Contacts of the helix formed by residues 56 - 68 (chain o) in PDB entry 6FF7
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 56 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6o ARG* 4.3 4.4 - - - +
54o PHE* 3.2 26.8 - - - +
55o GLU* 1.3 79.2 - - + +
57o ALA* 1.3 64.9 + - - +
58o GLU* 3.7 9.0 - - + +
59o ASP* 4.3 14.1 - - + +
60o ALA* 3.8 3.1 + - - +
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Residues in contact with ALA 57 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3o THR 5.6 4.0 - - - +
5o LYS* 3.9 28.8 - - + +
6o ARG* 5.0 1.6 - - + +
56o LEU* 1.3 72.9 - - - +
58o GLU* 1.3 68.2 + - - +
59o ASP 3.3 1.3 - - - -
60o ALA* 3.0 13.5 + - - +
61o ALA* 3.0 14.8 + - - +
167o MET* 4.6 18.8 - - + -
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Residues in contact with GLU 58 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56o LEU* 4.3 4.6 - - + +
57o ALA* 1.3 76.9 - - - +
59o ASP* 1.3 63.1 + - - +
61o ALA* 3.3 9.0 + - - +
62o ALA* 3.1 23.1 + - - +
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Residues in contact with ASP 59 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28o PRO* 3.9 3.8 - - - +
29o PHE* 5.1 6.1 - - + -
54o PHE* 4.6 8.5 - - + -
55o GLU* 5.7 0.4 - - + +
56o LEU* 4.3 19.5 + - + +
57o ALA 3.3 0.6 - - - -
58o GLU* 1.3 77.2 - - - +
60o ALA* 1.3 57.5 - - - +
62o ALA* 3.4 7.6 + - - +
63o ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 60 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5o LYS 3.2 26.0 - - - +
6o ARG 3.7 18.6 - - - +
8o LEU* 5.6 5.4 - - + -
28o PRO* 4.5 0.7 - - - -
29o PHE* 5.2 0.2 - - - -
54o PHE* 3.8 14.7 - - + +
56o LEU 3.8 3.8 + - - +
57o ALA 3.0 5.8 + - - +
59o ASP* 1.3 76.4 - - - +
61o ALA* 1.3 66.2 + - - +
63o ALA* 2.9 19.0 + - - +
64o ILE* 3.0 12.9 + - - +
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Residues in contact with ALA 61 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5o LYS* 4.7 2.1 + - + +
57o ALA 3.0 11.5 + - - +
58o GLU* 3.6 10.5 - - - +
60o ALA* 1.3 75.1 - - - +
62o ALA* 1.3 63.3 + - - +
64o ILE* 3.2 7.9 + - - +
65o ASP* 3.1 22.9 + - - +
215o TYR* 3.6 38.0 - - + +
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Residues in contact with ALA 62 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58o GLU 3.1 13.4 + - - +
59o ASP* 3.6 10.8 - - - +
61o ALA* 1.3 76.2 - - - +
63o ALA* 1.3 62.0 + - - +
65o ASP* 3.6 6.6 + - - +
66o ASN* 3.3 23.7 + - - +
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Residues in contact with ALA 63 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27o ILE* 2.7 18.2 - - - +
28o PRO* 0.6 67.1 - - + -
59o ASP 3.0 9.1 + - - +
60o ALA 2.9 9.7 + - - +
62o ALA* 1.3 77.2 - - - +
64o ILE* 1.3 53.7 + - - +
66o ASN* 4.7 2.2 - - - -
67o MET* 2.7 24.6 + - - +
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Residues in contact with ILE 64 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8o LEU* 5.8 5.6 - - + -
27o ILE* 5.3 0.7 - - - -
60o ALA 3.0 11.0 + - - +
61o ALA* 3.6 10.1 - - - +
63o ALA* 1.3 71.6 - - - +
65o ASP* 1.3 61.5 + - - +
66o ASN 2.9 1.6 - - - -
68o ASN* 2.7 37.0 + - - +
79o VAL* 4.2 24.9 - - + +
80o ASN* 5.0 7.6 - - - +
81o LEU 5.7 0.2 - - - +
215o TYR 5.0 5.6 - - - +
216o GLY* 6.0 2.7 - - - -
218o LYS 5.8 3.4 - - - +
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Residues in contact with ASP 65 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61o ALA 3.1 12.6 + - - +
62o ALA* 3.9 7.4 - - - +
64o ILE* 1.3 77.8 - - - +
66o ASN* 1.3 60.6 + - - +
68o ASN* 3.8 9.7 - - - +
215o TYR 5.0 6.8 + - - +
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Residues in contact with ASN 66 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27o ILE 4.9 1.3 - - - +
62o ALA 3.3 14.8 + - - +
63o ALA* 3.8 3.1 - - - +
64o ILE 2.8 1.8 + - - -
65o ASP* 1.3 77.4 - - - +
67o MET* 1.3 57.3 + - - +
68o ASN 2.8 25.1 + - - +
70o SER* 4.1 4.7 - - - -
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Residues in contact with MET 67 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26o PHE 4.2 2.7 - - - +
27o ILE* 2.5 53.8 + - + +
63o ALA 2.7 11.6 + - - +
66o ASN* 1.3 73.3 - - - +
68o ASN* 1.3 61.4 + - - +
69o GLU 3.1 1.0 + - - -
70o SER* 2.8 29.1 + - - -
77o ILE* 3.7 7.4 - - - +
79o VAL* 4.1 5.8 - - + +
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Residues in contact with ASN 68 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o ILE 2.7 28.3 + - - +
65o ASP* 3.8 12.0 - - - +
66o ASN 2.8 10.9 + - - +
67o MET* 1.3 68.5 - - - +
69o GLU* 1.3 70.7 + - + +
79o VAL* 3.8 22.9 - - - +
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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