Contacts of the strand formed by residues 103 - 109 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL 4.4 0.2 - - - -
70A GLU* 3.4 4.9 - - - -
71A ALA* 2.9 38.8 + - + +
73A VAL* 3.7 18.2 - - + -
78A TYR* 3.7 26.5 + + - +
81A PHE* 3.5 32.3 - + + -
82A LYS* 5.2 0.5 - - - +
94A CYS* 3.5 21.3 - - - -
95A TYR 3.0 18.2 - - - +
96A ARG* 3.5 31.7 - - + -
97A ILE* 4.1 3.8 - - - -
101A ALA* 3.7 5.1 - - - +
102A CYS* 1.3 85.4 - - + +
104A MET* 1.3 63.3 + - - +
105A LEU* 5.1 1.6 - - + +
137B ILE* 3.6 27.8 - - + +
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Residues in contact with MET 104 (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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68A ILE* 3.9 24.7 - - + -
69A VAL 3.4 4.3 - - - -
70A GLU* 3.8 29.6 - - + -
93A PHE* 3.7 12.4 - - + -
94A CYS* 3.5 0.4 - - - -
95A TYR* 2.7 34.7 + - + +
97A ILE* 4.0 16.7 - - + +
103A TYR* 1.3 75.3 - - - +
105A LEU* 1.3 59.5 + - - +
68B ILE* 4.1 23.3 - - + -
70B GLU* 4.4 1.3 - - - +
104B MET* 3.7 27.8 - - + +
131B HIS* 3.8 28.9 - - + +
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Residues in contact with LEU 105 (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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68A ILE* 3.5 8.3 - - - +
69A VAL* 2.9 60.9 + - + +
71A ALA* 5.2 3.1 - - + -
81A PHE* 4.2 12.6 - - + -
85A ILE* 3.9 24.5 - - + -
91A ILE* 4.3 6.7 - - + -
93A PHE* 2.8 26.9 - - - +
94A CYS* 3.8 24.0 - - + -
103A TYR* 5.1 3.1 - - + -
104A MET* 1.3 76.1 - - - +
106A LYS* 1.3 65.1 + - - +
107A ILE* 4.7 1.8 - - + +
118A PHE* 4.6 13.0 - - + -
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Residues in contact with LYS 106 (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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66A SER* 3.6 22.5 + - - -
67A CYS 3.4 10.5 - - - +
68A ILE* 3.8 4.5 - - + -
91A ILE* 3.6 6.9 - - - +
92A GLU* 2.9 60.1 + - + +
93A PHE* 3.2 36.4 + - + +
105A LEU* 1.3 75.8 - - - +
107A ILE* 1.3 63.0 + - - +
108A ASN* 3.8 6.1 - - - +
133A ILE* 3.7 14.4 - - + -
95B TYR* 2.9 37.0 + - + +
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Residues in contact with ILE 107 (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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66A SER* 3.2 6.1 + - - -
67A CYS* 3.0 58.2 + - + +
69A VAL* 4.1 14.6 - - + -
90A ASN* 3.5 13.0 - - + +
91A ILE* 4.1 16.4 - - + -
105A LEU* 4.2 2.2 - - + -
106A LYS* 1.3 74.3 - - - +
108A ASN* 1.3 74.4 + - - +
109A ALA* 4.5 11.7 - - + -
114A ALA 5.2 0.4 - - - +
115A VAL* 4.7 9.6 - - + -
118A PHE* 3.6 40.4 - - + -
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Residues in contact with ASN 108 (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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58A GLN* 3.8 30.9 + - + +
63A LEU* 4.1 25.0 + - + +
65A VAL 3.4 3.8 + - - +
66A SER* 2.8 28.3 + - - -
90A ASN* 3.0 37.5 + - + +
92A GLU* 3.4 24.3 + - - +
106A LYS* 3.8 13.7 - - - +
107A ILE* 1.3 77.2 - - - +
109A ALA* 1.3 63.2 + - - +
110A GLU* 4.7 0.3 - - - +
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Residues in contact with ALA 109 (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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63A LEU* 3.2 14.8 - - - +
65A VAL* 2.8 35.7 + - + +
107A ILE* 4.5 8.5 - - + -
108A ASN* 1.3 75.5 - - - +
110A GLU* 1.3 71.3 + - - +
111A SER 3.2 8.7 + - - +
114A ALA* 4.1 6.3 - - + -
115A VAL* 3.7 32.1 - - + +
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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