Contacts of the strand formed by residues 89 - 96 (chain C) in PDB entry 6PAI
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 TYR 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 3.1 8.4 - - - +
84C SER* 2.7 50.6 + - - +
86C CYS* 4.7 5.4 - - - -
87C GLY 3.5 0.2 - - - -
88C ARG* 1.3 130.9 + - + +
90C VAL* 1.3 66.3 + - - +
91C LEU* 5.4 2.0 - - + +
111C TRP* 3.7 32.5 - + + -
112C TRP 3.1 21.5 - - - +
113C GLU* 4.0 3.1 - - + -
114C PHE* 4.8 0.4 - - - -
123C VAL* 4.3 22.3 - - + +
187C VAL* 4.6 15.7 - - + -
188C PRO* 3.9 23.4 + - + +
189C PRO 4.4 3.3 + - - -
190C PRO* 5.1 0.3 - - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 5.9 1.6 - - + -
68C ILE* 5.9 1.8 - - + -
80C PHE* 3.4 34.1 - - + -
82C GLY* 3.1 16.2 - - - +
83C PHE* 3.8 33.2 - - + -
89C TYR* 1.3 76.3 - - - +
91C LEU* 1.3 68.9 + - - +
112C TRP* 2.7 40.2 + - + +
114C PHE* 4.1 15.8 - - + +
120C LEU* 4.6 8.5 - - + -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PHE* 3.9 0.5 - - - -
81C LEU* 2.8 63.1 + - + +
82C GLY 3.1 13.4 + - - +
83C PHE 6.1 0.4 - - - -
84C SER* 5.8 8.5 - - - +
89C TYR* 5.5 3.1 - - + +
90C VAL* 1.3 78.7 - - - +
92C SER* 1.3 53.4 + - - +
109C LEU* 3.9 13.0 - - + -
110C TYR 3.0 22.2 - - - +
111C TRP* 3.9 35.7 - - + +
112C TRP* 4.1 2.5 - - - -
142C VAL* 4.2 21.8 - - + -
144C GLU* 6.4 2.5 - - + -
152C VAL* 5.2 4.9 - - + -
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C HIS* 2.9 29.7 - - - -
79C ILE 3.1 20.6 - - - -
80C PHE* 3.5 20.9 - - - -
81C LEU* 3.9 7.9 - - - -
91C LEU* 1.3 74.9 - - - +
93C TYR* 1.3 60.6 + - - +
109C LEU* 3.3 6.8 - - - +
110C TYR* 2.9 29.7 + - - -
112C TRP* 3.3 11.3 + - - -
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLY 4.2 0.5 - - - +
78C HIS* 3.9 0.3 - - - -
79C ILE* 3.2 68.8 + - + +
81C LEU* 3.8 26.5 - - + -
92C SER* 1.3 76.0 - - - +
94C THR* 1.3 73.7 + - - +
95C SER* 4.4 10.1 - - - -
107C TYR* 4.1 15.0 - + + -
108C HIS 3.0 14.1 - - - +
109C LEU* 4.5 4.5 - - + -
110C TYR* 3.9 2.2 - - - -
128C LEU* 5.0 1.3 - - + -
137C ASP* 5.9 0.4 - - - -
138C LEU 4.9 6.4 + - - -
140C LEU* 3.8 51.1 + - + +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA 3.8 22.0 - - - +
77C GLY 4.0 4.5 - - - -
78C HIS* 3.9 21.3 - - + +
79C ILE* 5.8 0.2 - - - -
93C TYR* 1.3 80.2 - - - +
95C SER* 1.3 62.6 + - - +
96C SER* 4.1 6.1 + - - -
106C ILE 3.3 12.6 - - - +
107C TYR* 3.3 17.7 - - - -
108C HIS* 2.9 15.3 + - - +
110C TYR* 2.3 44.8 + - + +
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLY 4.9 3.8 + - - -
79C ILE* 5.6 6.2 - - - +
93C TYR* 4.4 9.2 - - - -
94C THR* 1.3 76.3 - - - +
96C SER* 1.3 58.6 + - - +
105C TYR* 3.3 20.0 - - - -
106C ILE 3.4 5.8 - - - -
107C TYR* 3.7 15.0 - - - -
137C ASP* 3.2 23.1 + - - -
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 5.4 5.0 - - - -
95C SER* 1.3 75.8 + - - +
97C SER* 1.3 65.0 + - - +
105C TYR* 3.6 5.3 - - - -
106C ILE* 2.9 47.8 + - - +
108C HIS* 5.3 1.6 + - - -
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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