Contacts of the helix formed by residues 45 - 49 (chain H) 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 LEU 45 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G VAL* 4.3 27.4 - - + -
119G GLN 5.1 0.7 - - - +
43H ARG* 4.1 28.5 - - + -
44H GLY* 1.3 70.6 - - - +
46H GLU* 1.3 64.1 + - + +
48H ILE* 3.3 16.9 + - + +
49H LEU* 3.2 31.9 + - + +
60H PHE* 3.8 20.6 - - + +
61H THR* 4.4 5.6 - - + +
63H ARG 4.3 0.2 - - - -
64H ALA* 3.6 42.2 - - + +
482H LEU* 5.2 5.6 - - + -
536H HIS* 2.8 24.2 + - + +
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLY* 3.4 0.6 - - - -
45H LEU* 1.3 76.8 + - - +
47H MET* 1.3 60.0 + - - +
48H ILE 3.5 0.5 + - - -
49H LEU* 3.5 15.3 + - - +
50H LYS* 3.6 12.6 + - - +
341H THR* 2.9 35.4 + - + +
358H LYS* 4.4 1.4 + - - -
480H PHE* 3.2 28.5 + - - +
481H GLN* 3.7 12.8 + - - +
482H LEU* 3.4 21.7 + - + +
535H VAL 5.3 0.5 - - - +
536H HIS* 3.2 20.8 + - + +
540H MG 2.0 32.8 - - - -
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Residues in contact with MET 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PRO* 3.6 19.4 - - + +
125G PRO* 3.9 28.9 - - + -
42H PHE* 3.8 27.8 - - - -
44H GLY* 3.3 7.8 + - - +
45H LEU 3.2 0.4 - - - -
46H GLU* 1.3 75.8 - - - +
48H ILE* 1.3 59.0 + - - +
50H LYS* 3.6 19.6 - - - +
341H THR* 3.9 25.4 - - + +
342H LYS* 5.3 0.4 - - - -
343H PRO* 3.8 26.9 - - + -
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G VAL* 3.3 21.5 - - + +
119G GLN* 3.8 18.8 - - - +
121G ALA* 3.8 13.7 - - + +
122G LYS 3.5 22.9 - - - +
123G PRO* 3.8 0.6 - - + +
125G PRO* 3.8 17.9 - - + -
43H ARG 4.5 0.4 - - - +
44H GLY 3.4 18.4 - - - +
45H LEU* 3.5 17.3 - - + +
47H MET* 1.3 74.3 - - - +
49H LEU* 1.3 59.3 + - - +
50H LYS 3.8 2.6 + - - +
52H ARG* 2.6 32.2 + - - +
60H PHE* 3.7 34.3 - - + -
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Residues in contact with LEU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 3.2 21.6 + - + +
46H GLU* 3.6 11.9 - - - +
48H ILE* 1.3 74.7 - - - +
50H LYS* 1.3 67.2 + - - +
51H GLY 3.1 0.3 + - - -
52H ARG* 2.8 27.3 + - + +
57H ALA* 4.4 11.9 - - - +
60H PHE* 3.5 38.4 - - + -
61H THR* 3.8 15.9 - - + -
477H ILE* 3.8 17.4 - - + +
480H PHE* 3.5 44.9 - - + -
482H LEU* 4.6 2.7 - - + -
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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