Contacts of the strand formed by residues 87 - 91 (chain C) in PDB entry 3JUT
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 ASN 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLU* 3.7 17.9 + - + +
80C ARG 3.3 3.9 - - - +
81C LEU* 3.3 32.3 + - - +
82C GLU* 4.7 0.7 - - - -
85C HIS 4.9 0.9 + - - -
86C TYR* 1.3 76.1 - - - +
88C THR* 1.3 63.3 + - - +
89C TYR* 3.3 34.6 + - + +
122C ILE 3.4 3.5 - - - +
123C LEU* 3.7 0.9 - - - -
124C PHE* 2.7 34.3 + - - +
126C PRO* 3.3 25.6 - - - +
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU 3.2 3.5 - - - +
79C GLU* 3.5 3.1 - - - -
80C ARG* 2.8 46.4 + - - +
82C GLU* 3.3 36.7 + - + +
87C ASN* 1.3 72.7 - - - +
89C TYR* 1.3 63.1 + - - +
90C ILE* 4.0 1.6 - - - +
100C PHE* 3.9 21.3 - - + -
117C TYR* 5.7 1.7 - - + -
122C ILE* 3.5 35.0 - - + +
123C LEU* 3.7 9.9 - - + -
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.9 24.7 - - + +
15C LEU* 6.5 0.4 - - + -
38C LEU* 3.8 8.7 - - + +
46C VAL* 3.9 13.0 - - + -
48C ILE* 3.8 20.0 - - + -
77C PHE* 4.3 8.1 - - + -
78C LEU 3.5 1.3 - - - -
79C GLU* 2.6 50.0 + - + -
87C ASN* 3.3 34.6 + - + -
88C THR* 1.3 73.8 - - - +
90C ILE* 1.3 61.6 + - - +
100C PHE* 3.2 4.4 - - - -
101C VAL* 2.7 56.3 + - + +
122C ILE 4.4 2.8 + - - -
124C PHE* 4.1 28.3 - + + -
126C PRO* 4.7 1.0 - - - +
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Residues in contact with ILE 90 (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 PHE* 3.0 5.9 - - - -
78C LEU* 2.6 57.6 + - + +
80C ARG* 4.9 6.7 - - + -
88C THR* 4.9 3.6 - - - +
89C TYR* 1.3 75.4 - - - +
91C SER* 1.3 75.4 + - - +
95C ALA* 3.4 34.8 - - + +
98C ASN* 3.4 34.1 - - + +
99C TRP 3.4 10.5 - - - +
100C PHE* 3.8 21.3 - - + -
117C TYR* 5.2 2.5 - - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET* 4.0 23.4 + - - +
74C GLU* 5.6 2.8 + - - -
76C LEU 3.8 1.5 + - - -
77C PHE* 3.5 17.9 - - - -
89C TYR 4.0 0.2 + - - -
90C ILE* 1.3 69.0 - - - +
92C LYS* 1.3 57.8 + - - +
93C LYS* 3.6 4.2 + - - +
94C HIS* 3.1 37.0 + - - -
95C ALA* 2.8 34.3 + - - +
99C TRP 2.9 18.4 + - - -
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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