - + +
128L ASN* 3.4 25.0 + - + -
129L TYR* 3.4 33.5 + + - -
132L SER* 3.6 22.6 - - - +
125R SER 4.7 5.2 - - - -
126R GLY* 3.3 27.4 - - - +
127R GLY 2.5 6.1 + - - -
128R ASN* 1.3 76.7 - - + +
130R ALA* 1.3 63.9 + - - +
132R SER* 3.0 3.4 + - - -
133R ALA* 3.0 17.9 + - - +
155R ILE* 5.0 1.1 - - - -
156R ALA* 4.0 14.6 - - + -
159R ILE* 3.6 30.7 - - + -
160R CYS* 4.3 12.6 - - + -
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Residues in contact with ALA 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR* 3.8 23.1 - - + -
4R VAL* 3.9 26.0 - - + -
122R ALA* 4.9 1.1 - - + -
126R GLY 3.2 0.8 + - - -
127R GLY 2.7 11.4 + - - +
129R TYR* 1.3 76.1 - - - +
131R LEU* 1.3 55.7 + - - +
133R ALA* 3.2 4.2 + - - +
134R ALA* 2.8 30.6 + - - +
152R SER* 3.5 27.7 + - - +
153R LEU* 4.7 0.2 - - + -
156R ALA* 3.7 2.1 - - + +
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Residues in contact with LEU 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159L ILE* 4.1 13.7 - - + -
26Q VAL 5.2 4.9 - - - +
27Q MET* 6.1 1.3 - - - +
4R VAL* 4.9 1.1 - - - -
120R ILE* 4.2 22.2 - - + +
122R ALA* 4.0 20.3 - - + +
127R GLY 2.9 5.1 + - - +
128R ASN* 3.5 25.6 - - - +
130R ALA* 1.3 78.3 - - - +
132R SER* 1.3 65.9 + - - +
134R ALA* 3.0 6.0 + - - +
135R ARG* 2.9 76.2 + - + +
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Residues in contact with SER 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L TYR* 3.8 28.9 - - - +
132L SER* 4.0 4.3 - - - -
133L ALA* 4.1 3.2 - - - -
155L ILE* 3.7 26.5 - - - +
159L ILE* 2.9 21.5 - - - +
128R ASN 2.7 27.9 + - - -
129R TYR 3.6 3.1 - - - -
131R LEU* 1.3 73.8 - - - +
133R ALA* 1.3 56.9 + - - +
135R ARG* 4.6 0.9 - - - -
136R ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L SER* 4.4 5.1 - - - +
136L ALA* 4.4 8.5 - - + -
129R TYR 3.0 11.9 + - - +
130R ALA* 3.3 9.0 - - - +
132R SER* 1.3 74.4 - - - +
134R ALA* 1.3 71.3 + - - +
136R ALA* 2.9 10.0 + - - +
137R LEU* 2.8 22.1 + - + +
152R SER* 3.5 22.2 - - - +
155R ILE* 4.1 24.9 - - + -
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Residues in contact with ALA 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R VAL* 4.5 2.5 - - + -
6R VAL* 4.1 11.9 - - + -
120R ILE* 3.4 32.8 - - + -
130R ALA 2.8 16.5 + - - +
131R LEU* 3.3 8.1 - - - +
133R ALA* 1.3 69.2 - - - +
135R ARG* 1.3 56.7 + - - +
137R LEU* 2.4 27.7 + - - -
138R VAL* 2.8 14.4 + - - -
148R ILE* 4.0 6.5 - - - -
152R SER* 2.9 16.3 + - - +
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Residues in contact with ARG 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155L ILE* 4.7 16.4 + - + +
158L ASP* 4.5 15.4 + - - +
159L ILE* 3.7 23.0 - - - +
26Q VAL 4.6 10.1 + - - -
27Q MET 4.8 8.9 + - - -
28Q LYS* 5.9 1.4 - - - +
116R GLU* 6.2 2.8 - - - +
118R ASP* 4.2 16.7 + - - +
120R ILE* 3.5 20.0 + - + +
131R LEU* 2.9 55.1 + - + +
132R SER* 4.0 4.3 - - - +
134R ALA* 1.3 75.0 - - - +
136R ALA* 1.3 64.8 + - - +
139R GLU* 3.0 49.2 + - - +
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Residues in contact with ALA 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L ALA* 4.0 8.3 - - - +
136L ALA* 4.1 2.2 - - + -
137L LEU* 3.2 28.7 - - + +
155L ILE* 3.6 19.0 - - + +
132R SER 3.0 17.3 + - - +
133R ALA* 2.9 17.0 + - - +
135R ARG* 1.3 78.9 - - - +
137R LEU* 1.3 62.1 + - - +
139R GLU* 5.2 0.2 - - - -
140R ASN* 3.2 27.2 + - - +
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Residues in contact with LEU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L ALA* 3.6 33.4 - - + +
137L LEU* 4.7 2.0 - - + -
140L ASN* 3.9 20.2 - - + +
133R ALA 2.8 10.3 + - - +
134R ALA 2.4 13.5 + - - +
136R ALA* 1.3 69.3 - - - +
138R VAL* 1.3 68.9 + - - +
139R GLU 2.7 4.2 + - - -
140R ASN* 2.7 14.3 + - - -
141R THR* 2.9 29.4 - - + +
143R LEU* 4.1 8.7 - - + -
148R ILE* 3.7 29.8 - - + -
151R LYS* 4.0 27.6 - - + -
152R SER* 4.1 7.0 - - - +
155R ILE* 6.4 0.2 - - + -
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Residues in contact with VAL 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R VAL* 3.4 25.4 - - + -
8R ARG* 3.9 29.2 + - + +
118R ASP* 4.7 14.1 - - + +
120R ILE* 3.7 24.9 - - + -
134R ALA 2.8 13.6 + - - +
135R ARG* 4.2 1.3 - - - +
137R LEU* 1.3 72.3 - - - +
139R GLU* 1.3 65.0 + - + +
141R THR 3.6 10.6 - - - +
148R ILE* 3.1 27.3 - - + +
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Residues in contact with GLU 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ILE* 5.0 10.4 - - - +
118R ASP* 4.7 11.9 - - + +
135R ARG* 3.0 41.6 + - - +
137R LEU 2.7 5.3 + - - -
138R VAL* 1.3 82.2 - - + +
140R ASN* 1.3 71.1 + - - +
141R THR 3.7 0.2 - - - -
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Residues in contact with ASN 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L LEU* 4.4 10.7 - - + +
141L THR* 5.1 10.0 - - + -
143L LEU* 4.4 15.2 - - + +
151L LYS* 3.0 49.9 + - - +
155L ILE* 5.7 1.2 - - - +
136R ALA* 3.2 24.8 + - - +
137R LEU 2.7 9.5 + - - -
139R GLU* 1.3 89.2 + - - +
141R THR* 1.3 60.1 + - - -
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Residues in contact with THR 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L ASN* 4.6 13.1 + - - -
141L THR* 6.1 0.7 - - - -
8R ARG* 2.7 26.5 + - - -
137R LEU* 2.9 43.9 + - + +
138R VAL 3.6 6.3 - - - +
139R GLU 3.7 1.0 - - - -
140R ASN* 1.3 81.9 - - - +
142R GLU* 1.3 69.6 + - - +
143R LEU* 3.2 41.2 - - + +
148R ILE* 4.7 0.2 - - + -
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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
------------------------------------------------------------
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