Contacts of the strand formed by residues 88 - 96 (chain X) in PDB entry 3G90
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 ARG 88 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82X TYR* 3.7 4.6 - - - -
83X ASP* 2.8 36.0 + - - +
86X LEU* 4.0 34.3 - - + +
87X ASP* 1.3 79.6 - - - +
89X ASN* 1.3 68.4 + - - +
90X VAL* 4.5 7.4 - - + -
127X LEU* 3.9 28.6 - - - +
147X GLU* 3.7 33.7 + - - +
148X LEU 5.5 0.2 - - - +
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Residues in contact with ASN 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ALA 3.3 6.3 - - - +
82X TYR* 3.6 29.3 + - - +
88X ARG* 1.3 84.5 + - - +
90X VAL* 1.3 65.3 + - - +
147X GLU* 4.9 0.2 - - - -
148X LEU* 3.6 37.2 + - + +
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Residues in contact with VAL 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X TYR* 3.7 29.6 - - + -
80X ALA* 3.5 4.0 - - - -
81X ALA* 2.9 40.5 + - + +
83X ASP* 3.9 21.8 - - + +
86X LEU* 5.8 0.2 - - + -
88X ARG* 4.4 6.3 - - + +
89X ASN* 1.3 79.5 - - - +
91X ALA* 1.3 58.9 + - - +
92X ILE* 4.0 10.5 - - + -
127X LEU* 3.6 25.1 - - + -
145X VAL* 3.7 12.6 - - + -
146X MET 3.5 9.9 - - - +
148X LEU* 3.9 9.8 - - - +
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Residues in contact with ALA 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X J72 3.4 33.4 - - + +
70X ILE* 4.5 0.7 - - + -
78X VAL* 4.3 3.6 - - + -
79X CYS 3.4 7.4 - - - +
90X VAL* 1.3 72.6 - - - +
92X ILE* 1.3 61.6 + - - +
144X LEU 3.5 0.9 - - - +
145X VAL* 3.4 5.2 - - - +
146X MET* 2.9 48.6 + - + +
147X GLU 4.3 0.2 - - - +
148X LEU* 3.8 16.8 - - + +
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Residues in contact with ILE 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X PHE* 3.8 13.2 - - + -
60X VAL* 4.3 12.8 - - + -
64X TYR* 3.6 45.5 - - + -
67X LEU* 4.7 4.0 - - + -
78X VAL* 3.2 4.6 - - - -
79X CYS* 2.7 42.0 + - + +
81X ALA* 3.8 15.9 - - + -
90X VAL* 4.0 10.5 - - + -
91X ALA* 1.3 78.5 - - - +
93X LYS* 1.3 62.9 + - - +
130X PHE* 4.8 0.4 - - + -
143X TYR* 3.9 32.5 - - + -
144X LEU 3.4 6.7 - - - +
145X VAL* 4.3 7.9 - - + -
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Residues in contact with LYS 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLN* 3.2 49.2 + - - +
76X GLY* 4.9 3.1 - - - -
77X ILE 3.5 10.5 - - - +
78X VAL* 4.1 10.5 - - + +
91X ALA 4.2 0.4 - - - -
92X ILE* 1.3 74.7 - - - +
94X LYS* 1.3 60.8 + - - +
95X LEU* 3.6 24.5 + - + -
107X ARG* 5.3 7.1 - - - +
111X GLU* 2.8 33.8 + - - +
142X VAL 3.4 2.3 - - - +
143X TYR* 3.2 7.0 - - - -
144X LEU* 2.9 49.3 + - + +
146X MET* 4.3 15.9 - - + -
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Residues in contact with LYS 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X SER* 5.0 8.4 - - - +
57X THR* 2.9 33.8 + - - +
58X PHE* 3.7 27.0 - - + -
76X GLY* 5.6 0.5 - - - -
77X ILE* 2.9 34.1 + - + +
92X ILE 4.0 1.0 + - - -
93X LYS* 1.3 71.1 - - - +
95X LEU* 1.3 69.7 + - - +
96X SER* 3.6 18.0 + - - +
141X ASP* 3.6 25.6 + - + -
142X VAL 3.6 2.7 - - - +
143X TYR* 3.6 34.2 + - + +
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Residues in contact with LEU 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X LYS* 3.6 38.8 + - + +
94X LYS* 1.3 73.2 - - - +
96X SER* 1.3 62.3 + - - +
97X ARG 3.5 0.9 + - - -
98X PRO* 3.5 12.3 - - + +
108X ALA* 4.3 27.8 - - + +
111X GLU* 4.2 7.2 - - - +
112X LEU* 5.7 1.8 - - + -
141X ASP* 3.2 6.8 - - - +
142X VAL* 2.6 68.3 + - + +
144X LEU* 3.9 20.0 - - + -
394X ILE* 6.4 0.2 - - + -
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Residues in contact with SER 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X ILE* 6.3 2.9 - - - -
94X LYS* 3.6 21.3 + - - +
95X LEU* 1.3 70.8 - - - +
97X ARG* 1.3 73.6 + - - +
98X PRO* 3.4 2.4 - - - +
100X GLN* 3.1 16.2 + - - -
141X ASP* 3.4 13.6 + - - -
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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