Contacts of the helix formed by residues 54 - 59 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.9 11.2 - - + +
42D LEU* 3.4 30.2 - - + +
44D VAL* 4.4 2.2 - - + +
50D LEU* 3.7 26.7 - - + -
52D PHE* 3.2 6.4 + - - +
53D ALA* 1.3 72.3 - - - +
55D ASP* 1.3 62.3 + - - +
57D LEU* 2.9 25.9 + - + +
58D THR* 3.8 17.3 + - + -
61D PHE* 3.7 25.7 - + - -
136D THR* 5.4 0.2 + - - -
197D ILE* 4.2 6.7 - - + -
204D TYR* 3.4 60.9 + + + -
207D VAL* 3.6 25.5 - - + +
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Residues in contact with ASP 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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53D ALA* 3.1 2.3 - - + -
54D TYR* 1.3 78.1 - - - +
56D ILE* 1.3 62.2 + - - +
57D LEU 3.0 1.3 + - - -
58D THR* 3.1 15.5 + - - -
59D THR 4.6 0.2 + - - -
136D THR* 2.6 31.6 + - - +
137D VAL 3.7 18.3 - - - +
138D LYS* 3.9 9.4 + - - -
139D TRP* 2.8 27.6 + - - +
161D LEU* 3.5 26.0 - - + +
197D ILE* 3.8 22.0 - - - +
204D TYR* 6.5 0.2 - - - -
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Residues in contact with ILE 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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18D VAL* 4.0 14.1 - - + -
52D PHE* 3.9 22.2 - - + -
53D ALA* 3.4 15.7 - - + +
54D TYR 3.0 0.8 + - - -
55D ASP* 1.3 75.6 - - - +
57D LEU* 1.3 61.8 + - + +
59D THR* 5.1 2.5 + - - -
60D VAL* 4.6 3.6 - - - +
93D MET* 4.6 5.9 - - - +
95D TYR* 3.5 33.7 + - + +
101D CYS* 4.1 9.9 - - - -
120D PHE* 3.4 35.9 - - + -
125D PHE* 4.3 4.5 - - + -
131D VAL* 3.8 41.1 - - + -
139D TRP* 4.6 2.3 - - - -
161D LEU* 4.9 4.9 - - + -
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Residues in contact with LEU 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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14D MET* 3.9 9.7 - - + +
23D PHE* 3.6 28.3 - - + -
25D ILE* 3.6 28.7 - - + -
50D LEU* 4.0 8.1 - - + -
52D PHE* 3.6 29.4 - - + -
54D TYR* 2.9 23.3 + - + +
56D ILE* 1.3 80.7 - - + +
58D THR* 1.3 63.4 + - - +
59D THR 3.4 1.3 - - - -
60D VAL* 3.0 17.4 + - - +
61D PHE* 3.3 24.2 + - + -
120D PHE* 3.9 23.1 - - + -
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Residues in contact with THR 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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54D TYR* 3.9 32.1 - - + +
55D ASP* 3.1 17.1 + - - +
57D LEU* 1.3 77.3 - - - +
59D THR* 1.3 60.1 + - - +
61D PHE* 3.1 11.2 + - - +
63D KZ4 2.9 23.9 + - - +
139D TRP* 3.3 17.3 + - - -
195D ILE* 3.3 19.2 - - - +
197D ILE* 4.1 13.5 - - + -
209D LEU* 3.9 23.6 - - + +
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Residues in contact with THR 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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55D ASP 4.6 0.6 + - - -
56D ILE 5.1 2.1 + - - -
57D LEU 3.4 0.6 - - - -
58D THR* 1.3 75.7 + - - +
60D VAL* 1.3 58.9 + - - +
63D KZ4 2.9 62.6 - - + -
91D ARG* 2.8 24.0 + - - -
93D MET* 4.0 8.3 - - - -
139D TRP* 3.7 34.2 - - + +
173D PHE* 3.4 26.1 - - + -
195D ILE* 3.9 4.0 - - + -
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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