Contacts of the strand formed by residues 50 - 57 (chain B) 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 ARG 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.5 22.0 - - - +
9A ILE 2.7 29.7 + - - -
10A ILE* 4.9 2.4 - - - +
11A ASP* 5.2 2.2 - - - +
43B ILE 5.4 0.2 - - - +
44B ARG* 2.7 26.3 + - - -
47B TYR* 3.0 25.3 + - + +
48B PRO 3.2 0.2 - - - -
49B ASP* 1.3 95.2 + - - +
51B VAL* 1.3 63.3 + - - +
52B PRO* 4.4 0.2 - - - +
72B LEU* 3.0 53.4 + - + +
73B VAL 3.2 7.0 - - - +
74B PRO* 3.5 21.0 - - + +
75B SER 4.1 0.7 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.7 13.0 - - - +
50B ARG* 1.3 81.4 - - - +
52B PRO* 1.3 64.9 - - - +
53B VAL* 3.5 17.0 - - + +
71B TYR 3.6 0.3 - - - +
72B LEU* 3.7 4.2 - - - -
73B VAL* 2.8 43.5 + - + +
75B SER* 4.4 14.4 - - - -
113B MET* 3.9 23.3 - - + +
114B GLY* 4.4 4.0 - - - +
117B TYR* 3.6 38.1 - - + -
127B LEU* 5.6 0.4 - - + -
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Residues in contact with PRO 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.6 23.6 - - + -
40B GLY* 4.8 0.9 - - - +
43B ILE* 3.7 22.9 - - + -
44B ARG* 3.8 15.5 - - + -
50B ARG 4.4 0.4 - - - +
51B VAL* 1.3 83.3 - - - +
53B VAL* 1.3 62.1 + - - +
71B TYR 3.4 6.3 - - - +
72B LEU* 4.1 3.3 - - + -
117B TYR* 3.7 13.5 - - + +
125B PHE 3.2 22.4 - - - +
126B PHE* 3.7 16.6 - - + -
127B LEU* 3.1 23.6 + - - +
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.9 0.6 - - - -
51B VAL* 3.5 20.4 - - + +
52B PRO* 1.3 78.3 - - - +
54B ILE* 1.3 66.7 + - - +
55B VAL* 3.9 13.5 - - + -
69B LYS 3.5 2.1 - - - +
70B LYS* 3.7 1.9 - - - -
71B TYR* 2.8 44.1 + - + +
73B VAL* 3.6 20.2 - - + -
82B PHE* 4.3 4.0 - - + -
113B MET* 3.9 13.2 - - + -
126B PHE* 4.5 0.6 - - - -
127B LEU* 3.4 19.5 - - + +
129B ILE* 3.8 29.2 - - + -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TYR* 3.8 28.5 - - + -
53B VAL* 1.3 73.9 - - - +
55B VAL* 1.3 63.1 + - - +
56B GLU* 3.5 33.7 - - + +
69B LYS* 3.3 8.3 - - + +
70B LYS* 3.5 32.3 - - + -
126B PHE* 3.7 26.2 - - + -
127B LEU 2.9 4.9 + - - -
128B TYR* 3.6 29.5 - - + -
129B ILE* 2.9 29.1 + - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.9 10.1 - - + -
54B ILE* 1.3 76.9 - - - +
56B GLU* 1.3 66.5 + - - +
66B LEU* 3.6 35.6 - - + +
69B LYS* 3.0 18.1 + - - +
71B TYR* 3.7 22.7 - - + -
82B PHE* 3.8 24.9 - - + -
86B ILE* 4.5 12.3 - - + -
100B PHE* 4.9 3.6 - - + -
129B ILE* 3.3 17.3 - - + +
131B TYR* 3.8 15.7 - - + -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS 4.5 4.6 - - - +
25B SER* 2.6 31.2 + - - -
26B THR* 3.2 9.9 + - - -
27B TYR* 2.7 25.8 + - - +
54B ILE* 3.5 21.3 - - + +
55B VAL* 1.3 80.5 - - - +
57B LYS* 1.3 66.3 + - - +
65B ASP* 5.4 2.2 - - - -
66B LEU* 6.3 0.2 - - - -
69B LYS* 3.0 28.3 + - + -
128B TYR* 4.5 2.3 - - - -
129B ILE 3.0 8.7 + - - +
130B ALA* 3.1 9.9 - - + -
131B TYR* 2.9 31.1 + - - -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS 5.2 4.7 - - - +
56B GLU* 1.3 77.4 - - - +
58B ALA* 1.3 77.7 + - - +
59B PRO* 3.7 7.4 - - - +
61B ALA* 3.5 25.0 + - + +
63B ILE* 3.1 40.1 + - + +
64B GLY 4.0 5.4 - - - +
65B ASP* 4.3 23.5 + - - +
130B ALA* 5.0 1.5 - - - +
131B TYR* 3.4 21.1 + - + +
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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