Contacts of the strand formed by residues 80 - 89 (chain A) in PDB entry 3FA6
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 PRO 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLU* 5.7 0.2 - - - +
73A GLU 3.7 7.4 - - - +
74A GLN* 4.0 16.8 - - + +
78A GLY 3.8 6.3 - - - +
79A ARG* 1.3 85.7 - - + +
81A CYS* 1.3 59.9 + - - +
99A LEU* 3.7 7.3 - - - +
100A LEU* 3.1 43.0 + - + +
101A LYS 4.8 0.2 + - - -
42B GLU* 4.1 10.8 - - - +
44B LYS* 5.4 8.3 - - + -
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Residues in contact with CYS 81 (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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72A GLU* 3.5 8.3 + - - +
73A GLU* 2.9 48.5 + - - +
74A GLN 4.0 2.5 - - - -
75A THR* 4.0 17.9 - - + -
79A ARG 4.1 1.8 - - - +
80A PRO* 1.3 75.9 - - - +
82A LYS* 1.3 59.3 + - - +
83A SER* 3.6 20.0 - - - -
97A GLN* 3.9 21.3 - - + -
98A LYS 3.2 23.3 - - - +
99A LEU* 4.3 0.9 - - - -
100A LEU* 3.9 8.4 - - - +
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Residues in contact with LYS 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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70A GLU* 3.7 34.6 + - + +
71A PHE 3.5 4.5 - - - -
72A GLU* 3.7 15.8 + - - +
81A CYS* 1.3 73.4 - - - +
83A SER* 1.3 60.9 - - - +
96A GLU 3.9 0.9 - - - +
97A GLN* 3.5 1.0 - - - -
98A LYS* 2.8 66.6 + - + +
99A LEU 5.3 0.4 - - - -
100A LEU* 3.3 25.7 - - - +
46B GLU* 3.5 21.2 + - - +
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Residues in contact with SER 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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70A GLU* 3.3 7.9 - - - +
71A PHE* 2.8 55.6 + - - -
73A GLU* 2.7 38.2 + - - +
81A CYS* 3.6 1.4 - - - -
82A LYS* 1.3 75.7 - - - +
84A LEU* 1.3 62.3 + - - +
95A CYS* 3.7 5.8 - - - -
96A GLU 3.3 4.7 - - - -
97A GLN* 3.6 12.1 - - - +
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Residues in contact with LEU 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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68A GLY* 3.4 39.0 - - - +
69A GLU 3.5 14.8 - - - +
70A GLU* 3.8 8.1 - - + +
71A PHE* 4.3 2.0 - - - -
83A SER* 1.3 77.8 - - - +
85A VAL* 1.3 64.2 + - - +
86A LYS* 3.7 30.7 + - - +
94A VAL 3.6 1.4 - - - +
95A CYS* 3.5 0.4 - - - -
96A GLU* 3.0 37.6 + - + +
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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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65A PHE* 3.8 35.7 - - + -
66A LYS 5.3 0.4 + - - +
67A VAL* 3.5 9.6 - - + +
68A GLY* 2.8 29.6 + - - +
69A GLU 5.0 1.0 + - - -
71A PHE* 3.8 19.7 - - + -
84A LEU* 1.3 75.4 - - - +
86A LYS* 1.3 67.7 + - - +
93A MET* 3.7 30.7 - - + -
94A VAL 3.2 6.7 - - - +
95A CYS* 3.8 22.9 - - + -
109A TRP* 4.0 10.1 - - + -
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Residues in contact with LYS 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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67A VAL* 4.0 4.9 - - - -
68A GLY* 5.2 5.4 - - - -
84A LEU* 3.7 30.8 - - + +
85A VAL* 1.3 84.3 - - - +
87A TRP* 1.3 68.7 + - - +
88A GLU 3.4 0.2 + - - -
93A MET* 3.3 2.6 - - - +
94A VAL* 2.9 35.4 + - + +
96A GLU* 6.4 3.8 - - + -
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Residues in contact with TRP 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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1A PRO* 5.6 3.1 - - + -
3A PHE* 3.8 33.9 - + - -
45A GLN* 4.1 10.8 - - - -
48A ASP* 2.9 28.1 + - - -
50A PHE* 3.8 30.5 - + - -
67A VAL* 3.6 21.2 - - + +
86A LYS* 1.3 77.7 - - - +
88A GLU* 1.3 61.5 + - - +
89A SER* 3.4 23.3 - - - +
90A GLU* 3.8 15.3 - - - -
92A LYS 3.6 16.2 - - - -
93A MET* 4.0 15.7 - - + -
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Residues in contact with GLU 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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86A LYS 3.4 3.6 + - - -
87A TRP* 1.3 74.6 - - - +
89A SER* 1.3 63.1 + - - +
92A LYS* 2.7 44.7 + - + +
94A VAL* 3.7 26.9 - - + +
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Residues in contact with SER 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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87A TRP* 3.4 16.3 - - - +
88A GLU* 1.3 82.0 + - - +
90A GLU* 1.3 65.3 + - - +
91A ASN* 3.0 6.8 + - - +
92A LYS* 3.2 34.4 + - - +
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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