Contacts of the helix formed by residues 46 - 53 (chain A) in PDB entry 1NW6
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A CYS* 1.3 77.3 - - - +
47A CYS* 1.3 66.2 + - - +
48A LEU* 2.7 41.0 + - - +
49A ASP* 3.1 32.0 + - - +
50A THR* 3.1 11.3 + - - -
84A TRP* 5.4 2.6 + - - -
272A ALA* 4.6 4.6 - - + +
401A SFG 2.9 28.6 + - - -
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Residues in contact with CYS 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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45A CYS 4.7 0.2 - - - -
46A ASP* 1.3 76.9 + - - +
48A LEU* 1.3 71.7 + - - +
50A THR* 3.3 4.1 + - - -
51A LEU* 3.0 34.6 + - + +
84A TRP* 4.4 3.6 - - - -
88A TRP* 4.0 23.1 - - - -
249A PHE* 3.6 39.6 - - + +
250A PHE* 3.8 23.1 - - + -
401A SFG 3.0 25.9 + - - +
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Residues in contact with LEU 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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46A ASP* 2.7 21.9 + - - +
47A CYS* 1.3 80.3 - - - +
49A ASP* 1.3 57.8 + - - +
51A LEU* 4.0 3.0 - - + +
52A ALA* 2.9 31.4 + - - +
84A TRP* 5.1 7.6 - - - +
87A ARG* 3.5 53.2 - - + +
88A TRP* 3.8 36.8 - - + +
91A GLU* 4.5 12.0 - - + +
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Residues in contact with ASP 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 CYS* 4.7 9.6 - - + +
46A ASP* 3.1 30.8 + - - +
48A LEU* 1.3 76.2 - - - +
50A THR* 1.3 67.7 + - - +
52A ALA* 3.6 6.0 + - - +
53A LYS* 3.4 30.4 + - - +
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Residues in contact with THR 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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45A CYS* 3.2 21.1 - - - -
46A ASP 3.1 7.2 + - - -
47A CYS* 3.5 10.1 - - - +
49A ASP* 1.3 77.7 - - - +
51A LEU* 1.3 66.7 + - + +
53A LYS* 2.9 19.8 + - - +
54A LEU* 3.5 12.2 + - + +
247A LEU* 4.3 23.3 - - + -
249A PHE* 4.5 4.9 - - + -
270A THR* 2.8 29.6 + - + +
305A ALA* 6.0 0.2 - - - -
308A PHE* 3.8 23.0 - - + -
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Residues in contact with LEU 51 (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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47A CYS 3.0 23.9 + - - +
48A LEU* 4.0 4.7 - - - +
50A THR* 1.3 81.4 - - + +
52A ALA* 1.3 60.4 + - - +
54A LEU* 3.0 14.7 + - - +
88A TRP* 4.0 15.9 - - + +
91A GLU* 3.7 27.6 - - + +
92A ALA 4.1 11.0 - - - +
94A ARG* 2.8 20.3 + - - +
95A VAL* 4.0 29.7 - - + +
247A LEU* 4.2 6.1 - - + -
249A PHE* 3.7 44.0 - - + -
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Residues in contact with ALA 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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48A LEU 2.9 19.6 + - - +
49A ASP* 3.9 7.4 - - - +
50A THR 3.2 0.2 - - - -
51A LEU* 1.3 76.2 - - - +
53A LYS* 1.3 61.2 + - + +
54A LEU 3.3 3.3 + - - +
91A GLU* 3.8 11.4 + - - +
94A ARG* 4.2 3.6 + - - +
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Residues in contact with LYS 53 (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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49A ASP* 3.4 17.7 + - - +
50A THR 2.9 11.3 + - - +
52A ALA* 1.3 79.5 - - + +
54A LEU* 1.3 62.7 + - - +
55A PRO* 4.0 5.4 - - - +
305A ALA* 4.1 35.6 - - + +
306A ALA* 5.0 4.4 - - - +
308A PHE* 3.9 15.7 - - + +
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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