Contacts of the helix formed by residues 44 - 57 (chain A) in PDB entry 5FZ9
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 ASP 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLU 4.5 1.2 + - - -
41A GLU 3.7 5.6 + - - +
42A PHE 3.2 3.3 - - - -
43A ALA* 1.3 77.7 - - + +
45A PRO* 1.3 70.6 - - - +
46A PHE* 3.3 16.6 + - - +
47A ALA* 3.1 30.1 + - + +
48A PHE* 3.1 22.5 + - - +
467A MET* 5.1 3.5 - - - +
469A GLN* 3.8 14.0 - - - +
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.4 11.2 - - - +
44A ASP* 1.3 87.6 - - - +
46A PHE* 1.3 71.2 + - + +
48A PHE* 3.4 1.8 + - + +
49A ILE* 2.9 39.7 + - + +
458A GLY* 3.9 30.7 - - - +
459A TRP* 3.6 42.4 - - + +
464A MET* 5.0 10.1 - - + -
467A MET* 4.5 6.7 - - + -
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 3.3 7.8 + - - +
45A PRO* 1.3 85.6 - - + +
47A ALA* 1.3 65.8 + - - +
49A ILE* 4.0 6.3 - - + +
50A HIS* 3.1 24.4 + - - +
464A MET* 3.8 25.8 - - + -
467A MET* 3.9 34.3 - - + -
469A GLN* 3.8 37.0 - - + +
470A SER* 3.8 34.5 - - - -
602A PHE* 4.3 11.7 - + - -
604A THR* 4.0 29.5 - - + +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU 5.8 0.7 - - - +
44A ASP* 3.1 31.0 + - + +
46A PHE* 1.3 78.1 - - - +
48A PHE* 1.3 57.4 + - - +
50A HIS* 3.4 7.5 + - - +
51A LYS* 3.0 27.6 + - - +
469A GLN* 4.7 1.0 + - - -
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.8 20.2 - + + -
37A PRO* 3.6 32.1 - - + -
41A GLU* 3.8 28.9 + - + +
42A PHE* 5.5 0.2 - - - -
44A ASP 3.1 16.6 + - - +
45A PRO* 3.6 5.8 - - + +
47A ALA* 1.3 75.3 - - - +
49A ILE* 1.3 67.8 + - + +
51A LYS* 3.0 23.7 + - + +
52A ILE* 3.0 51.5 + - + +
64A VAL* 4.0 23.1 - - + -
459A TRP* 4.1 20.4 - + + -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO* 2.9 29.1 + - + +
46A PHE* 4.0 7.6 - - + +
48A PHE* 1.3 79.4 - - + +
50A HIS* 1.3 62.9 + - - +
52A ILE* 3.4 10.6 - - + +
53A ARG* 3.2 23.1 + - + +
459A TRP* 5.0 4.3 - - + -
464A MET* 5.2 6.5 - - - -
506A TYR* 4.0 28.9 - - + +
508A ILE* 5.3 2.2 - - + -
580A ILE* 4.1 27.1 - - + -
582A PHE* 4.5 8.2 - - + -
602A PHE* 3.6 32.5 - - + -
604A THR* 5.2 5.6 - - + -
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE 3.1 19.0 + - - +
47A ALA* 3.6 7.0 - - - +
49A ILE* 1.3 78.7 - - - +
51A LYS* 1.3 64.0 + - - +
53A ARG* 3.3 29.7 + - - +
54A PRO* 4.0 3.6 - - - +
606A ASP* 3.2 35.3 + - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLU* 3.9 26.1 + - + +
47A ALA 3.0 13.1 + - - +
48A PHE* 3.0 21.7 + - + +
50A HIS* 1.3 81.8 - - - +
52A ILE* 1.3 60.4 + - + +
53A ARG 3.2 0.4 - - - -
54A PRO* 3.2 17.8 - - - +
55A ILE* 5.7 0.7 - - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.7 32.5 - - + -
48A PHE* 3.0 52.4 + - + +
49A ILE* 3.4 21.3 - - - +
51A LYS* 1.3 79.1 - - + +
53A ARG* 1.3 65.2 + - - +
54A PRO* 3.3 1.3 - - - -
55A ILE* 3.0 10.4 + - - +
56A ALA* 3.0 20.9 + - + -
62A CYS* 4.0 25.1 - - - -
64A VAL* 4.7 0.4 - - + -
580A ILE* 4.7 9.4 - - + -
582A PHE* 4.4 9.0 - - + -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE 3.2 12.3 + - - +
50A HIS* 3.3 26.8 + - - +
52A ILE* 1.3 77.7 - - - +
54A PRO* 1.3 69.0 - - + +
57A GLU* 3.1 48.0 + - - +
506A TYR* 3.8 14.8 - - - -
582A PHE* 3.7 22.0 - - + -
606A ASP* 3.5 31.8 + - - -
1769A NUK 3.1 42.3 - - + +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A HIS 4.0 4.0 - - - +
51A LYS 3.2 16.8 - - - +
52A ILE 3.4 1.8 - - - -
53A ARG* 1.3 98.9 - - + +
55A ILE* 1.3 66.2 + - + +
57A GLU* 4.1 11.8 - - - +
58A GLN* 3.6 19.8 + - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO* 4.0 22.2 - - + -
35A PHE* 4.1 20.6 - - + -
51A LYS 5.7 0.7 - - - +
52A ILE* 3.0 10.9 + - - +
54A PRO* 1.3 82.8 - - + +
56A ALA* 1.3 64.4 - - - +
57A GLU 3.3 0.2 - - - -
58A GLN* 3.1 22.7 + - - +
59A THR* 3.9 6.0 + - + +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO* 4.8 1.1 - - - -
35A PHE* 4.5 2.5 - - + -
52A ILE* 3.0 14.0 + - + +
55A ILE* 1.3 81.2 - - - +
57A GLU* 1.3 58.5 + - - +
59A THR* 3.1 11.9 + - - -
60A GLY* 2.9 29.3 + - - -
62A CYS* 3.9 24.5 - - + -
582A PHE* 3.5 34.0 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ARG* 3.1 41.6 + - - +
54A PRO* 4.1 8.9 - - - +
56A ALA* 1.3 76.9 - - - +
58A GLN* 1.3 80.4 + - - +
59A THR 3.6 0.2 + - - -
60A GLY* 4.1 3.2 + - - +
523A PRO* 3.6 14.2 - - - +
524A GLY 4.3 4.9 + - - -
525A TYR* 4.8 3.5 + - - -
582A PHE* 4.2 23.7 - - + -
1769A NUK 3.0 34.5 - - + +
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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