Contacts of the strand formed by residues 83 - 94 (chain A) in PDB entry 3F40
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 LYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ILE 3.3 1.9 - - - +
79A ASN* 3.3 1.1 - - - -
80A MSE 2.7 43.3 + - - +
81A ASN 4.7 3.6 - - - +
82A GLY* 1.3 82.8 - - - +
84A THR* 1.3 61.4 + - - +
85A ILE* 3.9 6.6 + - + +
109A PRO* 4.4 21.8 - - + +
110A LEU* 3.8 23.1 - - + -
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Residues in contact with THR 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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77A ASP* 3.9 32.3 - - + +
78A ILE 3.4 6.1 - - - +
79A ASN* 4.1 17.5 + - + +
82A GLY 3.9 3.4 + - - -
83A LYS* 1.3 73.1 + - - +
85A ILE* 1.3 67.5 + - - +
86A ALA 4.4 0.6 + - - +
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Residues in contact with ILE 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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77A ASP* 3.4 3.2 - - - -
78A ILE* 2.8 43.9 + - + +
80A MSE 4.4 12.3 - - - -
83A LYS* 4.4 5.6 - - + +
84A THR* 1.3 81.0 - - - +
86A ALA* 1.3 64.0 + - - +
87A ALA* 3.6 1.8 + - + +
105A PHE* 3.5 41.7 - - + -
106A ASP 4.0 17.0 - - - +
109A PRO* 4.1 25.4 - - + -
110A LEU* 4.2 27.6 - - + -
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Residues in contact with ALA 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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76A TYR 3.8 0.4 - - - +
77A ASP* 3.6 20.8 + - - +
84A THR 4.3 0.6 + - - -
85A ILE* 1.3 73.1 - - - +
87A ALA* 1.3 59.5 + - - +
105A PHE* 3.6 15.9 - - - +
106A ASP 5.0 0.5 + - - -
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Residues in contact with ALA 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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75A ILE* 3.7 8.2 - - - +
76A TYR* 2.9 38.4 + - + +
78A ILE* 3.7 31.0 - - + -
85A ILE* 3.6 1.1 + - + +
86A ALA* 1.3 76.4 - - - +
88A SER* 1.3 61.3 + - - +
103A VAL* 4.0 2.9 - - + -
104A TYR 3.3 13.7 - - - +
105A PHE* 3.9 13.2 - - + -
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Residues in contact with SER 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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73A CYS* 3.2 26.0 - - - -
74A LEU 3.3 4.9 - - - -
75A ILE* 3.7 16.8 - - - +
76A TYR* 4.1 2.7 - - - -
87A ALA* 1.3 74.4 - - - +
89A GLY* 1.3 57.1 + - - +
103A VAL* 3.5 0.7 - - - +
104A TYR* 2.8 51.9 + - - -
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Residues in contact with GLY 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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73A CYS* 3.2 5.9 - - - -
74A LEU 2.8 39.8 + - - -
76A TYR* 3.5 25.9 - - - -
88A SER* 1.3 73.8 + - - +
90A LEU* 1.3 60.5 + - - -
91A TYR* 3.5 9.7 - - - -
101A LEU* 4.0 4.3 - - - -
102A HIS 3.7 4.7 - - - -
103A VAL* 4.3 1.8 - - - -
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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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71A ASP* 4.1 28.5 - - + +
72A VAL 3.5 11.2 - - - +
73A CYS* 4.4 17.0 - - + -
88A SER 4.2 0.4 - - - -
89A GLY* 1.3 70.3 - - - -
91A TYR* 1.3 61.3 + - - +
92A HIS* 4.1 0.8 + - + -
100A SER* 3.8 1.0 + - - +
101A LEU* 3.3 5.1 - - - +
102A HIS* 2.8 56.4 + - + +
104A TYR* 4.1 25.4 - - + +
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Residues in contact with TYR 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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11A VAL* 4.2 29.2 - - + -
14A PHE* 4.2 22.3 - + - -
15A ILE* 3.6 10.2 - - + +
34A PHE* 6.1 0.4 - + - -
60A TYR* 5.0 1.9 - - - -
71A ASP* 3.3 6.9 - - - +
72A VAL 2.8 43.6 + - - +
74A LEU* 3.7 22.9 - - + -
76A TYR* 2.7 30.8 + - - -
89A GLY 3.5 19.3 - - - -
90A LEU* 1.3 72.6 - - - +
92A HIS* 1.3 59.9 + - - +
93A LEU* 3.8 4.8 - - + +
98A ILE* 4.2 26.5 - - + -
100A SER 3.4 5.4 - - - +
101A LEU* 3.5 33.4 - - + +
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Residues in contact with HIS 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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70A ASN* 3.4 25.3 + - + +
71A ASP* 2.7 27.0 + - - +
90A LEU* 4.1 1.3 + - + -
91A TYR* 1.3 74.1 - - - +
93A LEU* 1.3 56.8 + - - +
94A GLU* 2.8 34.4 + - + +
98A ILE* 3.5 5.5 - - - +
99A THR* 2.8 48.3 + - - +
100A SER* 3.0 29.3 + - - +
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Residues in contact with LEU 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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7A THR* 3.9 33.2 - - + +
10A LEU* 3.7 29.4 - - + -
11A VAL* 3.9 19.1 - - + -
67A GLU* 5.4 0.2 - - - +
70A ASN* 2.9 38.4 + - - +
72A VAL* 4.0 14.4 - - + -
91A TYR* 3.8 14.8 - - + +
92A HIS* 1.3 81.2 - - - +
94A GLU* 1.3 71.7 + - - +
96A GLY 5.9 0.7 - - - +
97A GLU 3.2 9.6 - - - +
98A ILE* 3.7 23.8 - - + -
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Residues in contact with GLU 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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70A ASN* 5.1 7.3 + - - +
92A HIS* 2.8 30.0 + - + +
93A LEU* 1.3 82.0 - - - +
95A LYS* 1.3 89.6 + - + +
96A GLY 3.1 2.9 - - - -
97A GLU* 3.0 21.7 + - - +
99A THR* 3.9 20.4 - - + +
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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