Contacts of the strand formed by residues 81 - 91 (chain A) in PDB entry 3B7C
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 ALA 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 2.9 33.1 + - + -
78A SER* 3.2 19.2 + - - +
80A TYR* 1.3 82.5 - - + +
82A ALA* 1.3 61.8 + - - +
104A LEU* 4.3 13.0 - - + -
105A VAL 3.3 9.0 - - - +
106A GLU* 4.5 8.3 - - + +
112A TRP* 3.6 5.1 - - - -
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Residues in contact with ALA 82 (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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6A ILE* 3.7 19.1 - - + -
74A ILE* 4.4 2.2 - - + -
75A LYS 3.2 14.8 - - - +
76A MSE 3.8 13.0 - - + -
77A LEU* 4.1 7.9 - - - +
81A ALA* 1.3 76.4 - - - +
83A MSE 1.3 64.0 + - - +
104A LEU* 3.5 6.6 - - - +
105A VAL* 2.9 49.3 + - + +
112A TRP* 4.2 0.4 - - + -
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Residues in contact with MSE 83 (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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73A GLU* 3.5 27.3 - - + +
74A ILE* 3.3 5.9 - - - +
75A LYS* 2.8 67.1 + - + +
77A LEU* 4.0 14.6 - - + +
82A ALA* 1.3 73.1 - - - +
84A VAL* 1.3 64.7 + - - +
85A VAL* 3.8 30.5 - - + -
102A THR* 5.8 2.9 - - - -
103A LEU 3.4 8.7 - - - +
104A LEU* 5.0 0.9 - - - +
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Residues in contact with VAL 84 (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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6A ILE* 3.6 27.8 - - + -
10A LEU* 3.8 26.5 - - + -
71A ILE* 4.1 15.0 - - + -
73A GLU 3.4 7.9 - - - +
74A ILE* 4.1 8.7 - - + -
83A MSE 1.3 79.3 - - - +
85A VAL* 1.4 63.2 + - - +
101A PHE* 3.9 10.1 - - + +
102A THR* 3.4 3.1 - - - -
103A LEU* 2.8 50.2 + - + +
105A VAL* 4.2 21.5 - - + -
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Residues in contact with VAL 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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71A ILE* 3.7 2.3 - - - +
72A LYS* 2.7 46.7 + - + +
73A GLU* 2.8 26.8 + - + +
83A MSE 3.8 33.7 - - + -
84A VAL* 1.4 76.4 - - - +
86A GLY* 1.3 55.7 + - - +
100A VAL* 6.5 0.7 - - + -
101A PHE* 3.5 7.4 - - - +
102A THR* 3.9 26.5 - - + -
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Residues in contact with GLY 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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70A THR 3.2 13.7 - - - -
72A LYS* 3.7 7.6 - - - -
85A VAL* 1.3 79.0 - - - +
87A ARG* 1.3 64.9 + - - +
100A VAL* 3.4 8.1 - - - +
101A PHE* 2.9 43.1 + - - +
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Residues in contact with ARG 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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68A LYS 4.0 0.2 - - - +
69A PHE* 3.5 0.9 - - - -
70A THR* 2.9 43.3 + - + +
72A LYS* 5.5 2.0 - - + +
86A GLY* 1.3 78.5 - - - +
88A TRP* 1.3 61.3 + - - +
89A ASP* 4.7 8.0 + - - +
98A THR* 3.2 36.4 + - - +
99A GLY* 3.2 16.7 + - - +
100A VAL* 3.6 20.1 - - + +
101A PHE* 3.4 9.6 - - - -
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Residues in contact with TRP 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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67A LEU* 4.5 4.9 - - + -
68A LYS 3.6 4.5 - - - +
69A PHE* 4.0 23.8 - - + -
87A ARG* 1.3 73.9 - - - +
89A ASP* 1.3 68.3 + - - +
90A LEU* 4.0 20.4 - - + -
97A PRO* 3.6 30.3 - - + -
98A THR* 3.1 17.2 + - - -
99A GLY* 2.9 59.5 + - - -
100A VAL 3.3 21.5 + - - +
101A PHE* 4.2 10.1 - + + -
119A SER* 4.4 9.4 - - - -
120A SER 3.4 7.8 + - - +
121A ASP* 3.7 20.6 - - + -
127A EDO 3.7 13.5 - - - -
128A EDO 5.7 1.1 - - - -
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Residues in contact with ASP 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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67A LEU* 3.5 6.2 - - - +
68A LYS* 2.9 37.9 + - + +
70A THR* 4.6 10.7 + - - -
87A ARG* 4.7 8.0 + - - +
88A TRP* 1.3 80.3 + - - +
90A LEU* 1.3 62.3 + - - +
96A THR 5.1 1.0 - - - +
97A PRO 3.5 4.5 - - - +
98A THR* 2.8 28.3 + - - -
126A EDO 3.4 21.9 - - - +
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Residues in contact with LEU 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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17A TRP* 3.6 32.5 - - + +
58A TYR* 5.4 0.9 - - - +
64A LEU 3.7 10.1 - - - +
65A GLY 4.4 0.9 - - - -
66A GLU 3.2 14.1 - - - +
67A LEU* 3.9 18.2 - - + -
88A TRP* 4.0 20.9 - - + -
89A ASP* 1.3 76.4 - - - +
91A LYS* 1.3 58.9 + - - +
92A ARG* 3.7 29.2 - - + +
96A THR* 3.1 27.9 - - - -
97A PRO* 2.9 21.7 + - + +
126A EDO 3.9 3.4 - - - -
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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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65A GLY* 3.5 5.5 - - - -
66A GLU* 2.8 42.2 + - + +
90A LEU* 1.3 72.5 - - - +
92A ARG* 1.3 68.6 + - - +
95A ASP 4.2 1.1 - - - -
96A THR* 4.3 15.0 - - + -
126A EDO 3.8 14.6 - - - +
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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