Contacts of the helix formed by residues 54 - 64 (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 PRO 54 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H ARG 3.5 4.5 - - - +
53H ASP* 1.3 86.7 - - - +
55H ARG* 1.3 58.7 + - - +
56H ASP 3.4 0.5 + - - -
57H ALA* 3.4 17.4 + - + +
58H GLN 4.6 0.9 + - - -
80H VAL* 3.9 26.4 - - + +
83H CYS* 6.2 0.2 - - - -
225H VAL* 4.9 1.6 - - - +
449H TYR* 3.5 20.6 - - + +
470H ILE* 3.7 22.7 - - + -
472H GLN* 4.3 8.5 - - + -
475H GLY 3.1 26.5 - - - +
476H LYS 3.8 2.0 - - - +
477H ILE* 3.8 22.9 - - + -
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Residues in contact with ARG 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G PHE* 3.9 18.2 - - - -
217G LEU* 5.4 3.4 - - - +
262G TYR* 3.4 74.2 + - + +
53H ASP* 2.8 18.8 + - - +
54H PRO* 1.3 77.1 - - - +
56H ASP* 1.3 61.0 + - - +
58H GLN* 4.3 8.9 + - - +
59H HIS* 3.9 5.9 - - - -
224H VAL* 5.4 3.4 - - - +
225H VAL* 4.7 15.1 - - + +
444H TYR* 4.7 8.1 + - - -
447H TRP* 3.8 32.5 - - + +
449H TYR* 3.7 12.6 - - - +
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Residues in contact with ASP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G SER* 3.7 7.2 - - - -
260G PRO* 3.2 24.5 - - - +
261G PHE* 3.0 38.1 + - + +
262G TYR* 4.6 1.7 + - - -
52H ARG* 5.2 7.1 - - + +
53H ASP* 2.8 26.7 + - + +
55H ARG* 1.3 78.9 - - - +
57H ALA* 1.3 66.3 + - - +
58H GLN 3.2 2.2 - - - -
59H HIS* 2.8 23.5 + - - +
60H PHE* 3.5 22.5 + - + -
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 4.4 13.7 - - + -
52H ARG* 6.0 0.8 - - - +
53H ASP 3.5 3.4 + - - -
54H PRO* 3.4 16.7 + - + +
56H ASP* 1.3 77.2 - - - +
58H GLN* 1.3 62.8 + - - +
60H PHE* 3.1 2.8 + - - +
61H THR* 2.8 29.7 + - + +
76H SER* 4.3 3.4 - - - +
80H VAL* 5.1 2.0 - - + -
477H ILE* 4.4 8.2 - - + +
480H PHE* 3.6 36.1 - - + -
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Residues in contact with GLN 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G TYR* 3.3 16.2 + - - -
54H PRO 4.6 1.8 + - - -
55H ARG 4.3 6.9 + - - +
56H ASP 3.0 1.4 + - - -
57H ALA* 1.3 79.1 - - - +
59H HIS* 1.3 77.0 + - + +
61H THR* 3.2 8.3 + - - -
62H GLN* 3.1 31.1 + - - +
73H ALA* 3.9 28.4 - - - +
76H SER* 3.8 8.0 - - - -
77H VAL* 3.5 14.5 - - + +
223H THR* 2.7 52.3 + - - +
224H VAL* 3.5 9.7 - - - +
225H VAL* 4.5 2.8 - - + +
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Residues in contact with HIS 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G HIS* 3.5 21.7 - + - -
247G ILE* 4.3 23.8 - - + +
255G TRP* 3.4 5.8 - - + -
261G PHE* 3.7 39.1 - + + +
262G TYR* 2.8 33.2 + + - -
55H ARG 3.9 11.0 - - - -
56H ASP 2.8 15.1 + - - +
58H GLN* 1.3 86.3 - - + +
60H PHE* 1.3 63.5 + - - +
62H GLN* 3.9 4.5 + - - +
63H ARG* 3.3 36.8 + - - +
220H THR 5.8 0.6 + - - -
221H GLN* 4.7 9.4 - - + +
223H THR 5.0 0.2 - - - -
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Residues in contact with PHE 60 (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* 4.0 12.6 - - + +
121G ALA* 3.8 13.2 - - + -
255G TRP* 3.5 52.3 - + - -
259G SER* 4.8 2.0 - - - -
261G PHE* 4.1 15.3 - + - -
45H LEU* 3.8 14.9 - - + +
48H ILE* 3.7 31.6 - - + -
49H LEU* 3.5 25.8 - - + -
52H ARG* 3.6 24.2 - - - -
56H ASP* 3.6 22.7 - - + -
57H ALA 3.1 2.4 + - - +
59H HIS* 1.3 77.6 - - - +
61H THR* 1.3 64.1 + - - +
63H ARG* 3.2 19.4 + - - +
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Residues in contact with THR 61 (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* 4.5 8.1 - - + -
49H LEU* 3.8 26.5 - - + -
57H ALA 2.8 22.4 + - - +
58H GLN* 3.2 7.4 + - - -
60H PHE* 1.3 65.9 - - - +
62H GLN* 1.3 70.7 + - - +
63H ARG 3.0 2.0 - - - -
64H ALA* 2.9 22.6 + - - +
72H HIS* 3.3 13.1 + - - +
76H SER* 3.0 24.3 + - - +
468H HIS* 3.8 11.7 - - + -
480H PHE* 4.0 11.0 - - + -
482H LEU* 4.0 12.8 - - + -
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Residues in contact with GLN 62 (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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58H GLN* 3.1 14.7 + - - +
59H HIS* 4.0 10.2 + - - +
60H PHE 3.2 0.2 - - - -
61H THR* 1.3 84.9 + - - +
63H ARG* 1.3 71.9 + - - +
64H ALA 3.1 2.1 + - - -
65H CYS 3.1 23.7 + - - +
69H THR* 5.1 0.2 - - - -
70H TYR 2.9 29.8 + - - +
72H HIS* 3.8 12.4 - - + -
73H ALA* 3.7 23.0 - - + +
219H HIS* 3.4 14.4 - - - +
220H THR* 3.0 44.2 + - - +
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Residues in contact with ARG 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G CYS* 3.2 7.9 - - - +
118G VAL* 4.0 12.6 - - + +
148G CYS* 3.0 39.0 + - - +
247G ILE* 4.3 18.2 - - - +
249G CYS* 4.8 3.6 - - - +
255G TRP* 3.7 18.4 - - + -
267G SF4 3.6 26.0 - - - -
43H ARG* 2.8 21.9 + - - -
45H LEU* 4.3 2.0 - - - +
59H HIS* 3.3 27.7 + - - +
60H PHE 3.2 11.2 + - - +
61H THR 3.0 1.2 - - - -
62H GLN* 1.3 95.8 - - - +
64H ALA* 1.3 61.4 + - - +
65H CYS 3.0 2.5 - - - +
216H LYS* 4.3 7.1 - - - +
219H HIS* 3.5 28.1 - - - +
220H THR 5.0 1.6 + - - -
221H GLN* 4.6 5.3 + - - -
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 2.7 25.6 + - - +
45H LEU* 3.6 19.4 - - + +
61H THR 2.9 18.5 + - - +
63H ARG* 1.3 80.4 - - - +
65H CYS* 1.3 60.0 + - - +
72H HIS* 4.1 20.2 - - + +
482H LEU* 4.4 4.0 - - + -
532H ALA* 3.1 19.5 - - - +
533H CYS* 5.0 1.6 - - - -
536H HIS* 4.3 14.1 - - + -
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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