Contacts of the helix formed by residues 51 - 59 (chain D) in PDB entry 3NZG
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 SER 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.6 35.3 - - - +
62B GLU 4.8 1.0 + - - -
64B GLU* 4.3 10.2 + - - -
68B LEU* 3.7 11.0 - - - +
97B GLN* 2.9 28.5 + - - -
50D GLY* 1.3 69.3 - - - -
52D PRO* 1.3 72.2 - - - +
53D ASP* 3.2 5.2 - - - -
54D ALA* 2.9 8.6 + - - +
55D ILE* 2.9 21.7 + - - +
102D LEU* 4.6 0.8 - - - +
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Residues in contact with PRO 52 (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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64B GLU* 4.3 2.2 - - - +
19D PRO* 3.5 28.6 - - + +
21D ASN* 3.7 23.1 - - - +
30D ASN* 3.6 30.5 - - + +
31D THR 4.0 5.4 - - - +
32D VAL* 3.4 23.7 - - + +
50D GLY 2.9 7.1 - - - +
51D SER* 1.3 82.0 - - - +
53D ASP* 1.3 60.1 + - - +
55D ILE* 3.8 1.6 - - - +
56D LEU* 2.8 28.4 + - - +
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Residues in contact with ASP 53 (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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57B ALA* 3.8 9.3 - - + +
60B ASN 4.1 5.9 - - - +
61B ILE* 3.7 24.1 - - - +
62B GLU 4.9 2.0 + - - -
19D PRO* 5.1 0.9 - - - +
51D SER* 3.6 15.8 - - - -
52D PRO* 1.3 77.3 - - + +
54D ALA* 1.3 66.7 + - - +
56D LEU* 3.8 10.5 - - + +
57D ALA* 3.2 23.0 + - - +
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Residues in contact with ALA 54 (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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54B ALA* 5.1 3.0 - - - +
57B ALA* 4.2 11.1 - - - +
58B TYR* 4.1 17.0 - - + -
61B ILE* 3.7 22.2 - - + -
102B LEU* 6.0 0.3 - - - +
51D SER* 2.9 12.6 + - - +
53D ASP* 1.3 81.2 + - - +
55D ILE* 1.3 59.3 + - - +
57D ALA* 3.4 3.5 + - - +
58D TYR* 3.0 27.4 + - - +
102D LEU* 4.2 21.9 - - + +
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Residues in contact with ILE 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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17D PHE* 3.8 28.9 - - + -
32D VAL* 3.9 17.7 - - + -
48D ALA* 4.4 4.9 - - + -
49D ASP 3.4 24.0 - - - +
50D GLY 4.0 5.6 - - - +
51D SER 2.9 18.9 + - - +
52D PRO 3.8 4.5 - - - +
54D ALA* 1.3 75.1 - - - +
56D LEU* 1.3 65.5 + - - +
58D TYR* 3.2 5.2 + - + +
59D ALA* 2.9 22.0 + - - +
102D LEU* 3.3 44.6 - - + +
105D PHE* 4.0 4.0 - - + -
106D ALA* 4.6 7.6 - - + +
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Residues in contact with LEU 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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17D PHE* 3.7 32.8 - - + +
19D PRO* 4.1 24.2 - - + -
32D VAL* 5.9 0.7 - - + -
52D PRO 2.8 19.4 + - - +
53D ASP* 3.8 9.9 - - + +
55D ILE* 1.3 77.0 - - - +
57D ALA* 1.3 62.9 + - - +
59D ALA* 3.2 11.9 + - - +
60D ASN* 3.1 38.2 + - - +
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Residues in contact with ALA 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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53B ASP* 3.9 19.1 - - + +
54B ALA* 4.2 3.6 - - - -
57B ALA* 3.4 33.4 - - + -
53D ASP 3.2 8.1 + - - +
54D ALA 3.7 1.8 - - - +
56D LEU* 1.3 78.3 - - - +
58D TYR* 1.3 62.3 + - - +
60D ASN* 3.2 15.1 + - - +
61D ILE* 3.3 15.9 + - - +
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Residues in contact with TYR 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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54B ALA* 4.3 12.9 - - + +
102B LEU* 4.7 11.4 - - + -
54D ALA 3.0 14.1 + - - +
55D ILE* 3.2 11.0 + - + +
57D ALA* 1.3 76.9 - - - +
59D ALA* 1.3 63.7 + - - +
60D ASN 3.1 1.4 + - - -
61D ILE* 3.3 28.7 + - + +
69D THR 5.1 1.0 + - - -
70D ASN* 4.7 0.2 + - - -
71D ILE* 4.3 19.3 + - + +
94D THR* 4.0 19.1 - - + +
97D GLN* 3.6 38.5 - - + +
98D GLY* 3.8 19.8 + - - -
102D LEU* 4.4 11.0 - - + -
103D GLY* 3.8 30.6 + - - -
106D ALA* 3.8 22.7 - - + -
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Residues in contact with ALA 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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17D PHE* 3.4 46.4 - - + -
55D ILE 2.9 17.3 + - - +
56D LEU 3.2 6.0 + - - +
58D TYR* 1.3 77.0 - - + +
60D ASN* 1.3 64.7 + - - +
61D ILE 3.7 0.7 - - - -
70D ASN* 3.1 19.0 + - - +
71D ILE* 4.3 10.8 - - + -
72D THR* 4.3 7.3 + - - +
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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