Contacts of the helix formed by residues 144 - 157 (chain A) in PDB entry 1G8I
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 THR 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.6 9.0 + - - -
142A GLU 3.2 0.9 + - - +
143A ASN* 1.3 96.8 + - - +
145A PRO* 1.3 73.1 - - - +
146A GLU* 3.4 17.2 + - - +
147A LYS* 3.1 39.7 + - - +
148A ARG 3.2 9.5 + - - -
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Residues in contact with PRO 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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122A LEU* 3.8 10.5 - - + -
125A VAL* 3.7 13.6 - - + +
126A ASP* 3.8 47.6 - - + +
129A TYR* 3.5 21.3 - - + -
143A ASN 4.6 0.4 - - - +
144A THR* 1.3 86.8 - - - +
146A GLU* 1.3 69.0 + - - +
148A ARG* 3.3 2.5 + - + +
149A VAL* 2.9 33.6 + - - +
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Residues in contact with GLU 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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118A ARG* 3.5 16.0 + - - +
122A LEU* 3.8 27.5 - - + +
144A THR* 3.4 17.0 - - - +
145A PRO* 1.3 90.8 - - - +
147A LYS* 1.3 58.7 + - + +
149A VAL* 3.4 0.8 + - - -
150A ASP* 2.9 34.4 + - - +
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Residues in contact with LYS 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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140A GLU* 2.9 30.3 + - - +
141A GLU* 3.5 24.9 - - - +
142A GLU* 4.4 0.9 - - - -
143A ASN* 2.6 35.6 + - - +
144A THR* 3.1 26.4 + - - +
146A GLU* 1.3 73.5 - - + +
148A ARG* 1.3 65.9 + - - +
150A ASP* 3.5 7.7 + - - +
151A ARG* 3.2 23.0 + - - +
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Residues in contact with ARG 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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125A VAL* 4.0 17.9 - - + -
129A TYR* 3.5 24.2 - - + +
142A GLU* 5.1 12.7 - - + +
144A THR 3.2 5.6 + - - +
145A PRO 3.6 7.6 - - - +
147A LYS* 1.3 76.4 - - - +
149A VAL* 1.3 65.3 + - - +
151A ARG* 3.3 19.5 + - - +
152A ILE* 3.1 55.3 + - - +
155A MET* 5.5 0.6 - - - -
176A ASP* 5.2 6.1 + - - -
178A SER* 5.5 3.0 + - - -
179A ILE* 4.8 14.1 - - - +
951A 1PE 3.6 38.1 + - - -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 3.7 42.6 - - + +
121A MET* 4.0 5.8 - - + -
122A LEU* 3.7 29.6 - - + +
125A VAL* 4.0 19.3 - - + -
145A PRO 2.9 21.6 + - - +
146A GLU* 3.9 4.9 - - - +
148A ARG* 1.3 76.9 - - - +
150A ASP* 1.3 62.2 + - - +
152A ILE* 3.7 4.9 - - - +
153A PHE* 3.0 38.7 + - + -
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Residues in contact with ASP 150 (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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118A ARG* 2.3 42.3 + - - +
146A GLU* 2.9 15.9 + - - +
147A LYS* 3.8 7.7 - - - +
148A ARG 3.3 0.4 - - - -
149A VAL* 1.3 75.5 - - - +
151A ARG* 1.3 59.2 + - - +
153A PHE* 3.4 4.6 + - - +
154A ALA* 2.8 30.9 + - - +
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Residues in contact with ARG 151 (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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141A GLU 6.1 0.4 - - - +
147A LYS 3.2 14.8 + - - +
148A ARG* 3.3 20.4 + - - +
150A ASP* 1.3 80.6 - - - +
152A ILE* 1.3 63.2 + - - +
154A ALA* 3.2 10.9 + - - +
155A MET* 2.9 69.4 + - - +
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Residues in contact with ILE 152 (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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121A MET* 3.5 32.5 - - + -
148A ARG* 3.1 55.0 + - - +
149A VAL 3.7 6.7 - - - +
150A ASP 3.3 0.2 - - - -
151A ARG* 1.3 76.1 - - - +
153A PHE* 1.3 59.8 + - + +
155A MET* 3.2 11.3 + - - -
156A MET* 2.9 61.9 + - + +
164A LEU* 4.5 3.1 - - + -
176A ASP* 5.3 0.4 - - - +
179A ILE* 4.5 4.9 - - + -
951A 1PE 4.1 19.1 - - - +
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Residues in contact with PHE 153 (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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116A ILE* 3.6 13.2 - - + -
117A THR 3.7 1.8 - - - -
118A ARG* 3.5 39.3 - - + +
121A MET* 3.8 26.9 - - + -
149A VAL* 3.0 30.3 + - + +
150A ASP* 4.1 4.0 - - - +
152A ILE* 1.3 76.3 - - + +
154A ALA* 1.3 67.1 + - - +
156A MET* 4.4 1.3 - - - +
157A ASP* 3.0 49.6 + - + +
162A GLY* 3.5 29.2 - - - -
163A LYS 3.9 0.4 - - - -
164A LEU* 3.7 22.7 - - + -
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Residues in contact with ALA 154 (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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150A ASP 2.8 18.8 + - - +
151A ARG* 3.2 15.7 + - - +
153A PHE* 1.3 76.4 - - - +
155A MET* 1.3 62.5 + - + +
157A ASP 4.8 5.5 + - - +
158A LYS* 6.1 0.3 - - - -
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Residues in contact with MET 155 (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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148A ARG* 5.5 1.1 - - - -
151A ARG* 2.9 67.5 + - - +
152A ILE* 3.7 14.4 - - - +
154A ALA* 1.3 79.1 - - - +
156A MET* 1.3 67.9 + - + +
157A ASP 5.5 0.2 - - - -
158A LYS* 4.2 15.8 - - - -
172A GLY* 4.8 9.0 - - - +
175A ALA* 5.8 2.5 - - + -
176A ASP* 3.3 39.0 - - + +
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Residues in contact with MET 156 (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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152A ILE* 2.9 41.1 + - + +
155A MET* 1.3 87.3 - - + +
157A ASP* 1.3 60.5 + - - +
158A LYS* 3.1 15.6 + - - +
164A LEU* 3.9 17.7 - - + -
168A GLU* 3.4 27.3 - - - +
169A PHE* 3.9 22.2 - - - +
172A GLY* 3.5 36.8 - - - +
173A SER* 3.7 7.4 - - - +
176A ASP* 5.5 0.9 - - + +
179A ILE* 3.5 31.9 - - + -
951A 1PE 4.2 5.4 - - - -
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 3.0 27.6 + - + +
154A ALA 4.8 4.6 - - - +
156A MET* 1.3 72.7 - - - +
158A LYS* 1.3 61.4 + - - +
159A ASN* 3.1 8.1 - - - +
160A ALA* 3.5 12.7 + - - +
161A ASP* 3.1 8.1 + - - +
162A GLY* 2.7 32.0 + - - -
163A LYS 3.7 7.0 - - - -
164A LEU* 3.7 14.7 - - + +
168A GLU* 4.0 0.9 - - - -
1599A CA 2.2 33.0 - - - -
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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