Contacts of the helix formed by residues 126 - 140 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2K THR* 3.3 29.9 + - - +
124K GLY 3.4 0.4 - - - -
125K SER* 1.3 80.7 + - - +
127K GLY* 1.3 63.3 + - - +
128K ASN 3.6 1.3 - - - -
129K TYR* 3.4 26.4 + - - +
130K ALA 3.1 17.2 + - - -
156K ALA* 3.5 1.5 - - - +
160K CYS* 4.2 9.1 - - - -
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Residues in contact with GLY 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 4.3 3.8 + - - +
122K ALA* 3.6 17.1 - - - +
123K ILE* 4.1 15.0 - - - -
124K GLY 3.3 11.9 + - - -
125K SER 3.1 5.7 - - - -
126K GLY* 1.3 73.5 - - - +
128K ASN* 1.3 56.3 + - - +
129K TYR 2.9 2.7 + - - -
130K ALA* 3.0 5.2 + - - +
131K LEU* 2.6 34.0 + - - +
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Residues in contact with ASN 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K GLY 5.5 2.0 + - - -
125K SER 4.8 8.7 + - - -
127K GLY* 1.3 73.5 - - - +
129K TYR* 1.3 55.3 + - + +
131K LEU* 3.1 16.1 - - - +
132K SER* 2.6 40.1 + - - -
25L THR* 3.7 26.8 + - - +
26L VAL 5.5 3.3 + - - +
129Q TYR* 3.4 37.5 + - + -
159Q ILE* 4.3 10.9 - - + +
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Residues in contact with TYR 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K SER 4.6 5.8 + - - -
126K GLY* 3.5 25.4 - - - +
127K GLY 2.9 1.6 + - - -
128K ASN* 1.3 79.1 - - + +
130K ALA* 1.3 67.3 + - - +
131K LEU 2.6 2.3 + - - -
132K SER* 2.8 10.0 + - - -
133K ALA* 2.9 12.4 + - - +
156K ALA* 3.8 17.0 - - + -
159K ILE* 3.6 26.7 - - + -
160K CYS* 4.4 9.0 - - + -
25P THR* 3.1 27.9 - - + +
128Q ASN* 3.5 21.9 + - + -
129Q TYR* 3.5 32.8 + + - -
132Q SER* 3.7 27.2 - - - +
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Residues in contact with ALA 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 3.6 27.6 - - + -
4K VAL* 4.0 24.6 - - + +
126K GLY 3.1 1.6 + - - -
127K GLY* 3.0 8.0 + - - +
129K TYR* 1.3 77.2 - - - +
131K LEU* 1.3 56.2 + - - +
133K ALA* 4.3 0.7 - - - -
134K ALA* 2.8 27.6 + - - +
152K SER* 3.2 29.1 - - - +
156K ALA* 3.4 6.0 - - + +
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Residues in contact with LEU 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K VAL* 4.9 0.7 - - - -
120K ILE* 3.8 25.4 - - + +
122K ALA* 4.0 17.9 - - + +
127K GLY 2.6 15.2 + - - +
128K ASN* 3.1 20.4 - - - +
129K TYR 2.6 3.8 + - - -
130K ALA* 1.3 67.9 - - - +
132K SER* 1.3 69.6 + - - +
134K ALA* 2.7 16.9 + - - +
135K ARG* 2.7 66.6 + - + +
26L VAL 5.4 3.1 - - - +
159Q ILE* 3.8 14.8 - - + -
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Residues in contact with SER 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K ASN 2.6 21.4 + - - -
129K TYR 2.8 3.5 + - - -
131K LEU* 1.3 73.7 - - - +
133K ALA* 1.3 67.6 + - - +
135K ARG* 3.2 5.1 + - - +
136K ALA* 2.9 20.8 + - - +
129Q TYR* 3.7 30.0 - - - +
132Q SER* 4.1 6.1 - - - -
133Q ALA* 4.4 2.9 - - - -
155Q ILE* 3.5 26.4 - - - +
159Q ILE* 3.5 17.3 - - - +
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Residues in contact with ALA 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K TYR 2.9 9.9 + - - +
130K ALA* 3.5 6.5 - - - +
131K LEU 2.9 0.4 + - - -
132K SER* 1.3 75.2 - - - +
134K ALA* 1.3 63.5 + - - +
