Contacts of the strand formed by residues 114 - 120 (chain B) in PDB entry 2C47
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.5 37.8 - - + +
59B GLU* 3.9 17.8 + - - -
76B LEU* 3.8 21.8 - - + -
77B GLU 3.3 9.0 - - - +
78B PRO* 3.7 34.8 - - + -
79B ILE* 3.6 12.2 - - - +
110B PRO* 3.4 5.9 - - - +
111B CSD 3.0 34.9 + - - +
112B GLY 3.1 1.4 - - - +
113B LYS* 1.3 95.3 - - + +
115B ASN* 1.3 68.4 + - - +
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Residues in contact with ASN 115 (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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76B LEU* 3.5 4.0 - - - -
77B GLU* 2.8 43.1 + - + +
78B PRO 4.9 0.9 - - - +
79B ILE* 3.3 30.1 - - - +
86B LEU* 3.6 6.4 - - + +
108B PHE* 4.1 25.1 - - + -
109B GLY* 3.3 22.9 - - - +
110B PRO* 3.5 11.5 - - - +
114B TYR* 1.3 76.3 - - - +
116B ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 116 (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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74B ILE* 3.9 11.7 - - + -
75B LYS 3.3 5.6 - - - +
76B LEU* 3.6 20.4 - - + -
86B LEU* 4.2 0.7 - - - -
107B TYR* 3.7 9.2 - - + +
108B PHE* 3.2 11.0 - - - -
109B GLY 2.6 36.6 + - - +
111B CSD 3.9 20.6 - - + +
115B ASN* 1.3 76.8 - - - +
117B MET* 1.3 59.4 + - - +
118B VAL* 4.0 1.3 - - + -
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Residues in contact with MET 117 (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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73B ALA 3.9 0.2 - - - +
74B ILE* 3.5 2.4 - - - -
75B LYS* 2.8 43.5 + - + +
86B LEU* 3.2 50.6 - - + +
89B GLU* 3.8 11.4 - - + +
90B TYR* 3.2 34.1 - - + +
93B TYR* 3.7 26.2 - - - -
105B VAL* 4.1 9.4 - - + -
107B TYR 3.3 8.7 - - - +
108B PHE* 4.3 2.2 - - + -
116B ALA* 1.3 73.2 - - - +
118B VAL* 1.3 62.7 + - - +
119B LEU* 3.9 17.4 + - + +
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Residues in contact with VAL 118 (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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46B PHE* 3.6 45.1 - - + -
72B VAL* 3.7 24.0 - - + -
73B ALA 3.6 3.4 - - - +
74B ILE* 4.5 14.8 - - + +
105B VAL* 3.5 5.4 - - - +
106B TYR* 2.8 33.9 + - + -
107B TYR* 2.9 46.2 + - + +
111B CSD 4.8 3.8 - - - +
116B ALA* 5.1 1.6 - - + -
117B MET* 1.3 73.7 - - - +
119B LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 119 (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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60B LEU* 4.5 12.1 - - + -
72B VAL* 3.3 7.4 - - - +
73B ALA* 2.8 38.0 + - + +
75B LYS* 4.5 8.5 - - + -
93B TYR* 4.0 20.9 - - + +
103B PRO* 4.5 5.4 - - + -
104B GLN 3.3 8.3 - - - +
105B VAL* 3.2 31.2 - - + -
106B TYR* 3.7 6.3 - - - -
117B MET* 3.9 23.1 - - - +
118B VAL* 1.3 77.5 - - - +
120B GLU* 1.3 67.0 + - - +
1300B 5ID 3.7 33.7 - - + +
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Residues in contact with GLU 120 (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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72B VAL* 5.2 1.1 - - - +
73B ALA* 4.4 0.2 - - - +
100B GLU* 5.2 10.7 - - - +
102B VAL 4.3 2.6 - - - +
103B PRO* 3.7 12.0 - - + +
104B GLN* 2.7 44.9 + - - +
106B TYR* 3.4 26.0 - - - +
119B LEU* 1.3 71.7 - - - +
121B LEU* 1.3 62.6 + - - +
122B LEU* 3.7 15.9 + - + +
185B HIS* 5.8 1.8 + - - -
1300B 5ID 2.7 31.0 + - - -
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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