Contacts of the helix formed by residues 45 - 49 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E VAL* 4.3 26.9 - - + -
119E GLN 5.1 1.3 - - - +
43F ARG* 4.1 27.4 - - + +
44F GLY* 1.3 71.0 - - - +
46F GLU* 1.3 64.3 - - + +
48F ILE* 3.3 17.7 + - + +
49F LEU* 3.2 32.4 + - + +
60F PHE* 3.8 19.3 - - + +
61F THR* 4.4 6.3 - - + +
63F ARG 4.3 0.7 - - - -
64F ALA* 3.6 42.0 - - + +
482F LEU* 5.2 5.2 - - + -
536F HIS* 2.8 23.7 + - + +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLY 3.4 0.8 - - - -
45F LEU* 1.3 77.4 - - - +
47F MET* 1.3 59.6 + - - +
48F ILE 3.5 0.2 + - - -
49F LEU* 3.5 15.3 + - - +
50F LYS* 3.6 12.8 + - - +
341F THR* 2.9 35.5 + - + +
358F LYS* 4.4 1.6 + - - -
480F PHE* 3.2 27.8 + - - +
481F GLN* 3.7 14.0 + - - +
482F LEU* 3.4 21.8 + - + +
535F VAL 5.3 0.5 - - - +
536F HIS* 3.2 20.6 + - + +
540F MG 2.0 33.0 - - - -
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Residues in contact with MET 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E PRO* 3.6 18.3 - - + +
125E PRO* 3.9 30.1 - - + -
42F PHE* 3.8 27.1 - - - -
44F GLY 3.3 7.6 + - - +
45F LEU 3.2 0.8 - - - -
46F GLU* 1.3 74.7 - - - +
48F ILE* 1.3 59.8 + - - +
50F LYS* 3.6 20.4 - - - +
341F THR* 3.9 25.8 - - + +
342F LYS* 5.3 0.2 - - - -
343F PRO* 3.8 27.1 - - + -
402J GLU* 5.7 0.2 - - - +
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Residues in contact with ILE 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 3.3 22.2 - - + +
119E GLN* 3.8 18.6 - - - +
121E ALA* 3.8 13.0 - - + +
122E LYS 3.5 24.0 - - - +
123E PRO* 3.8 0.8 - - + +
125E PRO* 3.8 17.3 - - + -
43F ARG 4.5 0.7 - - - +
44F GLY 3.4 19.5 - - - +
45F LEU* 3.3 15.5 + - + +
47F MET* 1.3 73.5 - - - +
49F LEU* 1.3 58.3 - - + +
50F LYS 4.0 2.3 - - - +
52F ARG* 2.6 32.5 + - - +
60F PHE* 3.7 34.1 - - + -
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 3.2 21.8 + - + +
46F GLU* 3.6 12.6 - - - +
48F ILE* 1.3 74.2 - - - +
50F LYS* 1.3 66.9 + - - +
51F GLY 3.1 0.2 + - - -
52F ARG* 2.8 27.6 + - + +
57F ALA* 4.4 11.4 - - + -
60F PHE* 3.5 39.5 - - + -
61F THR* 3.8 15.5 - - + -
477F ILE* 3.8 18.0 - - + +
480F PHE* 3.5 44.6 - - + -
482F 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