Contacts of the strand formed by residues 67 - 75 (chain N) in PDB entry 6CET
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 CYS 67 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M PHE* 5.5 1.8 - - - -
60N MET* 3.7 30.5 - - + -
61N GLU 3.3 13.7 - - - +
62N LYS* 4.0 15.0 - - - -
66N GLY* 1.3 80.7 - - - -
68N PRO* 1.3 67.0 - - - +
69N VAL* 4.0 4.5 + - + +
87N PHE 4.0 0.9 - - - +
88N VAL* 3.5 1.2 - - - +
89N CYS* 2.9 37.7 + - + +
90N ASP 5.1 2.0 - - - +
91N ALA* 3.7 23.5 - - - +
95N THR* 5.5 3.8 - - - +
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Residues in contact with PRO 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 4.9 12.1 - - + -
42N VAL* 5.6 6.7 - - + -
46N THR* 5.0 15.9 - - + -
49N GLU* 5.1 6.1 - - - +
59N ALA 4.2 0.5 - - - +
60N MET* 3.2 3.6 - - - +
61N GLU* 3.0 43.3 + - + +
62N LYS 4.6 0.4 - - - +
63N LYS* 4.1 23.6 - - + -
65N ILE* 6.0 0.2 - - + -
66N GLY 4.2 0.2 - - - -
67N CYS* 1.3 86.6 - - - +
69N VAL* 1.3 63.7 + - - +
70N CYS* 5.5 1.6 - - + -
87N PHE 3.8 4.5 - - - +
88N VAL* 3.7 22.9 - - + -
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Residues in contact with VAL 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 4.8 1.7 - - - -
58N THR* 5.3 6.1 - - - -
59N ALA 3.6 10.5 - - - +
60N MET* 3.7 24.5 - - + -
67N CYS 4.6 4.7 - - - +
68N PRO* 1.3 77.8 - - + +
70N CYS* 1.3 67.2 + - - +
86N GLY* 3.2 5.2 - - - -
87N PHE* 2.9 51.2 + - + +
89N CYS* 5.7 2.5 - - - -
98N LEU* 5.6 9.6 - - + -
99N GLU* 5.1 16.2 - - + -
102N VAL* 4.6 22.7 - - + -
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Residues in contact with CYS 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 5.9 3.1 - - + -
49N GLU* 4.2 15.0 - - - +
50N LEU* 3.6 16.2 - - + -
57N VAL 3.8 1.0 - - - +
58N THR* 3.6 2.8 - - - +
59N ALA* 2.9 38.8 + - + +
68N PRO* 5.5 2.0 - - + +
69N VAL* 1.3 80.5 - - - +
71N ILE* 1.3 63.9 + - - +
72N GLU* 3.2 20.1 - - - +
84N ASN* 2.8 36.1 - - - -
85N LEU 3.5 6.1 - - - +
86N GLY* 5.0 1.8 - - - -
102N VAL* 5.0 1.8 - - - -
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Residues in contact with ILE 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56N THR* 4.3 6.3 - - + -
57N VAL 3.3 28.7 - - - +
58N THR* 3.8 23.3 - - + -
70N CYS* 1.3 76.3 - - - +
72N GLU* 1.3 67.8 + - - +
73N HIS* 5.7 0.4 - - - +
84N ASN* 2.4 26.6 + - - -
85N LEU* 2.9 32.4 + - + +
102N VAL* 3.8 21.3 - - + +
103N LYS* 4.0 18.2 - - + -
106N ALA* 3.7 33.2 - - + -
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Residues in contact with GLU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N GLU* 3.7 16.8 - - - +
50N LEU 4.8 9.9 - - - +
51N GLN* 5.5 1.8 - - - -
52N ASN* 5.6 5.8 - - - +
54N LEU 4.3 13.5 - - - +
55N ILE* 4.7 11.1 - - + -
56N THR* 3.4 23.1 + - - -
57N VAL* 3.9 14.8 - - - +
59N ALA* 5.9 2.6 - - - +
70N CYS* 3.2 19.7 - - - +
71N ILE* 1.3 82.2 - - - +
73N HIS* 1.3 73.1 + - - +
74N LYS* 6.0 2.7 - - + -
82N LEU* 6.6 0.2 - - + -
83N PHE 3.2 10.8 - - - +
84N ASN* 3.3 22.3 - - - +
106N ALA* 5.6 0.5 - - - +
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Residues in contact with HIS 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N ILE* 4.8 8.3 - - + -
56N THR* 4.6 11.9 - - + +
71N ILE* 5.6 0.8 + - - +
72N GLU* 1.3 79.9 + - - +
74N LYS* 1.3 70.9 + - - +
75N LYS* 5.9 2.5 - - + -
81N LEU* 5.9 0.2 - - + -
82N LEU* 3.6 1.4 - - - +
83N PHE* 3.0 76.1 + + - +
84N ASN* 6.1 0.4 - - - -
85N LEU 6.4 0.4 - - - -
106N ALA* 4.0 17.8 + - + +
109N LEU* 4.3 8.9 - - + -
110N THR* 3.1 47.6 + - + +
113N GLU* 5.7 1.7 - - + +
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Residues in contact with LYS 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N GLN* 4.6 3.4 - - - +
52N ASN 2.7 31.9 + - - +
53N LYS* 3.2 35.2 - - - +
55N ILE* 3.8 30.5 - - + +
72N GLU* 6.0 2.2 - - + -
73N HIS* 1.3 86.1 - - - +
75N LYS* 1.3 67.6 + - - +
81N LEU* 3.1 9.4 - - - +
82N LEU* 3.7 33.1 - - + +
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Residues in contact with LYS 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N HIS* 5.9 2.9 - - + -
74N LYS* 1.3 77.4 - - - +
76N TYR* 1.3 88.9 + - + +
77N SER* 3.6 2.2 - - - -
81N LEU* 2.6 54.4 + - + +
113N GLU* 5.4 9.0 - - + -
114N LEU* 4.0 30.3 - - + +
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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