Contacts of the strand formed by residues 103 - 109 (chain B) in PDB entry 2CFX
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 TYR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.6 31.8 - - + +
69B VAL 4.3 0.2 - - - -
70B GLU* 3.3 5.5 - - - +
71B ALA* 2.8 39.9 + - + -
73B VAL* 3.9 10.5 - - + -
78B TYR* 3.7 19.8 + + - +
81B PHE* 3.4 30.7 - + + -
82B LYS* 5.3 0.3 - - - +
94B CYS* 3.7 22.0 - - - -
95B TYR 3.0 16.8 - - - +
96B ARG* 3.4 33.9 + - + -
97B ILE* 3.9 5.4 - - - +
101B ALA* 3.8 0.6 - - - +
102B CYS* 1.3 94.6 - - + +
104B MET* 1.3 63.9 + - - +
105B LEU* 5.1 1.6 - - + -
116H GLU* 5.1 2.1 + - - -
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Residues in contact with MET 104 (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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68A ILE* 4.0 24.5 - - + -
70A GLU* 4.9 0.2 - - - +
104A MET* 3.7 24.9 - - + +
131A HIS* 3.8 31.2 - - + +
68B ILE* 3.7 25.1 - - + -
69B VAL 3.4 3.6 - - - +
70B GLU* 3.5 34.1 - - + +
93B PHE* 3.7 12.7 - - + -
94B CYS* 3.4 1.1 - - - -
95B TYR* 2.8 37.2 + - + +
97B ILE* 3.8 19.3 - - + +
103B TYR* 1.3 73.0 - - - +
105B LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 105 (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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68B ILE* 3.2 10.0 - - - +
69B VAL* 2.8 61.4 + - + +
71B ALA* 5.0 7.2 - - + -
81B PHE* 4.3 10.8 - - + -
85B ILE* 4.1 22.2 - - + -
91B ILE* 4.4 6.7 - - + -
93B PHE* 2.9 24.7 - - - +
94B CYS* 3.8 23.3 - - + -
103B TYR* 5.1 0.9 - - + -
104B MET* 1.3 75.4 - - - +
106B LYS* 1.3 60.3 + - - +
107B ILE* 3.9 24.5 - - + -
118B PHE* 4.1 10.3 - - + -
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Residues in contact with LYS 106 (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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95A TYR* 2.9 36.9 + - + +
58B GLN* 5.9 1.0 - - - +
66B SER* 3.9 4.7 + - - -
67B CYS 3.3 11.9 - - - +
68B ILE* 3.9 5.8 - - + -
91B ILE* 3.5 6.8 - - - +
92B GLU* 2.8 66.9 + - + +
93B PHE* 3.1 31.8 + - + -
105B LEU* 1.3 76.5 - - - +
107B ILE* 1.4 62.1 + - - +
108B ASN* 3.8 16.9 - - - +
133B ILE* 3.8 17.9 - - - -
136B GLU* 5.6 0.4 + - - -
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Residues in contact with ILE 107 (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 VAL 3.9 0.3 - - - +
66B SER* 3.1 6.4 - - - -
67B CYS* 3.0 46.1 + - + +
69B VAL* 4.3 5.2 - - + -
90B ASN* 3.4 5.6 - - + +
91B ILE* 3.2 31.6 - - + -
105B LEU* 3.9 13.2 - - + -
106B LYS* 1.4 73.9 - - - +
108B ASN* 1.3 65.6 + - - +
109B ALA* 5.0 4.5 - - + -
115B VAL* 4.1 25.8 - - + -
118B PHE* 3.9 36.8 - - + -
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Residues in contact with ASN 108 (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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58B GLN* 3.8 27.0 + - - +
63B LEU* 4.0 27.1 + - + -
65B VAL 3.2 4.0 + - - +
66B SER* 2.8 32.1 + - - -
90B ASN* 3.1 34.8 + - + +
92B GLU* 3.1 29.4 + - - +
106B LYS* 3.8 11.1 - - - +
107B ILE* 1.3 74.0 + - - +
109B ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 109 (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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63B LEU* 3.1 28.5 - - - +
65B VAL* 2.7 17.8 + - + +
90B ASN* 5.4 0.4 - - - +
107B ILE* 5.0 5.6 - - + -
108B ASN* 1.3 77.4 - - - +
110B GLU* 1.3 65.5 + - - +
111B SER 3.2 7.8 + - - +
114B ALA* 4.0 11.2 - - + -
115B VAL* 3.7 31.4 - - + +
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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