Contacts of the helix formed by residues 54 - 59 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.9 13.4 - - + +
42A LEU* 3.4 29.7 - - + +
44A VAL* 4.4 2.3 - - + +
50A LEU* 3.7 26.7 - - + -
52A PHE* 3.2 7.0 + - - +
53A ALA* 1.3 72.1 - - - +
55A ASP* 1.3 62.8 + - - +
57A LEU* 2.9 24.4 + - + +
58A THR* 3.8 16.4 + - + -
61A PHE* 3.6 26.1 - + - -
197A ILE* 4.3 6.1 - - + -
204A TYR* 3.5 61.2 + + + -
207A VAL* 3.7 24.3 - - + +
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Residues in contact with ASP 55 (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 ALA* 3.1 3.1 - - + +
54A TYR* 1.3 78.0 - - - +
56A ILE* 1.3 62.3 + - - +
57A LEU 3.0 1.8 + - - -
58A THR* 3.0 16.0 + - - -
59A THR 4.6 0.2 + - - -
136A THR* 2.5 31.2 + - - +
137A VAL 3.6 18.5 - - - +
138A LYS* 3.8 9.5 + - - -
139A TRP* 2.8 27.3 + - - +
161A LEU* 3.5 25.4 - - + -
197A ILE* 3.6 22.7 - - - +
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Residues in contact with ILE 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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18A VAL* 4.0 12.3 - - + -
52A PHE* 3.6 26.0 - - + -
53A ALA* 3.3 17.9 - - + +
54A TYR 3.0 0.8 + - - -
55A ASP* 1.3 76.9 - - - +
57A LEU* 1.3 61.7 + - + +
59A THR* 5.0 2.5 + - - -
60A VAL* 4.6 0.7 - - - +
93A MET* 4.6 8.8 - - - +
95A TYR* 3.5 32.5 + - + +
101A CYS* 4.3 9.4 - - - -
120A PHE* 3.5 33.7 - - + -
125A PHE* 4.4 4.3 - - + -
131A VAL* 3.8 38.6 - - + -
139A TRP* 4.5 2.8 - - - -
161A LEU* 4.9 5.2 - - + -
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Residues in contact with LEU 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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14A MET* 4.0 6.7 - - + -
23A PHE* 3.7 24.2 - - + -
25A ILE* 3.6 29.6 - - + -
50A LEU* 4.1 7.2 - - + -
52A PHE* 3.6 30.3 - - + -
54A TYR* 2.9 22.4 + - + +
56A ILE* 1.3 80.9 - - + +
58A THR* 1.3 57.8 + - - +
59A THR 3.4 1.6 - - - -
60A VAL* 2.9 27.2 + - - +
61A PHE* 3.3 21.9 + - + -
120A PHE* 3.7 29.4 - - + -
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Residues in contact with THR 58 (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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54A TYR* 3.9 31.6 - - + +
55A ASP* 3.0 16.5 + - - +
57A LEU* 1.3 76.9 - - - +
59A THR* 1.3 58.2 + - - +
61A PHE* 3.1 11.0 + - - +
63A KZ4 2.8 24.8 + - - +
139A TRP* 3.3 17.7 + - - -
195A ILE* 3.4 19.6 - - - +
197A ILE* 4.1 14.1 - - + -
209A LEU* 3.8 24.4 - - + +
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Residues in contact with THR 59 (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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55A ASP 4.6 0.2 + - - -
56A ILE 5.0 2.2 + - - +
58A THR* 1.3 77.0 - - - +
60A VAL* 1.3 58.3 + - - +
63A KZ4 2.9 56.3 - - + -
91A ARG* 2.8 31.8 + - - -
93A MET* 4.0 8.5 - - - -
139A TRP* 3.8 35.0 - - + +
173A PHE* 3.4 23.4 - - + -
195A ILE* 4.0 2.9 - - + -
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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