Contacts of the strand formed by residues 67 - 73 (chain A) in PDB entry 1BMZ
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 GLY 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.6 13.7 - - - -
35A LYS 5.7 0.2 - - - -
65A VAL 3.5 1.8 + - - -
66A GLU* 1.3 76.8 - - - +
68A ILE* 1.3 65.3 + - - -
69A TYR* 3.6 11.1 - - - -
96A THR* 3.4 7.3 - - - +
97A ALA 2.9 28.7 + - - -
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Residues in contact with ILE 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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34A ARG* 3.5 4.3 - - - +
35A LYS* 2.8 60.2 + - + +
41A TRP* 3.6 19.2 - - + -
67A GLY* 1.3 74.4 - - - -
69A TYR* 1.3 61.0 + - - +
94A VAL* 3.9 16.8 - - + -
95A PHE 3.5 8.1 - - - +
96A THR* 3.8 18.6 - - + +
89B GLU* 4.0 17.9 - - + +
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Residues in contact with TYR 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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12A LEU* 6.2 0.2 - - + -
32A VAL* 4.2 16.8 - - + -
33A PHE 3.3 15.9 - - - +
34A ARG* 3.3 35.1 + - + -
41A TRP* 3.7 2.5 - - - -
44A PHE* 4.0 14.6 - + - -
64A PHE* 3.6 28.9 - + - -
65A VAL* 2.7 41.1 + - - +
67A GLY 3.6 21.5 - - - -
68A ILE* 1.3 74.7 - - - +
70A LYS* 1.3 59.7 + - - +
71A VAL 4.2 0.4 - - - -
93A VAL 3.7 0.9 - - - +
94A VAL* 3.3 5.9 - - - +
95A PHE* 2.8 51.2 + - + +
97A ALA* 3.7 17.0 - - + -
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Residues in contact with LYS 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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31A HIS 3.7 0.9 - - - +
32A VAL* 3.3 4.6 - - - +
33A PHE* 2.8 54.1 + - + +
41A TRP* 3.5 53.8 - - + +
69A TYR* 1.3 73.8 - - - +
71A VAL* 1.3 68.7 + - - +
72A GLU* 4.2 10.2 + - + +
92A GLU* 3.8 29.3 + - + +
93A VAL 3.3 4.5 - - - -
94A VAL* 3.8 18.2 - - + -
92B GLU* 5.0 4.9 - - - +
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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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12A LEU* 5.0 7.0 - - + -
14A VAL* 4.3 13.7 - - + -
30A VAL* 3.7 25.8 - - + -
31A HIS 3.7 2.5 - - - +
32A VAL* 4.4 16.6 - - + +
70A LYS* 1.3 75.4 - - - +
72A GLU* 1.3 62.0 + - - +
73A ILE* 4.1 13.8 + - + +
91A ALA 3.6 1.6 - - - +
92A GLU* 3.2 3.8 - - - -
93A VAL* 2.7 47.2 + - + +
95A PHE* 3.8 26.7 - - + -
107A ILE* 4.5 13.0 - - + -
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Residues in contact with GLU 72 (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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29A ALA 4.0 0.2 - - - +
30A VAL* 3.2 7.1 - - - +
31A HIS* 2.8 51.9 + - + +
33A PHE* 3.9 27.4 - - + -
70A LYS* 4.0 8.5 + - + -
71A VAL* 1.3 73.1 - - - +
73A ILE* 1.3 62.9 + - - +
74A ASP* 4.0 0.6 + - - +
90A HIS* 3.6 32.2 + - + -
91A ALA 3.4 2.0 - - - -
92A GLU* 2.8 27.4 - - - +
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Residues in contact with ILE 73 (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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14A VAL* 4.5 14.8 - - + -
16A VAL* 4.5 14.1 - - + -
28A VAL* 3.6 25.8 - - + -
29A ALA 3.7 2.9 - - - +
30A VAL* 4.5 9.6 - - + +
71A VAL* 4.3 15.3 - - + +
72A GLU* 1.3 76.8 - - - +
74A ASP* 1.3 58.2 + - - +
75A THR* 2.8 25.3 + - + -
90A HIS* 3.0 17.5 - - - +
91A ALA* 2.8 24.2 + - + +
93A VAL* 4.9 11.2 - - + -
107A ILE* 5.2 2.9 - - + -
109A ALA* 3.7 27.8 - - + -
111A LEU* 5.0 0.9 - - + -
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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