Contacts of the strand formed by residues 74 - 82 (chain B) in PDB entry 6J7Z
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 ILE 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.3 19.1 - - + -
67B ILE 3.7 5.2 - - - +
68B THR* 4.0 4.5 - - + -
72B LEU 3.4 4.4 + - - +
73B ASN* 1.3 68.2 - - - +
75B LEU* 1.3 64.0 + - - +
76B ALA 4.0 22.2 - - - +
77B GLU* 4.8 4.9 - - + +
201B SER* 6.0 4.3 - - - +
204B ILE* 4.0 33.4 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.3 46.4 - - - +
67B ILE* 2.6 17.2 + - + +
68B THR 3.9 0.9 - - - -
69B ASP* 3.6 35.9 - - + +
73B ASN* 3.6 18.6 - - + +
74B ILE* 1.3 76.7 - - - +
76B ALA* 1.3 60.6 + - + +
131B GLN* 5.5 0.2 - - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.5 5.4 - - - +
67B ILE* 2.9 35.8 + - + +
74B ILE* 3.6 7.2 - - - +
75B LEU* 1.3 80.7 - - + +
77B GLU* 1.3 60.9 + - - +
78B GLY 3.9 0.3 + - - -
127B PHE* 3.6 19.9 - - + -
131B GLN* 3.6 28.9 - - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.7 22.5 - - + +
74B ILE* 4.8 5.8 - - + +
76B ALA* 1.3 71.9 - - - +
78B GLY* 1.3 70.6 + - - +
80B ASN* 6.0 0.6 - - + +
127B PHE* 3.8 7.1 - - - -
197B LEU* 3.8 26.2 - - + +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS 2.9 20.8 + - - +
76B ALA 3.9 0.2 + - - -
77B GLU* 1.3 84.8 - - - +
79B PRO* 1.3 79.2 - - - +
80B ASN* 3.6 4.0 + - - +
127B PHE* 3.4 22.2 - - - -
197B LEU* 6.1 0.3 - - - +
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA* 3.6 0.3 - - - +
65B CYS 3.5 12.0 + - - -
78B GLY* 1.3 86.0 - - - +
80B ASN* 1.3 58.6 + - - +
81B LEU* 3.9 21.5 - - + -
123B GLU* 4.0 31.2 - - + +
124B PHE* 3.2 44.8 - - + -
127B PHE* 3.8 21.8 - - + -
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 4.1 15.1 - - - +
63B MET 3.5 5.2 - - - +
64B ALA* 3.8 16.7 - - + +
77B GLU* 6.0 1.1 - - + +
78B GLY 3.6 3.5 + - - +
79B PRO* 1.3 72.0 - - - +
81B LEU* 1.3 67.9 + - - +
82B ILE* 4.4 1.9 + - - +
195B ARG* 4.6 13.1 - - - +
197B LEU* 3.9 39.5 + - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.3 6.7 - - - +
63B MET 2.9 34.7 + - - +
79B PRO* 3.9 13.0 - - + -
80B ASN* 1.3 85.7 + - - +
82B ILE* 1.3 62.8 + - - +
83B ILE* 3.8 13.9 - - + +
115B ILE* 3.9 24.7 - - + -
120B ALA* 3.8 28.7 - - + -
123B GLU* 3.9 32.8 - - + +
124B PHE* 3.8 14.6 - - + -
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE 3.3 10.3 - - - +
62B GLU* 3.9 24.7 - - + +
80B ASN* 4.4 1.8 + - - +
81B LEU* 1.3 75.0 - - - +
83B ILE* 1.3 58.9 + - - +
106B LEU* 4.2 6.7 - - + -
109B ALA* 3.8 23.8 - - + +
110B VAL* 3.6 38.4 - - + +
113B SER* 2.7 27.6 + - - -
115B ILE* 3.6 15.1 - - - +
195B ARG* 4.4 12.6 - - - +
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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