Contacts of the helix formed by residues 92 - 102 (chain G) in PDB entry 2FRV
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 MET 92 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G HIS 4.7 0.7 - - - +
14G ASN* 2.9 56.1 - - - +
15G ALA 3.8 3.4 - - - -
76G ILE* 4.3 1.3 - - + -
77G PRO* 4.1 17.3 - - + -
82G GLY 4.6 0.4 + - - -
85G GLY* 3.0 43.1 + - - +
86G LYS* 3.7 7.0 - - - +
87G VAL* 4.4 11.4 - - + -
90G ARG 3.4 0.2 + - - -
91G ASN* 1.3 68.6 - - - +
93G TYR* 1.3 67.1 + - - +
95G ILE* 3.3 10.0 + - + +
96G CYS* 3.1 27.4 + - - -
20H HIS* 3.6 32.3 - - + +
41H LEU* 4.0 7.6 - - + -
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Residues in contact with TYR 93 (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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76G ILE* 3.5 24.9 - - + +
77G PRO 4.2 11.6 + - - +
78G MET* 3.7 26.2 - - + -
81G GLY 5.8 1.1 - - - +
82G GLY* 5.7 2.0 - - - -
91G ASN* 3.2 6.8 - - + +
92G MET* 1.3 78.2 - - - +
94G ASP* 1.3 72.4 + - - +
96G CYS* 3.5 1.6 + - - +
97G ALA* 2.9 38.9 + - + +
134G ALA 3.7 9.9 - - - -
135G LEU* 3.3 26.9 - - + -
137G LYS* 2.8 33.6 + - - -
138G LEU* 3.9 9.4 - - - +
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Residues in contact with ASP 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E THR* 3.6 24.3 - - - +
216E GLU* 3.4 32.2 - - - +
90G ARG* 3.8 4.5 + - - -
91G ASN* 2.8 33.0 + - - +
93G TYR* 1.3 88.4 - - - +
95G ILE* 1.3 65.4 + - - +
97G ALA* 3.3 5.2 + - - +
98G GLU* 3.1 23.0 + - - +
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Residues in contact with ILE 95 (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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12G LEU* 4.3 17.9 - - + -
57G GLU* 5.7 4.5 - - - +
60G LEU* 4.3 11.7 - - + -
87G VAL* 3.6 38.4 - - + +
90G ARG* 3.4 55.4 - - + +
91G ASN 3.1 10.0 + - - +
92G MET* 3.3 8.5 + - + +
94G ASP* 1.3 77.5 - - - +
96G CYS* 1.3 55.9 + - - +
98G GLU* 3.2 1.9 + - - +
99G VAL* 2.9 42.4 + - + +
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Residues in contact with CYS 96 (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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12G LEU* 4.0 21.1 - - - -
14G ASN* 3.4 32.8 - - - -
72G ILE* 4.4 7.0 - - + -
76G ILE* 3.9 15.7 - - + -
92G MET 3.1 18.8 + - - +
93G TYR 3.8 3.4 - - - +
95G ILE* 1.3 72.6 - - - +
97G ALA* 1.3 64.0 + - - +
99G VAL 4.4 0.4 - - - +
100G ALA* 2.9 36.0 + - - +
135G LEU* 3.7 19.8 - - + +
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Residues in contact with ALA 97 (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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93G TYR* 2.9 36.7 + - + +
94G ASP* 3.3 5.8 + - - +
96G CYS* 1.3 77.8 - - - +
98G GLU* 1.3 56.4 + - - +
101G PRO* 2.9 25.8 - - - +
135G LEU* 4.4 2.0 - - - +
138G LEU* 3.4 29.4 - - + +
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Residues in contact with GLU 98 (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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215E TYR* 2.7 24.3 + - - -
264E ALA* 4.2 32.1 - - + +
60G LEU* 6.5 0.2 - - - -
61G HIS* 4.8 3.6 + - - -
64G ILE* 3.7 26.2 - - + +
90G ARG* 2.7 35.8 + - - +
94G ASP 3.1 9.4 + - - +
95G ILE* 3.5 7.9 - - - +
96G CYS 3.1 0.2 - - - -
97G ALA* 1.3 78.3 - - - +
99G VAL* 1.3 65.1 + - + +
101G PRO* 3.8 2.3 - - - +
102G LYS* 3.1 32.7 + - - +
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Residues in contact with VAL 99 (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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10G VAL* 4.2 7.0 - - + -
12G LEU* 4.1 12.6 - - + -
60G LEU* 4.4 10.5 - - + -
64G ILE* 3.9 31.0 - - + -
68G PHE* 3.7 16.6 - - + -
70G CYS* 4.0 20.9 - - - -
95G ILE* 2.9 35.3 + - + +
98G GLU* 1.3 78.1 - - + +
100G ALA* 1.3 68.3 + - - +
102G LYS* 3.0 22.9 + - - +
103G ALA 3.6 3.8 + - - -
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Residues in contact with ALA 100 (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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70G CYS* 4.3 8.7 - - - -
72G ILE* 4.1 18.2 - - + -
96G CYS* 2.9 20.4 + - - +
99G VAL* 1.3 76.7 - - - +
101G PRO* 1.3 65.9 - - + +
103G ALA* 3.2 21.0 + - - +
106G VAL* 3.6 13.9 - - + +
135G LEU* 4.0 12.1 - - + -
140G VAL* 3.9 18.3 - - + +
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Residues in contact with PRO 101 (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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96G CYS 3.4 1.3 - - - +
97G ALA 2.9 29.2 - - - +
98G GLU 3.8 3.1 - - - +
99G VAL 3.4 4.0 - - - -
100G ALA* 1.3 94.5 - - + +
102G LYS* 1.3 60.9 + - + +
103G ALA 3.4 4.7 + - - +
138G LEU* 4.0 35.7 - - + +
139G GLY 6.3 0.4 - - - -
140G VAL* 4.1 9.8 - - + -
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Residues in contact with LYS 102 (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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264E ALA 3.7 24.9 + - - -
64G ILE* 3.9 41.5 - - + +
66G GLY 4.4 5.4 - - - +
68G PHE* 3.6 16.4 - - + -
98G GLU* 3.1 26.2 + - - +
99G VAL 3.0 6.9 + - - +
101G PRO* 1.3 79.6 - - + +
103G ALA* 1.3 60.4 + - - +
104G LYS* 4.1 7.8 + - - -
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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