Contacts of the helix formed by residues 59 - 67 (chain D) in PDB entry 3N3B
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 PRO 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.7 35.9 - - + -
46D VAL* 3.9 9.4 - - + -
47D PRO* 3.8 17.5 - - + +
49D TYR* 4.1 18.8 - - + -
56D GLY 5.3 0.7 - - - +
57D ALA 3.5 7.4 - - - +
58D VAL* 1.3 94.0 - - + +
60D ARG* 1.3 65.4 + - - +
61D GLN* 3.3 5.8 - - - +
62D VAL* 3.2 19.3 + - + +
63D ILE* 3.2 10.8 + - - +
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Residues in contact with ARG 60 (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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32D GLU* 3.4 34.6 + - - +
58D VAL 3.8 0.8 + - - -
59D PRO* 1.3 72.0 - - - +
61D GLN* 1.3 60.0 + - - +
63D ILE* 3.3 15.1 + - + +
64D ARG* 3.0 35.5 + - + +
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Residues in contact with GLN 61 (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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7D PHE* 3.4 35.6 - - + -
28D ILE* 3.7 16.5 - - + +
29D PRO 3.4 17.0 - - - +
30D LEU* 2.8 27.6 + - - +
31D ASN 4.3 7.2 - - - +
32D GLU* 3.3 32.2 + - - +
36D ILE* 5.5 0.7 - - - +
59D PRO* 3.3 1.9 - - - +
60D ARG* 1.3 80.3 + - - +
62D VAL* 1.3 58.0 + - - +
64D ARG* 3.6 7.4 + - - +
65D PHE* 3.0 27.7 + - - +
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Residues in contact with VAL 62 (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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7D PHE* 3.8 33.2 - - + -
28D ILE* 4.5 9.0 - - + -
44D LEU* 4.0 18.2 - - + -
46D VAL* 3.8 17.7 - - + -
58D VAL* 3.8 14.4 - - + -
59D PRO* 3.2 16.7 + - + +
61D GLN* 1.3 73.6 - - - +
63D ILE* 1.3 60.4 + - - +
65D PHE* 3.3 6.3 + - + +
66D LEU* 2.9 47.0 + - + +
97D ILE* 4.1 5.4 - - + -
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Residues in contact with ILE 63 (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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58D VAL* 3.5 35.9 - - + +
59D PRO 3.2 9.3 + - - +
60D ARG* 3.5 17.7 - - + +
62D VAL* 1.3 76.5 - - - +
64D ARG* 1.3 57.8 + - + +
66D LEU* 3.2 5.8 + - - +
67D ASN* 2.9 53.6 + - - +
100D LYS* 5.5 12.6 - - - +
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Residues in contact with ARG 64 (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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32D GLU* 3.7 31.9 + - - +
33D ARG* 4.3 20.6 - - - +
34D GLU 5.1 4.8 + - - +
36D ILE* 5.8 1.5 - - + +
60D ARG* 3.0 23.2 + - + +
61D GLN* 3.8 7.4 - - - +
62D VAL 3.4 0.2 - - - -
63D ILE* 1.3 76.6 - - + +
65D PHE* 1.3 59.9 + - - +
67D ASN* 3.8 19.8 + - - +
68D ASP* 4.0 6.6 + - - +
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Residues in contact with PHE 65 (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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5D VAL* 3.8 22.9 - - + -
28D ILE* 3.8 18.6 - - + -
36D ILE* 3.7 43.3 - - + +
37D GLN* 5.0 0.4 - - - -
38D VAL* 4.3 10.3 - - + -
42D TYR* 3.3 39.0 - + - -
44D LEU* 4.2 6.1 - - + -
61D GLN 3.0 18.9 + - - +
62D VAL 3.5 4.5 - - - +
64D ARG* 1.3 78.9 - - - +
66D LEU* 1.3 71.8 + - + +
68D ASP* 3.6 6.3 + - - +
71D ASN* 3.4 56.9 - - + +
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Residues in contact with LEU 66 (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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42D TYR* 4.0 16.6 - - - +
44D LEU* 4.2 7.2 - - + -
58D VAL* 5.4 1.8 - - + -
62D VAL* 2.9 35.7 + - + +
63D ILE* 4.0 5.6 - - - +
65D PHE* 1.3 82.1 - - + +
67D ASN* 1.3 64.2 + - - +
68D ASP 3.1 8.3 + - - +
72D ARG* 3.0 38.1 + - + +
75D LEU* 3.8 26.7 - - + -
97D ILE* 4.0 27.8 - - + -
101D CYS* 4.5 9.9 - - - -
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Residues in contact with ASN 67 (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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63D ILE* 2.9 40.5 + - - +
64D ARG* 3.9 15.2 - - - +
65D PHE 3.3 0.6 - - - -
66D LEU* 1.3 74.3 - - - +
68D ASP* 1.3 62.4 + - - +
69D GLU* 3.5 5.5 + - - +
72D ARG* 3.5 18.3 + - - +
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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