Contacts of the strand formed by residues 84 - 95 (chain A) in PDB entry 1BMA
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 GLU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.1 4.7 - - + -
72A VAL 3.3 8.5 - - - +
73A GLY 3.9 6.1 - - - +
74A GLU* 3.8 21.3 - - - +
79A GLN 3.6 1.2 - - - +
80A ASN* 3.1 12.5 - - - +
81A ASN* 2.8 22.4 + - - +
82A GLY 3.1 10.1 + - - -
83A THR* 1.3 85.1 + - - +
85A GLN* 1.3 63.0 + - - +
86A TYR* 3.6 38.8 + - + +
280A CA 2.5 24.4 - - - -
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Residues in contact with GLN 85 (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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70A VAL 3.8 1.0 - - - +
71A VAL* 3.5 4.9 - - - +
72A VAL* 3.0 44.9 + - + +
83A THR 3.7 3.0 + - - +
84A GLU* 1.3 78.6 - - - +
86A TYR* 1.3 63.3 + - - +
87A VAL* 4.2 1.6 - - + +
116A GLN* 5.6 2.3 + - - -
118A VAL* 3.5 11.9 - - + +
119A THR* 2.9 54.7 + - - +
121A ASN* 4.0 8.7 - - - +
124A VAL* 3.5 20.6 - - - +
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Residues in contact with TYR 86 (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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69A ARG* 3.5 42.0 - - - +
70A VAL 3.6 3.1 - - - +
71A VAL* 3.5 29.8 - - + -
74A GLU* 4.6 4.2 + - - -
80A ASN* 5.2 2.6 + - - -
84A GLU* 3.6 39.9 + - + +
85A GLN* 1.3 74.1 - - - +
87A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 87 (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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69A ARG* 3.5 6.0 - - - +
70A VAL* 2.9 45.5 + - + +
85A GLN* 5.1 2.5 - - + +
86A TYR* 1.3 77.0 - - - +
88A GLY* 1.3 69.0 + - - +
114A LEU* 3.9 24.9 - - + -
115A ALA* 3.9 2.7 - - + +
116A GLN* 3.5 48.7 - - + +
118A VAL* 4.0 17.3 - - + -
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Residues in contact with GLY 88 (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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68A PHE 4.2 7.2 - - - -
69A ARG* 4.5 3.4 - - - -
87A VAL* 1.3 77.8 - - - +
89A VAL* 1.3 63.4 + - - -
90A GLN 3.8 0.2 - - - -
114A LEU* 3.5 5.5 - - - +
115A ALA* 2.8 34.2 + - - +
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Residues in contact with VAL 89 (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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33A LEU* 4.6 0.2 - - + -
68A PHE* 3.5 37.4 + - + +
69A ARG* 4.4 0.9 - - - -
70A VAL* 4.2 16.8 - - + -
88A GLY* 1.3 71.9 - - - +
90A GLN* 1.3 62.0 + - - +
91A LYS 4.0 10.8 - - - +
92A ILE* 3.7 33.9 - - + -
112A LEU* 4.0 27.8 - - + -
113A ARG 3.8 3.1 - - - +
114A LEU* 4.5 4.3 - - + +
115A ALA* 5.1 0.7 - - - -
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Residues in contact with GLN 90 (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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88A GLY 3.6 1.6 + - - -
89A VAL* 1.3 76.6 - - - +
91A LYS* 1.3 59.7 + - + +
113A ARG* 2.7 44.6 + - - +
114A LEU 3.9 6.3 - - - +
115A ALA* 3.8 29.3 + - + +
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Residues in contact with LYS 91 (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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89A VAL* 3.7 1.7 - - - +
90A GLN* 1.3 80.7 - - + +
92A ILE* 1.3 67.6 + - - +
93A VAL* 4.2 16.8 - - + +
111A LEU 3.9 0.7 - - - +
112A LEU* 3.4 3.6 - - - -
113A ARG* 2.8 54.5 + - + +
255A ASN* 3.0 31.2 - - + +
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Residues in contact with ILE 92 (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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62A VAL* 3.8 37.0 - - + +
66A LEU 5.8 0.2 - - - +
68A PHE* 4.0 28.9 - - + -
89A VAL* 3.7 20.0 - - + -
91A LYS* 1.3 79.3 - - - +
93A VAL* 1.3 63.9 + - - +
94A VAL* 3.9 13.8 + - + +
110A ALA* 5.0 0.4 - - + -
111A LEU 3.8 3.4 - - - -
112A LEU* 3.8 10.8 - - + -
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Residues in contact with VAL 93 (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 TRP* 4.3 6.7 - - + -
91A LYS* 4.2 15.9 - - + -
92A ILE* 1.3 76.5 - - - +
94A VAL* 1.3 64.9 + - - +
96A PRO* 6.2 0.2 - - + -
110A ALA* 3.4 1.4 - - - -
111A LEU* 2.9 43.1 + - + +
247A TRP* 3.8 17.5 - - + +
251A VAL* 3.8 35.2 - - + -
255A ASN* 4.1 16.6 - - - +
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Residues in contact with VAL 94 (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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59A ALA* 3.5 25.4 - - + +
62A VAL* 3.8 30.7 - - + +
92A ILE* 3.9 12.8 + - + +
93A VAL* 1.3 79.5 - - - +
95A HIS* 1.3 77.3 + - - +
96A PRO* 3.3 7.3 - - - +
98A TRP* 3.7 16.6 - - + -
109A ILE 4.0 3.4 - - - -
110A ALA* 4.1 3.1 - - + -
247A TRP* 3.9 4.0 - - - -
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Residues in contact with HIS 95 (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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94A VAL* 1.3 74.1 - - - +
96A PRO* 1.4 72.9 - - + +
97A TYR* 3.2 24.2 + + - +
98A TRP* 3.1 17.0 + - - +
107A TYR* 3.4 44.4 - + + +
109A ILE* 3.1 25.4 + - + +
244A TYR* 3.8 31.9 - + - -
247A TRP* 3.7 34.8 - + - +
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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