Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 5NS3
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 4.9 16.8 - - + -
52A ILE* 1.3 84.7 - - + +
54A GLU* 1.3 65.9 + - - +
56A ALA* 3.4 5.5 + - - +
57A ALA* 2.9 41.0 + - + +
70A VAL* 3.9 29.6 - - + -
72A ARG* 5.6 1.6 - - - +
87A PRO* 3.7 32.1 - - + -
90A LEU* 4.6 7.9 - - + +
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Residues in contact with GLU 54 (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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52A ILE* 3.2 48.6 + - - +
53A LEU* 1.3 86.2 - - - +
55A LYS* 1.3 60.1 + - + +
57A ALA* 3.7 5.1 - - - +
58A GLN* 3.0 29.0 + - - +
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Residues in contact with LYS 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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52A ILE* 3.5 17.4 + - - +
53A LEU 3.3 0.4 - - - -
54A GLU* 1.3 78.8 - - + +
56A ALA* 1.3 67.1 + - - +
58A GLN* 3.3 5.9 + - - +
59A GLU* 2.9 55.3 + - + +
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Residues in contact with ALA 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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41A GLN* 5.5 7.6 + - + +
43A LEU* 4.5 17.3 - - + -
52A ILE 3.1 15.7 + - - +
53A LEU* 3.4 3.6 + - - +
55A LYS* 1.3 77.7 - - - +
57A ALA* 1.3 57.5 + - - +
59A GLU* 3.6 7.2 + - - +
60A LEU* 3.0 30.1 + - - +
90A LEU* 3.6 17.0 - - + +
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Residues in contact with ALA 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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53A LEU* 2.9 24.1 + - + +
54A GLU* 3.7 5.4 - - - +
56A ALA* 1.3 75.7 - - - +
58A GLN* 1.3 58.2 + - - +
60A LEU 3.4 0.5 + - - -
61A ALA* 2.9 32.0 + - - +
68A PRO* 3.6 15.4 - - + +
70A VAL* 6.1 0.7 - - + -
90A LEU* 3.5 23.7 - - + +
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Residues in contact with GLN 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 GLU 3.0 17.5 + - - +
55A LYS* 4.0 5.8 - - - +
57A ALA* 1.3 73.6 - - - +
59A GLU* 1.3 60.9 + - + +
61A ALA* 3.6 13.6 - - - +
62A LEU* 2.9 35.2 + - + +
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Residues in contact with GLU 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 LYS* 2.9 55.6 + - + +
56A ALA* 3.9 6.5 - - - +
58A GLN* 1.3 73.6 - - + +
60A LEU* 1.3 64.9 + - - +
62A LEU* 3.1 13.0 + - + +
63A ILE* 3.0 34.8 + - + +
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Residues in contact with LEU 60 (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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39A ILE* 4.0 13.9 - - + -
41A GLN* 4.2 26.4 - - + +
56A ALA 3.0 18.5 + - - +
57A ALA* 3.9 3.4 - - - +
59A GLU* 1.3 75.3 - - - +
61A ALA* 1.3 59.7 + - - +
63A ILE* 3.5 7.0 + - + +
64A THR* 2.8 44.5 + - + +
68A PRO* 4.0 16.4 - - + -
90A LEU* 3.9 33.4 - - + +
91A ARG 4.6 0.4 - - - +
92A VAL* 4.3 9.9 - - + -
155A MET* 3.9 27.6 - - + -
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Residues in contact with ALA 61 (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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57A ALA 2.9 19.3 + - - +
58A GLN* 3.6 19.7 - - - +
60A LEU* 1.3 74.5 - - - +
62A LEU* 1.3 56.8 + - - +
65A GLY* 2.8 33.6 + - - -
66A GLN 3.3 24.1 + - - +
67A LYS* 4.8 2.0 - - - -
68A PRO* 3.8 8.4 - - + +
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Residues in contact with LEU 62 (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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58A GLN* 2.9 24.3 + - + +
59A GLU* 3.1 11.6 + - + +
61A ALA* 1.3 76.3 - - - +
63A ILE* 1.3 64.1 + - + +
64A THR 3.5 0.3 + - - -
65A GLY* 3.8 5.2 + - - -
105A LYS* 5.2 5.2 + - - -
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Residues in contact with ILE 63 (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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59A GLU* 3.0 25.8 + - + +
60A LEU* 4.2 8.1 - - + +
61A ALA 3.4 0.2 - - - -
62A LEU* 1.3 78.9 - - + +
64A THR* 1.3 60.4 + - + +
102A PHE* 3.9 31.7 - - + +
105A LYS* 4.5 22.3 + - + +
155A MET* 5.7 6.5 - - + -
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Residues in contact with THR 64 (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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39A ILE* 3.9 19.3 - - + -
60A LEU* 2.8 31.1 + - + +
61A ALA 3.7 0.2 + - - -
63A ILE* 1.3 81.2 - - + +
65A GLY* 1.3 62.0 + - - +
66A GLN* 3.2 22.2 + - - +
92A VAL* 3.8 23.7 - - + +
94A LEU* 4.0 21.9 - - + +
98A ARG* 3.8 20.4 - - - +
102A PHE* 4.6 8.9 - - + +
105A LYS* 6.1 1.6 - - - -
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Residues in contact with GLY 65 (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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61A ALA 2.8 13.4 + - - -
62A LEU 3.8 4.8 + - - -
63A ILE 3.7 1.2 - - - -
64A THR* 1.3 78.4 - - - +
66A GLN* 1.3 57.3 + - - +
98A ARG* 3.3 18.4 + - - -
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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