Contacts of the helix formed by residues 145 - 154 (chain B) in PDB entry 3GBN
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 ASP 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.5 2.7 - - - -
30B GLN* 3.3 9.4 + - - +
143B LYS* 4.1 4.7 - - + +
144B CYS* 1.3 74.5 - - - +
146B ASP* 1.3 59.9 + - - +
147B ALA* 3.3 12.0 + - - +
148B CYS* 2.8 25.0 + - - +
149B MET* 2.8 24.8 + - - +
162B TYR* 5.2 1.0 + - - -
185B EDO 3.3 26.9 - - - -
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B HIS* 3.7 18.2 + - - -
28B ASN* 3.0 21.2 + - - +
30B GLN* 3.0 39.5 + - - +
145B ASP* 1.3 73.0 - - - +
147B ALA* 1.3 57.5 + - - +
149B MET* 3.3 5.9 + - - +
150B GLU* 2.9 30.3 + - - +
153B ARG* 4.5 3.4 + - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ASP* 3.2 12.1 + - - +
146B ASP* 1.3 77.9 - - - +
148B CYS* 1.3 63.2 + - - +
150B GLU* 3.4 2.2 + - - -
151B SER* 3.1 17.8 + - - -
180B NAG 3.1 26.2 + - - +
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Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B HIS* 3.7 17.5 - - - -
144B CYS* 2.2 46.9 - - - -
145B ASP* 2.8 21.0 + - - +
147B ALA* 1.3 74.3 - - - +
149B MET* 1.3 63.2 + - - +
151B SER* 2.7 25.9 + - - -
152B VAL* 3.2 7.3 + - - +
157B TYR* 4.3 8.3 - - - -
162B TYR* 3.6 30.2 + - + +
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASP* 4.1 2.5 - - + -
12A THR 3.3 22.0 - - - +
13A ILE* 4.2 8.8 - - + +
26B HIS* 3.7 23.3 - - + -
27B GLN 3.9 13.9 - - - +
28B ASN* 3.8 15.0 - - + +
140B PHE* 3.8 28.7 - - + -
144B CYS* 3.5 21.1 - - + +
145B ASP 2.8 19.4 + - - +
146B ASP* 3.6 8.3 - - - +
148B CYS* 1.3 73.2 - - - +
150B GLU* 1.3 61.8 + - - +
152B VAL* 3.1 8.4 + - - +
153B ARG* 3.0 45.0 + - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ASP 2.9 17.7 + - - +
147B ALA* 3.8 5.8 - - - +
149B MET* 1.3 78.0 - - - +
151B SER* 1.3 57.9 + - - +
153B ARG* 2.7 39.5 + - - +
154B ASN* 2.9 35.4 + - - +
180B NAG 3.7 22.2 - - - +
181B GOL 2.8 25.2 + - - -
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ALA 3.1 12.0 + - - -
148B CYS* 2.7 23.3 + - - -
150B GLU* 1.3 74.3 - - - +
152B VAL* 1.3 63.2 + - - +
154B ASN* 3.0 11.0 - - - +
155B GLY 3.1 0.3 + - - -
156B THR* 2.9 45.8 + - - -
157B TYR* 3.1 20.8 + - - -
158B ASP 4.6 0.9 + - - -
162B TYR* 5.4 2.3 + - - -
180B NAG 4.1 11.8 + - - -
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 19.5 - - + -
24B TYR* 4.6 2.5 + - + -
122B VAL* 3.9 32.3 - - + +
125B GLN* 3.0 30.1 + - - +
126B LEU* 3.9 14.8 - - + -
140B PHE* 4.2 16.4 - - + -
148B CYS 3.2 13.0 + - - +
149B MET* 3.1 7.7 + - - +
151B SER* 1.3 77.8 + - - +
153B ARG* 1.3 60.9 - - - +
154B ASN 3.2 1.0 + - - -
155B GLY 3.2 3.6 + - - -
157B TYR* 3.7 25.4 - - + -
183B EDO 4.6 1.4 + - - -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.4 4.4 - - + +
24B TYR* 3.4 50.5 + - + -
26B HIS* 3.4 18.8 + - - +
35B ALA* 4.0 16.0 - - - +
36B ALA 5.6 0.4 - - - -
146B ASP* 4.5 3.8 + - - +
149B MET* 3.0 32.5 + - - +
150B GLU* 2.7 52.9 + - - +
152B VAL* 1.3 77.1 - - - +
154B ASN* 1.3 58.2 + - - +
181B GOL 3.3 26.7 - - - -
182B CL 3.2 30.8 - - - +
183B EDO 3.3 11.3 + - - -
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU* 2.9 22.2 + - - +
151B SER* 3.0 7.4 - - - +
152B VAL 3.1 0.2 - - - -
153B ARG* 1.3 77.8 - - - +
155B GLY* 1.3 59.3 + - - +
156B THR* 2.6 29.0 + - - +
180B NAG 1.3 78.9 + - + +
181B GOL 4.1 17.3 - - - -
183B EDO 3.5 8.4 + - - -
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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