Contacts of the helix formed by residues 54 - 59 (chain F) in PDB entry 6NQN
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 TYR 54 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F ILE* 3.9 9.7 - - + +
42F LEU* 3.5 32.8 + - + +
44F VAL* 4.3 8.6 - - + +
50F LEU* 3.7 30.7 - - + -
52F PHE* 3.2 8.1 + - - +
53F ALA* 1.3 71.5 - - - +
55F ASP* 1.3 64.6 + - - +
57F LEU* 2.9 27.5 + - + +
58F THR* 3.8 17.6 + - + -
61F PHE* 3.7 26.4 - + - -
136F THR* 5.2 0.4 + - - -
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Residues in contact with ASP 55 (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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53F ALA* 3.1 2.1 - - + -
54F TYR* 1.3 79.1 - - - +
56F ILE* 1.3 60.2 + - + +
57F LEU 3.0 0.2 - - - -
58F THR* 3.1 20.5 + - - +
136F THR* 2.5 39.9 + - + +
137F VAL 3.6 21.2 - - - +
138F LYS* 4.4 10.9 - - - -
139F TRP* 2.7 38.8 + - + +
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Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 4.0 16.8 - - + -
52F PHE* 3.5 29.4 - - + -
53F ALA* 3.1 17.7 - - + +
54F TYR 3.0 0.4 + - - -
55F ASP* 1.3 78.4 - - + +
57F LEU* 1.3 62.3 + - + +
59F THR* 5.0 2.9 + - - -
60F VAL* 4.6 2.8 - - - +
93F MET* 4.7 6.4 - - - +
95F TYR* 3.5 32.4 + - + +
101F CYS* 4.3 8.5 - - - -
120F PHE* 3.5 26.6 - - + -
125F PHE* 4.4 4.9 - - + -
131F VAL* 3.7 39.0 - - + -
136F THR* 5.8 1.6 - - + -
139F TRP* 4.5 2.7 - - + -
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Residues in contact with LEU 57 (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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14F MET* 4.1 5.4 - - + -
23F PHE* 3.7 19.5 - - + -
25F ILE* 3.7 29.6 - - + -
50F LEU* 4.2 2.5 - - + -
52F PHE* 3.7 27.1 - - + -
54F TYR* 2.9 31.3 + - + +
56F ILE* 1.3 79.5 - - + +
58F THR* 1.3 58.1 + - - +
59F THR 3.4 1.8 - - - -
60F VAL* 2.9 27.8 + - - +
61F PHE* 3.4 20.8 + - + -
120F PHE* 3.6 35.7 - - + -
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Residues in contact with THR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F LEU* 6.1 1.1 - - + -
54F TYR* 3.8 33.4 - - + +
55F ASP* 3.1 23.8 + - - +
57F LEU* 1.3 77.3 - - - +
59F THR* 1.3 59.1 + - - +
60F VAL 3.0 0.2 - - - -
61F PHE* 3.1 12.3 + - + +
63F KZ4 2.9 29.5 + - - +
139F TRP* 3.3 17.7 + - - -
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Residues in contact with THR 59 (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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55F ASP 4.6 0.4 + - - -
56F ILE 5.1 1.6 + - - -
57F LEU 3.3 0.6 + - - -
58F THR* 1.3 77.0 - - - +
60F VAL* 1.3 58.3 + - - +
63F KZ4 2.9 66.9 - - + -
91F ARG* 2.8 31.5 + - - -
93F MET* 3.9 14.4 - - - +
139F TRP* 3.8 38.1 - - + +
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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