Contacts of the helix formed by residues 54 - 64 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D ARG 3.5 4.9 - - - +
53D ASP* 1.3 87.1 - - - +
55D ARG* 1.3 59.0 + - - +
56D ASP 3.4 0.3 + - - -
57D ALA* 3.4 17.6 + - + +
58D GLN 4.6 0.7 + - - -
80D VAL* 3.9 25.6 - - + +
225D VAL* 4.9 1.6 - - - +
449D TYR* 3.5 20.0 - - + +
470D ILE* 3.7 22.7 - - + -
472D GLN* 4.3 8.3 - - + -
475D GLY 3.1 27.1 - - - +
476D LYS 4.2 2.2 - - - +
477D ILE* 3.8 22.4 - - + -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PHE* 3.9 18.2 - - - -
217C LEU* 5.4 3.0 - - - +
262C TYR* 3.4 72.7 + - + +
53D ASP* 2.8 19.7 + - - +
54D PRO* 1.3 76.0 - - - +
56D ASP* 1.3 60.5 + - - +
58D GLN* 4.3 9.0 + - - +
59D HIS* 3.9 5.9 + - - -
80D VAL* 5.9 0.2 - - + -
224D VAL* 5.4 3.2 - - - +
225D VAL* 4.7 14.1 - - + +
444D TYR* 4.7 7.6 + - - -
447D TRP* 3.8 31.9 - - + +
449D TYR* 3.7 13.0 - - - +
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C SER* 3.7 7.9 - - - -
260C PRO* 3.2 24.3 - - - +
261C PHE* 3.0 38.2 + - + +
262C TYR* 4.6 2.1 + - - -
52D ARG* 5.2 6.8 - - + +
53D ASP* 2.8 27.6 + - - +
55D ARG* 1.3 78.9 - - - +
57D ALA* 1.3 67.3 + - - +
58D GLN 3.2 2.7 - - - -
59D HIS* 2.8 23.6 + - - +
60D PHE* 3.5 22.2 + - + -
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 4.4 13.7 - - + -
52D ARG* 6.0 0.8 - - - +
53D ASP 3.5 3.8 + - - -
54D PRO* 3.4 17.1 + - + +
56D ASP* 1.3 76.2 - - - +
58D GLN* 1.3 62.5 + - - +
60D PHE* 3.1 3.9 + - - +
61D THR* 2.8 29.9 + - + +
76D SER* 4.3 2.7 - - - +
80D VAL* 5.1 2.0 - - + -
477D ILE* 4.4 8.4 - - + +
480D PHE* 3.6 36.6 - - + -
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C TYR* 3.3 16.2 + - - -
54D PRO 4.6 1.6 + - - -
55D ARG 4.3 7.7 + - - +
56D ASP 3.0 1.4 + - - -
57D ALA* 1.3 79.4 - - - +
59D HIS* 1.3 78.6 + - + +
61D THR* 3.2 8.2 + - - -
62D GLN* 3.1 30.3 + - - +
73D ALA* 3.9 27.0 - - - +
76D SER* 3.8 8.4 - - - -
77D VAL* 3.5 14.8 - - + +
223D THR* 2.7 51.0 + - - +
224D VAL* 3.5 8.7 - - - +
225D VAL* 4.5 3.4 - - + +
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C HIS* 3.5 22.1 - + - -
247C ILE* 4.3 23.4 - - + +
255C TRP* 3.4 5.9 - - + -
261C PHE* 3.7 39.5 - + + +
262C TYR* 2.8 32.4 + + - -
55D ARG 3.9 10.5 - - - -
56D ASP 2.8 15.9 + - - +
58D GLN* 1.3 85.6 - - + +
60D PHE* 1.3 63.7 + - - +
62D GLN* 3.9 5.1 + - - +
63D ARG* 3.3 36.2 + - - +
221D GLN* 4.7 9.7 - - + +
223D THR 5.0 0.2 - - - -
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 4.0 12.4 - - + +
121C ALA* 3.8 13.2 - - + -
255C TRP* 3.5 51.4 - + - -
259C SER* 4.8 2.0 - - - -
261C PHE* 4.1 15.3 - + - -
45D LEU* 3.8 13.4 - - + +
48D ILE* 3.7 31.9 - - + -
49D LEU* 3.5 25.1 - - + -
52D ARG* 3.6 24.5 - - - -
56D ASP* 3.6 23.3 - - + -
57D ALA 3.1 2.8 + - - +
59D HIS* 1.3 78.1 - - - +
61D THR* 1.3 63.5 + - - +
63D ARG* 3.2 19.4 + - - +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 4.5 7.6 - - + -
49D LEU* 3.8 27.1 - - + -
57D ALA 2.8 22.3 + - - +
58D GLN* 3.2 7.4 + - - -
60D PHE* 1.3 67.1 - - - +
62D GLN* 1.3 70.6 + - - +
63D ARG 3.0 2.0 - - - -
64D ALA* 2.9 23.1 + - - +
72D HIS* 3.3 12.9 + - - +
76D SER* 3.0 25.3 + - - +
468D HIS* 3.8 11.9 - - + -
480D PHE* 4.0 10.3 - - + -
482D LEU* 4.0 12.6 - - + -
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLN* 3.1 15.1 + - - +
59D HIS* 4.0 10.0 + - - +
60D PHE 3.2 0.4 - - - -
61D THR* 1.3 85.3 + - - +
63D ARG* 1.3 71.3 + - - +
64D ALA 3.1 2.3 + - - -
65D CYS 3.1 22.9 + - - +
68D CYS 5.2 0.2 - - - +
70D TYR 2.9 30.3 + - - +
72D HIS* 3.8 12.1 - - + -
73D ALA* 3.7 22.6 - - + +
219D HIS* 3.4 14.5 - - - +
220D THR* 3.0 44.9 + - - +
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C CYS* 3.2 7.7 - - - +
118C VAL* 4.0 11.5 - - + +
148C CYS* 3.0 38.9 + - - +
247C ILE* 4.3 18.5 - - - +
249C CYS* 4.8 3.2 - - - +
255C TRP* 3.7 19.5 - - + -
267C SF4 3.6 27.6 - - - -
43D ARG* 2.8 21.7 + - - -
45D LEU* 4.3 2.4 - - - +
59D HIS* 3.3 28.2 + - - +
60D PHE 3.2 11.4 + - - +
61D THR 3.0 1.8 - - - -
62D GLN* 1.3 94.6 - - - +
64D ALA* 1.3 61.4 + - - +
65D CYS 3.0 2.5 - - - +
216D LYS* 4.3 6.9 - - - +
219D HIS* 3.5 27.5 - - - +
220D THR 5.0 1.2 + - - -
221D GLN* 4.6 5.3 + - - -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ARG* 2.7 26.7 + - - +
45D LEU* 3.6 18.1 - - + +
61D THR 2.9 17.7 + - - +
63D ARG* 1.3 80.4 - - - +
65D CYS* 1.3 59.0 + - - +
72D HIS* 4.1 20.9 - - + +
482D LEU* 4.4 3.6 - - + -
532D ALA* 3.1 18.2 - - - +
533D CYS* 5.0 1.8 - - - -
536D HIS* 4.3 15.0 - - + -
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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