Contacts of the helix formed by residues 19 - 26 (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 GLY 19 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G CYS* 3.2 15.3 + - - -
18G THR* 1.3 77.5 - - - +
20G CYS* 1.3 58.1 + - - +
21G SER 3.4 0.2 - - - -
22G GLU* 3.9 2.9 - - - -
23G SER 3.1 19.4 + - - -
149G PRO* 3.4 14.6 - - - +
267G SF4 3.9 10.8 - - - -
66H GLY* 3.6 25.4 - - - -
218H PRO* 3.7 7.1 - - - +
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Residues in contact with CYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G TYR* 4.0 2.7 - - - -
19G GLY* 1.3 75.9 - - - +
21G SER* 1.3 62.9 + - - +
23G SER* 3.0 21.3 + - - -
24G VAL* 3.5 9.4 + - - +
73G GLU* 3.1 26.9 + - + +
109G ILE* 3.7 15.2 - - + +
110G GLY* 3.2 32.1 - - - -
149G PRO* 3.9 4.5 - - - -
150G PRO* 3.8 14.4 - - - -
267G SF4 2.3 33.0 - - - -
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Residues in contact with SER 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G TYR* 3.6 6.5 + - - -
13G HIS* 2.9 22.2 + - - -
16G GLU* 4.1 0.2 + - - -
18G THR* 3.5 12.5 + - - +
19G GLY 3.4 0.2 - - - -
20G CYS* 1.3 73.3 - - - +
22G GLU* 1.3 64.7 + - - +
24G VAL* 3.0 22.1 + - - +
25G LEU* 3.5 13.7 + - - +
45G HIS* 4.0 20.9 - - - -
47G THR* 4.7 3.6 - - - -
73G GLU* 2.4 32.7 + - - -
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Residues in contact with GLU 22 (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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18G THR* 3.2 17.6 + - + +
19G GLY 4.2 0.7 - - - +
20G CYS 3.5 0.2 - - - -
21G SER* 1.3 75.4 - - - +
23G SER* 1.3 61.7 + - - +
24G VAL 3.1 0.7 + - - -
25G LEU* 3.3 27.1 + - - +
26G ARG* 2.8 56.4 + - - +
66H GLY 3.7 12.8 - - - +
67H VAL* 3.7 34.7 - - + +
106H HIS* 4.0 6.9 - - - -
110H VAL* 4.6 13.4 - - - +
115H LEU* 6.1 0.7 - - - +
218H PRO* 3.8 13.0 - - + -
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Residues in contact with SER 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLY 3.1 18.2 + - - -
20G CYS* 3.0 11.6 + - - -
21G SER 3.2 0.4 - - - -
22G GLU* 1.3 75.8 - - - +
24G VAL* 1.3 68.1 + - - +
26G ARG* 3.2 8.7 + - - +
109G ILE* 4.6 2.1 - - - +
149G PRO* 3.9 13.6 - - - +
150G PRO* 3.8 25.5 + - - +
152G PRO* 3.1 34.2 - - - +
155G PHE* 6.0 0.9 - - - +
218H PRO* 3.8 13.4 - - - +
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Residues in contact with VAL 24 (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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11G TYR* 4.5 11.9 - - + +
20G CYS 3.6 14.1 - - - +
21G SER* 3.0 10.3 + - - +
23G SER* 1.3 79.6 + - - +
25G LEU* 1.3 57.9 + - + +
26G ARG 3.0 7.2 + - - -
27G THR* 3.0 32.8 + - - +
32G VAL* 4.4 7.1 - - + +
35G LEU* 4.5 18.6 - - + -
36G ILE* 6.1 0.2 - - + -
42G MET* 6.0 5.8 - - + -
45G HIS* 6.3 0.7 - - - +
109G ILE* 4.0 10.8 - - + -
152G PRO* 5.1 3.8 - - + -
155G PHE* 3.7 40.2 - - + -
156G VAL* 4.8 3.1 - - + -
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Residues in contact with LEU 25 (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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21G SER* 3.5 10.5 + - - +
22G GLU* 3.3 38.8 + - + +
24G VAL* 1.3 75.2 - - + +
26G ARG* 1.3 64.1 + - - +
27G THR* 3.4 4.2 + - - +
32G VAL* 4.1 33.5 - - + +
45G HIS* 6.1 1.1 - - - +
47G THR* 6.3 2.7 - - + -
48G LEU* 4.7 28.7 - - + -
110H VAL* 5.4 9.6 - - + -
114H HIS* 6.3 1.6 - - + +
200H LEU* 5.3 7.4 - - + -
203H GLN* 2.8 34.2 + - - +
204H VAL* 3.7 3.8 - - - +
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Residues in contact with ARG 26 (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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22G GLU* 2.8 58.3 + - - +
23G SER* 3.5 12.8 - - - +
24G VAL 3.0 1.8 - - - -
25G LEU* 1.3 79.4 - - - +
27G THR* 1.3 67.8 + - - +
28G VAL* 3.4 12.0 + - - +
152G PRO* 4.0 12.1 - - + +
234G ASN* 4.3 9.9 - - - +
235G GLN* 4.7 6.4 + - - +
66H GLY 5.0 2.0 + - - -
67H VAL 5.8 1.2 + - - -
69H THR* 5.7 1.4 - - - +
106H HIS* 3.4 18.5 + - - -
203H GLN* 3.1 25.6 + - - -
204H VAL* 4.4 11.2 - - + +
207H ALA* 3.3 20.4 - - - +
217H ASN* 2.8 45.4 + - - +
218H PRO* 4.0 2.8 - - - +
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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