Contacts of the strand formed by residues 177 - 183 (chain r) in PDB entry 5GJQ
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 177 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18r ASP* 3.6 3.6 - - - +
19r ARG* 3.4 48.3 + - - +
20r VAL* 5.8 0.9 - - - +
30r ASP* 3.6 11.4 + - + +
175r LEU 3.6 1.1 - - - -
176r PRO* 1.3 99.2 - - + +
178r PHE* 1.3 71.4 + - - +
193r ASN* 5.5 3.8 - - + -
194r ILE 3.5 4.7 - - - -
195r SER* 3.8 17.9 - - - -
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Residues in contact with PHE 178 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3r TYR* 3.9 16.8 - + - -
16r ALA* 5.0 1.1 - - + -
17r SER* 3.2 24.2 - - - +
18r ASP* 4.0 13.9 - - + -
19r ARG* 3.9 4.3 - - - -
164r LEU* 3.6 54.3 - - + -
167r LEU* 4.8 4.3 - - + -
168r GLN* 3.9 11.0 - - - -
175r LEU* 3.7 38.6 - - + -
176r PRO 4.3 1.1 - - - -
177r THR* 1.3 82.2 - - - +
179r SER* 1.3 66.4 + - - +
180r VAL* 3.5 3.0 + - + +
193r ASN* 3.5 10.2 - - - +
194r ILE* 2.9 40.8 + - + +
196r PHE* 4.2 6.1 - + - -
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Residues in contact with SER 179 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16r ALA* 3.1 4.3 - - - +
17r SER* 3.0 45.7 + - - -
19r ARG* 3.0 31.6 + - - +
32r HIS 4.7 1.0 + - - -
33r ASP* 4.2 16.2 + - - -
35r MET* 3.7 9.8 - - - +
178r PHE* 1.3 73.2 - - - +
180r VAL* 1.3 61.0 + - - +
181r ARG* 4.5 12.4 + - - -
193r ASN* 3.9 9.5 + - - -
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Residues in contact with VAL 180 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14r LEU* 3.8 16.8 - - + -
15r VAL 3.4 6.1 - - - +
16r ALA* 4.0 10.5 - - + -
157r VAL* 5.4 1.8 - - + -
160r LEU* 3.9 11.4 - - + -
164r LEU* 5.3 0.2 - - + -
178r PHE* 3.5 10.4 + - + +
179r SER* 1.3 81.8 - - - +
181r ARG* 1.3 69.7 + - - +
190r ASP* 4.0 0.9 - - - +
191r LEU* 3.0 51.3 + - + +
192r ASP 4.1 10.9 + - - +
193r ASN* 4.6 2.8 + - - -
194r ILE* 3.5 33.0 - - + -
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Residues in contact with ARG 181 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14r LEU* 3.7 4.6 - - - +
15r VAL* 2.9 33.5 + - - +
33r ASP* 2.3 42.0 + - - -
35r MET* 3.3 31.3 - - + +
37r LYS* 4.1 21.5 - - - +
43r LEU* 3.9 23.3 - - + -
179r SER* 4.5 9.6 + - - -
180r VAL* 1.3 81.6 + - - +
182r ILE* 1.3 64.7 + - - +
188r ILE* 4.0 15.7 - - + -
189r HIS 3.4 8.7 - - - +
190r ASP* 2.8 38.2 + - - +
191r LEU* 4.5 0.4 - - - +
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Residues in contact with ILE 182 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12r TYR* 3.9 26.7 - - + -
13r VAL 3.4 13.9 - - - +
14r LEU* 4.1 17.5 - - + -
153r ARG* 4.1 29.6 - - + +
157r VAL* 5.7 1.3 - - + -
181r ARG* 1.3 79.9 - - - +
183r ILE* 1.3 73.0 + - - +
184r ASP* 5.4 0.4 - - - +
187r GLY 3.5 1.7 - - - +
188r ILE* 3.6 1.3 - - - -
189r HIS* 2.8 51.9 + - + +
191r LEU* 3.8 25.8 - - + -
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Residues in contact with ILE 183 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12r TYR* 3.4 4.0 - - - +
13r VAL* 2.8 44.2 + - + +
15r VAL* 5.4 1.8 - - + -
41r LYS* 3.7 30.1 - - - +
42r ILE 4.5 0.4 - - - -
43r LEU* 3.6 48.2 - - + +
105r ALA* 3.8 27.8 - - + +
106r GLY* 4.1 2.7 - - - -
107r TYR* 4.4 8.6 - - + +
182r ILE* 1.3 78.8 - - - +
184r ASP* 1.3 69.2 + - - +
187r GLY 3.4 12.6 - - - +
188r ILE* 4.3 7.6 - - + -
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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