136K ALA* 2.9 15.3 + - - +
137K LEU* 2.9 17.1 + - - +
152K SER* 3.3 19.1 - - - +
155K ILE* 3.5 35.2 - - + -
132Q SER* 4.0 5.9 - - - +
136Q ALA* 4.0 11.2 - - + -
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Residues in contact with ALA 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K VAL* 4.5 3.6 - - + -
6K VAL* 3.9 8.3 - - + -
120K ILE* 3.9 22.7 - - + -
130K ALA 2.8 17.0 + - - +
131K LEU* 2.7 8.9 + - - +
133K ALA* 1.3 70.1 - - - +
135K ARG* 1.3 57.6 + - - +
137K LEU* 3.2 2.1 + - - +
138K VAL* 2.8 35.9 + - - +
148K ILE* 3.6 17.7 - - + -
152K SER* 2.9 14.5 + - - +
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Residues in contact with ARG 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K GLU* 4.9 8.9 - - - +
118K ASP* 3.6 29.1 + - - -
120K ILE* 3.9 18.3 + - + +
131K LEU* 2.7 62.5 + - + +
132K SER* 3.5 9.6 - - - +
134K ALA* 1.3 71.5 - - - +
136K ALA* 1.3 57.1 + - - +
138K VAL* 3.2 0.9 + - - +
139K GLU* 2.9 51.9 + - - +
26L VAL 4.5 8.3 + - - -
27L MET 5.4 3.8 + - - -
155Q ILE* 4.7 12.9 + - + +
158Q ASP* 4.4 12.7 + - - +
159Q ILE* 4.0 20.2 - - - +
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Residues in contact with ALA 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K SER 2.9 11.3 + - - +
133K ALA 2.9 11.0 + - - +
135K ARG* 1.3 77.0 - - - +
137K LEU* 1.3 61.8 + - + +
139K GLU* 3.2 3.3 + - - -
140K ASN* 2.9 39.5 + - - +
133Q ALA* 4.2 13.2 - - + +
136Q ALA* 4.0 7.6 - - + -
137Q LEU* 3.6 25.6 - - + -
155Q ILE* 4.7 9.5 - - + +
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Residues in contact with LEU 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ALA* 2.9 6.5 + - + +
134K ALA 3.8 4.5 - - - +
136K ALA* 1.3 77.7 - - + +
138K VAL* 1.3 59.6 + - - +
141K THR* 2.5 38.0 - - + +
143K LEU* 4.3 13.9 - - + -
148K ILE* 3.6 37.7 - - + +
151K LYS* 3.9 28.0 - - + -
152K SER* 4.1 9.0 - - - +
155K ILE* 5.3 0.9 - - + -
136Q ALA* 3.2 44.0 - - + +
137Q LEU* 4.5 3.4 - - + +
140Q ASN* 4.4 10.1 - - + +
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Residues in contact with VAL 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 4.1 13.2 - - + -
7K ARG 6.0 0.4 - - - +
8K ARG* 3.5 34.7 + - + +
118K ASP* 4.9 15.0 - - + +
120K ILE* 3.4 25.6 - - + -
134K ALA 2.8 26.4 + - - +
135K ARG 3.8 3.1 - - - +
137K LEU* 1.3 79.2 - - - +
139K GLU* 1.3 66.8 + - + +
140K ASN 3.6 0.2 + - - -
141K THR 3.7 3.5 + - - +
148K ILE* 3.2 22.2 - - + -
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Residues in contact with GLU 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K ASP* 5.3 7.9 - - + +
135K ARG* 2.9 37.0 + - - +
136K ALA* 4.0 2.5 - - - +
138K VAL* 1.3 80.7 - - + +
140K ASN* 1.3 70.8 + - - +
141K THR 3.7 0.8 + - - -
154Q ARG* 5.9 2.6 - - - -
155Q ILE* 4.0 20.6 - - - +
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Residues in contact with ASN 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K ALA* 2.9 20.9 + - - +
139K GLU* 1.3 90.7 + - - +
141K THR* 1.3 65.7 + - + +
137Q LEU* 3.8 30.9 - - + +
141Q THR* 4.5 13.7 + - - +
143Q LEU* 4.5 17.8 - - + +
151Q LYS* 4.5 11.8 - - - +
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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