Contacts of the strand formed by residues 90 - 95 (chain C) in PDB entry 3U7U
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 90 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TYR* 3.6 2.9 - - - +
85C LEU* 3.6 5.9 - - - -
86C TYR* 2.8 60.2 + + + +
87C GLU* 3.9 11.0 - - - -
89C ARG* 1.3 126.7 + - + +
91C ALA* 1.3 61.0 + - - +
92C LEU 3.8 13.9 - - - +
93C ALA* 4.3 5.2 - - + -
121C GLY* 3.4 13.5 - - - +
122C VAL 4.1 4.3 - - - -
123C TYR* 3.6 53.1 - + + -
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Residues in contact with ALA 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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61C TYR* 3.4 8.3 - - - +
62C VAL* 2.9 25.9 + - - +
80C ILE* 3.5 19.3 - - + +
82C GLY* 4.5 0.7 - - - -
85C LEU* 3.7 9.2 - - + +
90C TYR* 1.3 73.5 - - - +
92C LEU* 1.4 54.8 + - - +
117C ILE* 3.4 24.9 - - + -
119C ASN 3.3 26.0 - - - +
120C GLY 4.1 1.3 - - - -
121C GLY 2.7 11.0 + - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.4 33.9 - - + +
64C VAL* 5.3 0.4 - - + -
72C LEU* 6.2 0.4 - - + -
77C LEU* 5.9 0.4 - - + -
80C ILE* 4.1 12.3 - - + -
90C TYR* 3.8 2.7 - - - +
91C ALA* 1.4 77.5 - - - +
93C ALA* 1.3 56.8 + - - +
94C ILE* 3.9 31.6 - - + -
111C LEU* 4.6 11.9 - - + -
114C LEU* 4.2 21.8 - - + -
117C ILE* 4.5 6.5 - - + -
121C GLY 3.2 3.9 + - - +
122C VAL* 3.4 27.5 - - + -
123C TYR 2.8 32.2 + - - -
124C VAL* 4.8 1.8 - - + -
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL 2.9 10.9 + - - +
63C LEU* 3.5 21.2 - - + +
64C VAL 2.8 32.9 + - - +
86C TYR* 4.0 20.6 - - + -
90C TYR* 4.3 10.1 - - + -
92C LEU* 1.3 74.4 - - - +
94C ILE* 1.3 57.9 + - - +
95C PHE* 4.1 10.8 - - + -
123C TYR* 3.2 11.4 - - + +
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Residues in contact with ILE 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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64C VAL* 3.1 19.1 - - + +
72C LEU* 4.9 3.4 - - + -
92C LEU* 3.9 35.6 - - + -
93C ALA* 1.3 75.7 - - - +
95C PHE* 1.3 60.3 + - - +
97C ASN* 3.4 17.5 - - - +
106C LEU* 4.0 20.9 - - + -
109C LEU* 4.0 27.6 - - + -
111C LEU* 4.4 5.8 - - + -
123C TYR 2.7 8.3 + - - +
124C VAL* 3.2 25.6 - - + +
125C ASP 3.0 24.3 + - - +
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Residues in contact with PHE 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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11C LEU* 3.9 24.0 - - + -
63C LEU* 3.7 21.1 - - + -
64C VAL 3.1 5.5 + - - -
65C ALA* 3.1 28.1 - - + +
66C LEU* 3.4 1.1 + - + -
86C TYR* 3.8 31.0 - + - -
93C ALA* 4.1 8.3 - - + -
94C ILE* 1.3 71.6 - - - +
96C LEU* 1.4 87.4 + - + +
97C ASN* 3.0 14.1 + - - +
123C TYR* 3.5 40.2 - + + +
125C ASP 3.0 18.4 - - - +
126C GLN* 4.7 0.9 - - + -
127C ASN* 5.7 0.7 - - - +
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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