Contacts of the strand formed by residues 95 - 101 (chain C) in PDB entry 1P27
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 GLU 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASP* 5.3 3.8 - - - +
70C THR* 3.5 23.3 + - - +
90C ILE 3.9 0.7 - - - +
91C VAL* 3.5 6.8 - - - +
92C ILE* 3.0 59.6 + - + +
94C ASP* 1.3 81.8 - - + +
96C HIS* 1.3 59.4 + - - +
97C ILE* 3.9 9.6 - - + -
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Residues in contact with HIS 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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27A ARG* 4.8 3.8 - - - -
29A ASP* 6.2 0.4 - - - -
31A LYS* 5.8 2.0 - - - -
6C TYR* 5.3 0.9 - + - -
89C GLU* 3.3 34.7 - - + +
90C ILE 2.3 36.1 + - - -
91C VAL* 2.7 35.2 - - + +
94C ASP 3.6 4.3 + - - +
95C GLU* 1.3 72.5 - - - +
97C ILE* 1.3 71.4 + - - +
98C SER* 5.8 0.4 - - - -
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Residues in contact with ILE 97 (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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69C ILE* 5.6 0.4 - - + -
70C THR* 3.5 46.2 - - + +
72C GLU 4.6 4.9 - - - +
73C ASP* 5.8 2.7 - - - +
88C LEU 4.4 1.1 - - - -
89C GLU* 3.4 3.1 - - - -
90C ILE* 3.0 51.7 + - + +
92C ILE* 4.3 2.5 - - + -
95C GLU* 3.9 18.4 - - + +
96C HIS* 1.3 86.3 - - - +
98C SER* 1.3 63.6 + - - +
99C PHE* 3.9 31.2 - - + -
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Residues in contact with SER 98 (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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31A LYS* 4.8 8.7 + - - -
8C ARG* 5.6 1.0 + - - -
73C ASP* 5.6 1.9 - - - +
74C ASP* 3.8 9.4 + - - +
88C LEU 3.3 5.0 + - - -
89C GLU* 3.8 23.0 + - - +
96C HIS* 5.8 1.0 - - - -
97C ILE* 1.3 77.5 + - - +
99C PHE* 1.3 68.8 + - - +
100C THR* 5.8 1.3 - - - -
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Residues in contact with PHE 99 (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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69C ILE* 3.7 41.1 - - + -
72C GLU 3.7 24.0 - - - -
73C ASP* 4.0 3.8 - - - -
74C ASP* 3.3 15.7 - - - +
77C TRP* 3.3 42.6 - + + -
87C GLU* 3.3 6.5 - - - +
88C LEU* 2.8 55.0 + - + +
90C ILE* 5.4 1.3 - - + -
97C ILE* 3.9 28.3 - - + -
98C SER* 1.3 76.3 + - - +
100C THR* 1.3 65.4 + - - +
101C THR* 4.3 1.1 - - - +
122C PHE* 4.4 10.3 - + + -
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Residues in contact with THR 100 (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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74C ASP* 2.9 21.7 + - - +
77C TRP* 5.2 0.7 - - - +
78C PRO 4.2 2.6 - - - +
79C PRO* 5.0 0.9 - - - +
80C PRO* 3.3 32.3 - - + +
85C ARG* 3.6 21.1 + - - +
86C GLN 3.4 8.3 - - - +
87C GLU* 4.2 7.3 - - + +
98C SER* 5.5 2.1 - - - -
99C PHE* 1.3 77.6 + - - +
101C THR* 1.3 63.7 + - - +
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Residues in contact with THR 101 (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 TRP* 3.4 45.4 - - + -
78C PRO* 2.7 36.1 - - + +
80C PRO* 3.4 15.4 - - - +
85C ARG* 3.2 6.6 - - - -
86C GLN* 2.9 27.6 + - - +
99C PHE* 5.1 0.5 - - - +
100C THR* 1.3 74.0 + - - +
102C SER* 1.3 70.5 + - - +
104C ILE* 5.3 3.4 - - + -
119C LEU* 4.5 5.4 - - + -
122C PHE* 4.3 15.0 - - - -
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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