Contacts of the strand formed by residues 103 - 109 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ILE* 3.4 25.6 - - + +
116E GLU* 5.3 0.9 + - - -
70G GLU* 3.5 5.7 - - - +
71G ALA* 2.7 42.5 + - + -
73G VAL* 3.6 18.8 - - + -
78G TYR* 3.7 30.4 + + - +
81G PHE* 3.4 31.9 - + + -
82G LYS* 5.0 1.2 - - - +
94G CYS* 3.8 22.4 - - - -
95G TYR 3.0 17.9 - - - +
96G ARG* 3.4 29.0 + - + -
97G ILE* 4.2 5.4 - - - -
101G ALA* 3.6 1.3 - - - +
102G CYS* 1.3 88.4 - - + +
104G MET* 1.3 58.1 + - - +
105G LEU* 4.2 1.1 - - + +
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Residues in contact with MET 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 3.7 32.5 - - + -
70D GLU* 5.0 0.2 - - - +
104D MET* 4.1 14.8 - - + -
131D HIS* 3.7 23.6 - - + +
68G ILE* 3.7 30.1 - - + -
69G VAL 3.5 3.4 - - - -
70G GLU* 3.8 29.6 - - + +
93G PHE* 3.7 13.5 - - + -
94G CYS* 3.6 0.9 - - - -
95G TYR* 2.8 36.5 + - + +
97G ILE* 3.5 30.4 - - + +
103G TYR* 1.3 71.3 - - - +
105G LEU* 1.3 59.3 + - - +
131G HIS* 5.0 0.2 - - - -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ILE* 3.4 9.2 - - - +
69G VAL* 2.9 58.2 + - + +
71G ALA* 5.0 6.7 - - + -
81G PHE* 4.0 18.2 - - + -
85G ILE* 3.9 27.6 - - + -
91G ILE* 4.1 8.3 - - + -
93G PHE* 3.1 18.8 - - - +
94G CYS* 3.9 16.4 - - + -
103G TYR* 5.3 0.4 - - + -
104G MET* 1.3 73.5 - - - +
106G LYS* 1.3 72.2 + - - +
107G ILE* 4.5 2.7 - - + +
118G PHE* 4.2 18.4 - - + -
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Residues in contact with LYS 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 3.0 36.4 + - + +
58G GLN* 6.1 0.2 - - - +
66G SER* 3.5 22.9 + - - -
67G CYS 3.4 10.5 - - - +
68G ILE* 4.0 5.4 - - + -
91G ILE* 3.3 10.6 - - - +
92G GLU* 2.8 62.5 + - + +
93G PHE* 3.0 36.2 + - + -
105G LEU* 1.3 75.9 - - - +
107G ILE* 1.3 62.6 + - - +
108G ASN* 3.8 7.0 - - - +
133G ILE* 3.9 10.3 - - + -
136G GLU* 5.7 0.2 + - - -
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Residues in contact with ILE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G VAL 4.0 0.2 - - - +
66G SER* 3.4 6.8 + - - -
67G CYS* 2.9 57.9 + - + +
69G VAL* 4.0 15.3 - - + -
88G LEU* 5.7 0.4 - - + -
89G PRO 5.2 4.7 - - - +
90G ASN* 3.6 4.5 - - + +
91G ILE* 4.2 11.4 - - + -
105G LEU* 4.7 6.3 - - + -
106G LYS* 1.3 76.2 - - - +
108G ASN* 1.4 78.4 + - - +
109G ALA* 4.5 8.9 - - + +
114G ALA 5.7 0.2 - - - +
115G VAL* 4.8 7.6 - - + -
118G PHE* 3.5 46.9 - - + -
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Residues in contact with ASN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLN* 3.7 30.7 + - - +
63G LEU* 4.1 26.4 + - + -
65G VAL 3.5 3.7 + - - +
66G SER* 2.9 26.9 + - - -
90G ASN* 3.0 41.2 + - + +
92G GLU* 3.3 24.6 + - - +
106G LYS* 3.8 11.3 - - - +
107G ILE* 1.4 76.5 - - - +
109G ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LEU* 3.0 29.6 - - - +
65G VAL* 2.8 16.8 + - + +
90G ASN* 5.5 0.4 - - - +
107G ILE* 4.5 8.7 - - + +
108G ASN* 1.3 77.3 - - - +
110G GLU* 1.3 64.1 + - - +
111G SER 3.4 8.5 + - - +
114G ALA* 4.2 10.1 - - + -
115G VAL* 3.5 32.8 - - + +
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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