Contacts of the strand formed by residues 127 - 132 (chain C) in PDB entry 7BRU
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 LEU 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 5.4 0.2 - - + -
52C PRO 3.1 15.3 + - - +
53C VAL* 3.3 22.1 - - + +
54C ILE* 2.9 29.1 + - - +
102C VAL* 4.2 22.2 - - + -
113C MET* 4.3 6.5 - - + +
116C LEU* 4.2 25.1 - - + +
117C TYR* 3.9 37.2 - - + +
120C HIS* 4.3 9.0 - - + +
121C HIS* 4.4 4.3 - - - +
126C PHE* 1.3 72.2 - - - +
128C TYR* 1.3 76.1 + - - +
129C ILE* 4.1 17.3 - - + -
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Residues in contact with TYR 128 (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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25C SER* 3.7 31.6 - - - -
27C TYR* 4.4 3.1 - + - -
28C LYS* 3.8 12.9 - - + +
36C ARG* 3.2 20.2 + - - -
54C ILE* 3.8 25.1 - - + -
56C GLU* 4.6 2.0 - - - -
101C PHE 3.9 2.6 - - - +
102C VAL* 3.7 22.3 - - - +
103C ASN 5.1 0.5 + - - -
120C HIS 5.2 2.0 + - - -
122C GLU* 4.1 12.6 - - + -
124C ASP* 2.8 32.9 + - - -
126C PHE* 3.6 23.3 + - + +
127C LEU* 1.3 77.1 - - - +
129C ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 129 (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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53C VAL* 3.6 24.7 - - + -
54C ILE 2.9 21.5 + - - +
55C VAL* 3.3 9.9 - - + -
56C GLU* 3.1 17.0 + - - +
79C VAL* 5.3 4.3 - - + -
82C PHE* 4.5 10.1 - - + -
100C PHE* 3.9 35.2 - - + -
101C PHE 3.5 4.9 - - - +
102C VAL* 3.9 16.4 - - + -
107C PRO* 6.1 1.6 - - + -
113C MET* 4.0 21.8 - - + -
116C LEU* 6.2 0.9 - - + -
127C LEU* 4.0 10.0 + - + -
128C TYR* 1.3 74.1 - - - +
130C ALA* 1.3 73.0 + - - +
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Residues in contact with ALA 130 (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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56C GLU* 3.2 11.7 - - + +
57C LYS 5.3 0.2 - - - -
58C ALA 4.7 3.4 - - - +
100C PHE* 3.3 4.2 - - - -
101C PHE* 2.6 45.9 + - + +
128C TYR 4.1 1.0 - - - -
129C ILE* 1.3 75.7 - - - +
131C TYR* 1.3 60.6 + - - +
137C TYR* 3.7 35.0 - - + -
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Residues in contact with TYR 131 (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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55C VAL* 3.5 16.8 - - + -
56C GLU* 2.9 40.1 + - - -
57C LYS* 3.6 11.5 - - + +
58C ALA* 3.0 24.1 + - - -
61C ALA* 4.1 1.0 - - - +
63C ILE* 3.2 29.6 - - + -
64C GLY 3.2 10.3 + - - -
65C ASP* 3.6 4.2 + - - -
66C LEU* 3.1 52.0 + - + +
86C ILE* 5.6 0.7 - - + -
90C ILE* 3.8 12.6 - - + -
98C LEU* 3.7 16.4 - - + -
99C PHE 3.0 12.1 - - - +
100C PHE* 3.7 19.7 - + + -
101C PHE* 4.7 1.1 - - - -
130C ALA* 1.3 75.2 - - - +
132C SER* 1.3 62.2 + - - +
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Residues in contact with SER 132 (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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58C ALA* 3.9 10.3 - - - +
61C ALA* 3.7 17.9 - - - +
63C ILE* 4.6 1.6 - - - -
98C LEU* 3.5 9.7 - - - +
99C PHE* 2.8 32.4 + - - +
101C PHE* 3.8 17.3 - - - -
131C TYR* 1.3 81.6 - - - +
133C ASP* 1.3 74.7 + - - +
134C GLU* 2.8 28.3 + - - +
136C VAL 5.1 0.4 - - - -
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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