Contacts of the strand formed by residues 89 - 96 (chain X) in PDB entry 1SHU
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 ALA 89 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84X VAL 3.2 11.2 - - - +
85X PHE* 3.9 3.6 - - + -
88X GLN* 1.3 76.5 - - - +
90X THR* 1.3 70.9 + - - +
122X GLU* 3.6 35.9 + - + +
123X GLY* 3.8 4.7 - - - +
126X LEU* 3.6 22.2 - - + +
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Residues in contact with THR 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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51X LYS* 5.1 5.4 + - - +
83X ILE* 3.4 2.1 - - - -
84X VAL* 2.9 50.2 + - - +
88X GLN* 5.1 9.4 - - + -
89X ALA* 1.3 82.3 - - - +
91X ILE* 1.3 62.4 + - - +
92X ILE* 3.4 11.8 + - - +
126X LEU* 3.8 8.7 - - - -
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Residues in contact with ILE 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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81X SER* 4.3 0.4 - - - +
82X PHE 3.7 5.4 - - - +
83X ILE* 4.1 3.6 - - + -
90X THR* 1.3 72.0 - - - +
92X ILE* 1.3 60.4 + - - +
93X LEU 3.7 4.7 - - - +
94X PRO* 3.5 43.0 - - + +
126X LEU* 3.9 34.0 - - + +
129X GLU* 5.9 1.3 - - + +
130X GLN* 3.8 35.9 - - + +
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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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82X PHE* 2.9 15.7 + - + +
84X VAL* 3.8 41.5 - - + -
90X THR* 3.4 8.5 + - - +
91X ILE* 1.3 74.6 - - - +
93X LEU* 1.3 59.9 + - - +
94X PRO* 3.8 6.2 - - - +
105X GLY* 4.1 13.7 - - - +
108X ASP* 3.7 39.2 - - + +
109X LEU* 4.3 9.6 - - + -
112X VAL* 5.4 7.6 - - + -
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Residues in contact with LEU 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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80X LEU 3.6 19.5 - - - +
81X SER* 2.8 21.8 + - - -
82X PHE* 3.0 58.2 + - + +
91X ILE* 3.7 3.6 - - - -
92X ILE* 1.3 77.5 - - - +
94X PRO* 1.3 75.0 - - + +
96X THR* 3.8 13.2 - - + -
101X LYS* 3.3 35.2 - - + +
102X ILE* 3.9 17.3 - - + -
105X GLY* 4.5 7.0 - - - -
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Residues in contact with PRO 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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91X ILE* 3.5 23.5 - - + +
92X ILE 3.8 6.7 - - - +
93X LEU* 1.3 93.6 - - + +
95X LEU* 1.3 69.3 + - - +
96X THR* 3.2 16.8 + - - +
130X GLN* 3.8 4.3 - - - +
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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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44X ASP* 3.8 16.2 - - + +
45X LEU 4.6 1.6 - - - +
46X TYR* 3.3 28.3 - - + +
79X ARG* 3.5 69.8 + - + +
80X LEU 3.4 11.4 - - - -
81X SER* 3.7 6.3 - - - +
93X LEU 3.6 1.2 + - - -
94X PRO* 1.3 72.4 - - - +
96X THR* 1.3 61.2 + - - +
130X GLN* 3.2 21.4 + - + +
134X ALA* 4.8 7.0 - - + -
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Residues in contact with THR 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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79X ARG* 3.8 11.2 - - - +
80X LEU 2.9 29.8 + - - +
93X LEU* 3.8 22.4 - - + -
94X PRO 3.5 13.0 - - - +
95X LEU* 1.3 78.3 - - - +
97X GLY* 1.3 60.7 + - - +
98X ASP* 3.1 32.4 + - - +
101X LYS* 4.1 16.7 + - + +
102X ILE* 3.8 9.4 - - + +
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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