Contacts of the helix formed by residues 126 - 140 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J THR* 3.1 29.2 + - - +
125J SER* 1.3 80.2 + - - +
127J GLY* 1.3 66.7 + - - +
128J ASN 3.7 0.4 - - - -
129J TYR* 3.4 25.9 - - - +
130J ALA 3.2 14.6 + - - -
156J ALA* 3.4 2.3 - - - +
160J CYS* 4.1 9.1 - - - -
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Residues in contact with GLY 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 4.1 3.6 - - - +
122J ALA* 3.9 18.2 - - - +
123J ILE* 3.9 15.9 - - - -
124J GLY 3.2 12.3 + - - -
125J SER 3.1 5.9 - - - -
126J GLY* 1.3 73.2 - - - +
128J ASN* 1.3 68.7 + - - +
129J TYR 2.7 2.1 + - - -
130J ALA* 2.8 6.2 + - - +
131J LEU 2.8 18.5 + - - -
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Residues in contact with ASN 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 4.8 0.8 + - - +
125J SER 4.9 7.7 + - - -
126J GLY 3.7 0.2 - - - -
127J GLY* 1.3 72.0 - - - +
129J TYR* 1.3 54.1 + - + +
131J LEU* 3.1 16.3 - - - +
132J SER* 2.6 39.7 + - - -
25K THR* 3.5 38.4 + - - +
26K VAL 5.4 2.9 - - - +
129P TYR* 3.3 27.8 + - + -
159P ILE* 4.2 11.2 - - + +
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Residues in contact with TYR 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J SER 4.6 5.2 - - - -
126J GLY* 3.4 27.6 - - - +
127J GLY 2.7 4.2 + - - -
128J ASN* 1.3 75.7 - - + +
130J ALA* 1.3 67.0 + - - +
131J LEU 2.7 1.7 + - - -
132J SER* 2.8 10.5 + - - -
133J ALA* 2.9 12.7 + - - +
156J ALA* 3.7 18.4 - - + -
159J ILE* 3.6 28.5 - - + -
160J CYS* 4.4 9.9 - - + -
25O THR* 3.3 22.8 - - + +
128P ASN* 3.4 28.2 + - + -
129P TYR* 3.6 28.7 + + - -
132P SER* 3.7 22.2 - - - +
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Residues in contact with ALA 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 3.7 25.6 - - + -
4J VAL* 4.0 25.6 - - + +
126J GLY 3.2 1.2 + - - -
127J GLY 2.8 10.5 + - - +
129J TYR* 1.3 76.5 - - - +
131J LEU* 1.3 56.0 + - - +
133J ALA* 3.9 0.7 - - - -
134J ALA* 2.9 26.7 + - - +
152J SER* 3.1 35.1 - - - +
153J LEU 4.6 0.2 - - - +
156J ALA* 3.4 2.3 - - + +
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Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J VAL* 4.9 0.7 - - - -
120J ILE* 3.9 25.8 - - + +
122J ALA* 4.1 18.6 - - + +
127J GLY 2.8 11.2 + - - +
128J ASN* 3.1 19.7 - - - +
129J TYR 2.7 3.6 + - - -
130J ALA* 1.3 70.1 - - - +
132J SER* 1.3 67.9 - - - +
134J ALA* 2.7 7.8 + - - +
135J ARG* 2.7 76.1 + - + +
26K VAL 5.4 3.6 - - - +
159P ILE* 3.8 15.3 - - + -
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Residues in contact with SER 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J ASN 2.6 25.2 + - - -
129J TYR 3.3 3.6 - - - -
131J LEU* 1.3 73.3 - - - +
133J ALA* 1.3 63.4 + - - +
135J ARG* 3.5 4.5 + - - +
136J ALA* 3.0 23.2 + - - +
129P TYR* 3.6 37.6 - - - +
132P SER* 3.9 6.3 - - - -
133P ALA* 4.3 3.0 - - - -
155P ILE* 3.7 19.1 - - - +
159P ILE* 3.6 16.6 - - - +
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Residues in contact with ALA 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J TYR 2.9 10.1 + - - +
130J ALA* 3.5 2.9 - - - +
131J LEU 2.9 0.2 + - - -
132J SER* 1.3 75.9 - - - +
134J ALA* 1.3 54.8 + - - +
136J ALA* 2.8 24.8 + - - +
