Contacts of the helix formed by residues 172 - 183 (chain D) in PDB entry 3GBA
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 ASN 172 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ILE* 6.6 0.2 - - + -
59D GLY 5.3 6.7 - - - +
137D VAL* 3.6 15.3 - - - -
170D VAL* 3.4 6.4 - - - +
171D LYS* 1.3 104.4 - - + +
173D SER* 1.3 64.4 + - - +
174D ASP* 3.4 9.6 + - - +
175D GLU* 3.0 25.8 + - - +
176D GLY 3.1 15.9 + - - -
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 2.8 40.8 + - - -
137D VAL* 3.7 9.0 - - - +
172D ASN* 1.3 75.4 - - - +
174D ASP* 1.3 62.2 + - - +
176D GLY* 3.1 3.2 + - - -
177D ILE* 2.9 43.4 + - - +
187D LEU* 4.6 1.6 - - - +
189D MET* 4.7 3.4 - - - -
258D DYH 3.3 25.2 - - - -
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Residues in contact with ASP 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 5.0 18.7 + - - +
172D ASN* 3.3 9.9 + - - +
173D SER* 1.3 78.6 - - - +
175D GLU* 1.3 63.4 + - - +
177D ILE* 3.4 13.8 + - - +
178D GLN* 3.0 33.4 + - + +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ARG* 4.6 2.4 + - - -
169D LEU 4.6 1.4 - - - +
170D VAL* 3.5 18.1 - - + +
171D LYS* 3.0 38.8 + - - +
172D ASN* 3.0 23.0 + - - +
174D ASP* 1.3 76.0 - - - +
176D GLY* 1.3 58.7 + - - +
178D GLN* 3.5 5.7 + - - +
179D ARG* 3.0 29.3 + - + +
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Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D VAL* 3.8 25.5 - - - +
172D ASN 3.1 7.5 + - - -
173D SER 3.1 7.5 + - - -
175D GLU* 1.3 77.2 - - - +
177D ILE* 1.3 55.9 + - - +
179D ARG* 3.2 4.7 + - - +
180D VAL* 3.0 32.4 + - - +
185D TYR* 4.2 1.5 - - - -
187D LEU* 3.8 18.4 - - - -
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.5 3.1 - - + -
173D SER* 2.9 30.3 + - - +
174D ASP* 3.8 13.7 - - - +
176D GLY* 1.3 72.0 - - - +
178D GLN* 1.3 63.8 + - - +
180D VAL* 3.2 9.6 + - - +
181D LEU* 2.9 46.7 + - + +
189D MET* 3.9 22.0 - - + -
197D VAL* 3.6 42.4 - - + -
201D ASN* 5.0 3.4 - - - +
204D LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ASP* 3.0 24.6 + - + +
175D GLU* 3.8 6.5 - - - +
177D ILE* 1.3 82.6 - - - +
179D ARG* 1.3 56.4 + - - +
181D LEU* 3.3 21.7 + - - +
182D THR* 2.8 46.6 + - + +
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Residues in contact with ARG 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLU* 3.0 26.5 + - - -
167D SER* 2.9 30.5 + - - -
168D ALA* 3.7 19.4 + - - +
169D LEU 3.7 9.1 + - - -
170D VAL* 3.8 10.9 - - - +
175D GLU* 3.0 15.2 + - - +
176D GLY* 3.2 9.2 + - - +
178D GLN* 1.3 78.1 - - - +
180D VAL* 1.3 61.7 + - - +
182D THR* 4.0 4.7 - - - -
183D THR* 2.7 47.1 + - + +
185D TYR* 3.4 33.7 - - + +
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Residues in contact with VAL 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.0 14.1 - - + +
114D TYR* 4.1 16.2 - - - -
115D ARG* 4.5 8.9 + - - +
176D GLY 3.0 18.9 + - - +
177D ILE 3.6 6.7 - - - +
179D ARG* 1.3 74.8 - - - +
181D LEU* 1.3 62.3 + - - +
183D THR 3.3 12.0 - - - +
185D TYR* 3.5 35.9 - - + +
187D LEU* 3.7 22.9 - - + +
204D LEU* 3.7 33.0 - - + +
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ARG* 5.7 1.0 + - - -
177D ILE* 2.9 33.0 + - + +
178D GLN* 3.7 23.3 - - - +
179D ARG 3.3 0.2 - - - -
180D VAL* 1.3 78.9 - - - +
182D THR* 1.3 64.7 + - + +
183D THR 4.8 0.2 - - - -
201D ASN* 3.9 22.9 - - - +
203D ASN* 3.8 28.8 + - - +
204D LEU* 3.8 26.0 - - + -
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Residues in contact with THR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ARG* 5.5 0.9 - - - -
178D GLN* 2.8 33.7 + - + +
179D ARG* 4.0 1.6 - - - -
181D LEU* 1.3 84.5 - - + +
183D THR* 1.3 74.8 + - - +
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Residues in contact with THR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ARG* 3.2 14.5 + - - -
133D GLU* 5.7 0.3 + - - -
179D ARG* 2.7 37.9 + - + +
180D VAL 3.3 7.8 - - - +
181D LEU 3.7 0.4 - - - -
182D THR* 1.3 94.0 - - - +
184D ASP* 1.3 60.1 + - - +
185D TYR* 3.0 20.6 + - - +
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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