Contacts of the strand formed by residues 66 - 71 (chain A) in PDB entry 1BV1
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 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.0 36.6 - - + +
56A ILE 3.2 14.4 - - - +
57A SER* 4.2 1.8 - - - +
58A PHE* 3.8 7.2 - - - -
64A PHE 3.6 0.8 - - - -
65A LYS* 1.3 107.4 - - + +
67A VAL* 1.3 72.0 + - - +
68A LYS* 3.9 17.3 - - + -
87A GLU* 2.7 35.4 + - - +
88A GLY* 3.5 21.0 - - - -
89A GLY* 3.0 25.9 + - - -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS 3.7 0.3 - - - +
55A LYS* 3.5 4.0 - - - -
56A ILE* 2.9 52.8 + - + +
58A PHE* 4.0 17.7 - - + -
64A PHE* 6.4 0.2 - - + -
66A TYR* 1.3 76.1 - - - +
68A LYS* 1.3 61.3 + - - +
69A ASP* 3.6 17.0 - - - +
85A VAL* 3.3 33.9 - - + -
87A GLU 3.4 11.7 - - - +
88A GLY 3.8 10.3 - - - +
89A GLY* 4.3 5.4 - - - -
90A PRO* 4.4 3.8 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.7 27.9 - - + +
53A ILE* 4.6 10.8 - - + -
54A LYS 3.3 9.6 - - - +
55A LYS* 4.4 11.4 - - - +
66A TYR* 3.9 15.2 - - + -
67A VAL* 1.3 76.7 - - - +
69A ASP* 1.3 65.2 + - - +
85A VAL* 3.5 0.7 - - - -
86A ILE* 2.8 36.4 + - + +
87A GLU* 2.8 59.3 + - + +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR 3.7 0.2 - - - +
53A ILE* 3.2 8.7 - - - +
54A LYS* 3.0 36.5 + - + +
56A ILE* 3.3 26.1 - - + +
67A VAL* 3.6 10.8 - - - +
68A LYS* 1.3 80.5 - - - +
70A ARG* 1.3 62.2 + - - +
71A VAL* 4.3 1.6 - - + -
83A TYR* 3.8 31.6 - - + -
84A SER 3.0 6.3 - - - +
85A VAL* 3.5 18.6 - - - +
86A ILE* 4.9 1.1 - - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY* 4.6 9.0 - - - -
52A THR 3.2 5.2 - - - +
53A ILE* 3.4 25.7 - - + +
69A ASP* 1.3 74.9 - - - +
71A VAL* 1.3 69.6 + - - +
72A ASP* 3.0 26.9 + - - +
83A TYR* 3.0 7.8 - - - +
84A SER* 2.8 48.5 + - - +
86A ILE* 3.9 28.2 - - + +
97A LYS* 5.0 11.1 - - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY 4.1 8.1 - - - +
49A GLY 3.7 18.8 - - - +
50A PRO* 3.4 2.7 - - + +
51A GLY* 2.8 30.1 + - - -
52A THR* 2.9 29.9 + - + +
54A LYS* 5.2 9.6 - - + -
69A ASP* 5.7 1.1 - - + +
70A ARG* 1.3 75.0 - - - +
72A ASP* 1.3 59.4 + - - +
73A GLU 4.1 3.1 - - - +
74A VAL* 3.5 32.3 - - + -
81A TYR* 3.5 28.3 - - + +
82A ASN 3.9 3.1 - - - +
83A TYR* 4.2 2.2 - - + -
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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