137J LEU* 2.8 16.1 + - + +
152J SER* 3.2 25.8 - - - +
155J ILE* 3.5 31.2 - - + -
132P SER* 4.0 5.1 - - - +
136P ALA* 3.9 11.0 - - - -
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Residues in contact with ALA 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J VAL* 4.6 3.6 - - + -
6J VAL* 3.9 17.7 - - + -
120J ILE* 3.9 12.8 - - + -
130J ALA 2.9 14.1 + - - +
131J LEU* 2.7 7.8 + - - +
133J ALA* 1.3 70.3 - - - +
135J ARG* 1.3 54.1 + - - +
137J LEU 3.1 1.2 + - - -
138J VAL* 2.7 40.2 + - - +
148J ILE* 3.5 19.1 - - + -
149J VAL* 6.3 0.2 - - - -
152J SER* 2.9 17.6 + - - +
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Residues in contact with ARG 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J GLU* 4.8 10.7 - - - +
118J ASP* 3.5 28.7 + - - -
120J ILE* 3.9 17.8 + - + +
131J LEU* 2.7 64.5 + - + +
132J SER* 3.7 7.4 - - - +
134J ALA* 1.3 72.1 - - - +
136J ALA* 1.3 61.3 + - - +
138J VAL* 4.0 0.3 - - - +
139J GLU* 3.1 43.9 + - - +
26K VAL 4.5 8.7 + - - -
27K MET 5.5 3.4 + - - -
155P ILE* 4.6 14.9 + - + +
158P ASP* 4.3 13.3 + - - +
159P ILE* 4.0 19.8 - - - +
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Residues in contact with ALA 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER 3.0 12.9 + - - +
133J ALA 2.8 10.3 + - - +
135J ARG* 1.3 77.6 - - - +
137J LEU* 1.3 58.6 + - - +
138J VAL 3.2 0.3 + - - -
139J GLU* 3.3 2.4 + - - -
140J ASN* 2.9 38.7 + - - +
133P ALA* 4.1 12.6 - - + +
136P ALA* 3.9 11.9 - - + -
137P LEU* 3.6 25.6 - - + -
155P ILE* 4.7 8.9 - - + +
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Residues in contact with LEU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ALA* 2.8 8.5 + - + +
134J ALA 3.8 3.6 - - - +
136J ALA* 1.3 73.5 - - + +
138J VAL* 1.3 61.2 + - - +
141J THR* 2.8 38.0 - - + +
143J LEU* 4.3 14.3 - - + +
148J ILE* 3.6 32.4 - - + +
151J LYS* 3.6 31.4 - - + -
152J SER* 4.2 7.9 - - - +
155J ILE* 5.3 1.6 - - + -
136P ALA* 3.2 44.9 - - + +
137P LEU* 4.4 2.5 - - + +
140P ASN* 4.3 11.7 - - + +
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Residues in contact with VAL 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J VAL* 4.0 13.9 - - + -
8J ARG* 3.4 33.3 + - + +
118J ASP* 5.0 13.7 - - + +
120J ILE* 3.6 26.2 - - + -
134J ALA 2.7 25.2 + - - +
135J ARG 4.0 2.0 - - - +
137J LEU* 1.3 75.6 - - - +
139J GLU* 1.3 65.7 + - + +
141J THR 3.8 3.1 + - - +
148J ILE* 3.2 23.6 - - + -
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Residues in contact with GLU 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J ASP* 5.2 8.6 - - + +
135J ARG* 3.1 35.5 + - - +
136J ALA* 4.0 1.7 - - - +
138J VAL* 1.3 83.2 - - + +
140J ASN* 1.3 70.8 + - - +
141J THR 3.7 0.7 + - - -
154P ARG* 6.0 1.9 - - - -
155P ILE* 4.0 21.1 - - - +
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Residues in contact with ASN 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J ALA* 2.9 21.5 + - - +
139J GLU* 1.3 92.3 + - - +
141J THR* 1.3 67.7 + - + +
137P LEU* 3.8 31.7 - - + +
141P THR* 4.4 13.4 + - + -
143P LEU* 4.5 17.3 - - + +
151P LYS* 4.5 11.6 - - - +
155P ILE* 5.8 2.4 - - - +
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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