Contacts of the strand formed by residues 65 - 73 (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 VAL 65 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B LEU* 4.8 12.8 - - + -
63G LEU 3.1 4.2 - - - +
64G PRO* 1.3 85.7 - - + +
66G SER* 1.3 67.2 + - - +
67G CYS* 4.7 2.0 - - - -
107G ILE 4.0 0.3 - - - +
108G ASN* 3.5 3.6 - - - -
109G ALA* 2.8 35.3 + - + +
110G GLU 4.7 1.8 - - - +
111G SER* 4.0 12.1 - - - +
112G LEU* 4.0 35.9 - - + +
115G VAL* 3.7 30.5 - - + -
132G VAL* 5.2 3.1 - - + -
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Residues in contact with SER 66 (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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112B LEU* 5.8 0.8 - - - +
64G PRO 4.2 1.9 + - - -
65G VAL* 1.3 76.8 - - - +
67G CYS* 1.3 58.9 + - - +
106G LYS* 3.5 11.5 + - - -
107G ILE 3.4 2.7 + - - -
108G ASN* 2.9 27.9 + - - -
132G VAL* 3.7 3.9 - - - +
133G ILE* 2.7 57.9 + - - +
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Residues in contact with CYS 67 (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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134B PHE* 5.4 0.4 - - - -
65G VAL* 4.7 1.6 - - - -
66G SER* 1.3 77.9 - - - +
68G ILE* 1.3 61.9 + - - +
69G VAL* 4.1 1.1 - - + -
105G LEU 4.0 0.2 - - - +
106G LYS* 3.4 6.1 - - - +
107G ILE* 2.9 44.4 + - + +
112G LEU* 5.6 0.2 - - - -
115G VAL* 3.7 28.9 - - - +
130G THR* 3.5 30.3 - - + -
131G HIS 3.3 9.6 - - - +
132G VAL* 4.0 18.2 - - - -
133G ILE* 3.9 8.1 - - - -
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Residues in contact with ILE 68 (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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93D PHE* 5.1 0.7 - - + -
95D TYR* 3.9 16.4 - - + -
97D ILE* 4.2 12.1 - - + -
104D MET* 4.0 22.2 - - + -
67G CYS* 1.3 72.6 - - - +
69G VAL* 1.3 66.9 + - - +
70G GLU 4.2 0.2 - - - -
93G PHE* 3.9 22.4 - - + -
104G MET* 3.7 33.4 - - + -
105G LEU 3.4 7.4 - - - +
106G LYS* 4.0 8.5 - - + -
131G HIS* 2.7 50.7 + - + +
133G ILE* 3.8 28.2 - - + +
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Residues in contact with VAL 69 (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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67G CYS* 4.1 7.4 - - + -
68G ILE* 1.3 84.3 - - - +
70G GLU* 1.3 66.7 + - - +
71G ALA* 3.8 2.6 + - + +
104G MET* 3.5 1.9 - - - -
105G LEU* 2.9 54.6 + - + +
107G ILE* 4.0 26.2 - - + -
115G VAL* 5.5 0.7 - - + -
118G PHE* 4.4 9.9 - - + -
119G ILE* 4.2 9.9 - - + -
128G THR* 3.8 31.4 - - + -
129G VAL 3.4 5.4 - - - +
130G THR* 4.1 11.7 - - + +
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Residues in contact with GLU 70 (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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70D GLU* 4.6 11.6 - - - +
131D HIS* 5.6 4.0 + - - -
68G ILE 4.2 0.6 - - - -
69G VAL* 1.3 74.8 - - - +
71G ALA* 1.3 58.5 + - - +
97G ILE* 5.3 0.2 - - + -
100G ALA* 6.0 1.2 - - - +
101G ALA* 3.6 27.3 + - + +
103G TYR 3.5 3.8 - - - +
104G MET* 3.8 26.0 - - + +
127G GLN 3.6 0.5 - - - +
128G THR* 3.2 6.4 - - - -
129G VAL* 3.0 48.7 + - + +
131G HIS* 2.7 32.5 + - - +
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Residues in contact with ALA 71 (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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69G VAL* 3.8 5.4 + - + +
70G GLU* 1.3 75.2 - - - +
72G THR* 1.3 61.8 + - - +
73G VAL 4.1 0.7 - - - +
81G PHE* 4.0 32.1 - - + -
101G ALA* 3.6 0.7 - - - +
102G CYS* 2.8 26.8 + - - +
103G TYR* 2.7 26.0 + - + +
105G LEU* 5.0 5.4 - - + -
126G ALA* 4.3 4.9 - - + -
127G GLN 3.1 7.2 - - - +
128G THR* 4.9 6.1 - - + -
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Residues in contact with THR 72 (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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127E GLN* 6.3 3.6 - - + -
71G ALA* 1.3 71.9 - - - +
73G VAL* 1.3 70.2 + - - +
100G ALA 4.0 10.3 + - - +
101G ALA* 3.5 20.4 - - - +
102G CYS* 3.7 13.0 - - - -
126G ALA* 3.1 2.7 - - - -
127G GLN* 2.7 62.5 + - - +
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Residues in contact with VAL 73 (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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74E LYS* 5.9 0.9 + - - -
72G THR* 1.3 80.2 - - - +
74G LYS* 1.3 61.8 + - - +
75G ASN 4.3 0.3 + - - -
76G ALA* 4.0 7.2 + - - -
77G ASP 3.3 40.8 - - - +
78G TYR* 3.9 16.9 + - + +
81G PHE* 3.9 25.8 - - + -
102G CYS* 3.3 15.7 - - - -
103G TYR* 3.6 32.1 - - + -
125G TYR 3.7 4.7 - - - +
126G ALA* 4.1 0.7 - - + -
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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