Contacts of the helix formed by residues 63 - 79 (chain B) in PDB entry 3NPC
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 ASN 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE 3.2 0.6 - - - -
62B GLN* 1.3 89.0 + - - +
64B GLN* 1.3 63.3 + - - +
65B THR* 3.2 9.2 + - - -
66B HIS* 3.0 43.1 + - - -
67B ALA* 3.1 24.1 + - - +
349B ILE* 3.5 11.4 - - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 1.3 75.2 - - - +
65B THR* 1.3 53.8 + - - +
67B ALA* 3.4 2.3 + - - +
68B LYS* 2.8 65.0 + - - +
346B GLU* 5.7 1.0 - - - +
347B HIS 2.8 26.7 + - - +
348B ALA* 4.0 1.4 - - - +
349B ILE* 3.8 24.4 - - + +
352B TRP* 3.0 24.6 + - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASN* 3.2 8.4 + - - -
64B GLN* 1.3 78.1 - - - +
66B HIS* 1.3 69.5 + - + +
68B LYS* 3.6 10.8 + - - +
69B ARG* 3.1 63.1 + - - +
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA* 3.2 38.3 + - + +
37B GLN* 4.7 9.5 + - + +
58B SER 5.1 1.4 + - - -
60B PRO* 3.0 19.3 - - + +
62B GLN* 3.8 29.8 + - + -
63B ASN* 3.0 41.3 + - - +
65B THR* 1.3 80.6 - - + +
67B ALA* 1.3 59.9 + - - +
69B ARG* 3.6 8.0 + - - +
70B ALA* 3.0 30.8 + - - +
173B ALA* 6.4 0.4 - - + -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PRO 2.7 16.3 + - - +
61B PHE* 4.1 3.6 - - - -
63B ASN 3.1 16.1 + - - +
64B GLN 3.7 3.1 - - - +
66B HIS* 1.3 74.3 - - - +
68B LYS* 1.3 65.2 + - - +
70B ALA 3.2 0.7 + - - -
71B TYR* 3.0 26.5 + - - +
349B ILE* 4.0 6.5 - - + -
352B TRP* 3.6 38.4 - - + -
356B ILE* 3.8 8.3 - - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLN* 2.8 52.2 + - - +
65B THR* 3.8 10.1 + - - +
66B HIS 3.4 0.2 - - - -
67B ALA* 1.3 71.9 - - - +
69B ARG* 1.3 60.1 + - + +
71B TYR* 4.0 3.8 - - - +
72B ARG* 3.1 31.0 + - - +
345B ARG 5.9 0.2 - - - -
346B GLU* 5.7 12.7 - - - +
352B TRP* 3.6 31.4 - - + -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 3.1 38.7 + - + +
65B THR* 3.1 43.7 + - - +
66B HIS* 3.9 7.0 - - - +
68B LYS* 1.3 80.0 - - + +
70B ALA* 1.3 64.1 + - - +
71B TYR 3.3 0.2 - - - -
72B ARG* 3.8 24.8 - - - +
73B GLU* 3.2 18.7 + - - +
173B ALA* 4.6 11.1 - - - +
365B B96 3.4 25.2 - - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.2 21.4 - - + +
60B PRO* 3.3 37.5 - - + -
66B HIS 3.0 11.9 + - - +
67B ALA 3.2 3.5 + - - +
69B ARG* 1.3 74.7 - - - +
71B TYR* 1.3 65.0 + - - +
73B GLU* 3.9 4.2 - - - +
74B LEU* 3.2 29.7 + - - +
356B ILE* 4.3 6.5 - - + -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ALA 3.0 16.9 + - - +
68B LYS 4.0 1.8 - - - +
70B ALA* 1.3 75.1 - - - +
72B ARG* 1.3 67.0 + - - +
74B LEU* 3.2 5.9 + - + +
75B VAL* 2.9 33.3 + - + +
78B LYS* 5.5 0.7 + - - -
343B GLU* 2.4 53.6 + - + -
347B HIS* 6.1 0.9 - - - -
352B TRP* 3.5 30.7 - + + -
355B LEU* 4.0 42.0 - - + +
356B ILE* 4.0 11.1 - - + +
359B GLU* 3.7 35.0 + - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 3.1 24.3 + - - +
69B ARG* 3.7 28.3 + - - +
70B ALA 3.4 0.2 - - - -
71B TYR* 1.3 79.9 - - + +
73B GLU* 1.3 55.7 + - - +
75B VAL* 3.2 5.5 + - - +
76B LEU* 2.9 47.7 + - + +
338B TYR* 3.9 25.4 - - + +
343B GLU* 6.1 0.4 - - - -
344B GLU* 4.6 7.9 - - - -
365B B96 3.8 28.9 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 2.8 28.8 + - - -
57B LEU* 3.7 14.2 - - - +
69B ARG 3.2 17.1 + - - +
70B ALA 3.9 4.3 - - - +
72B ARG* 1.3 77.9 - - - +
74B LEU* 1.3 63.6 + - + +
76B LEU* 3.6 0.5 + - - +
77B LEU* 3.1 39.3 + - + +
106B LEU* 3.8 17.3 - - + +
365B B96 2.7 65.5 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 5.3 4.0 - - + -
70B ALA 3.2 17.3 + - - +
71B TYR* 3.2 9.2 + - - +
73B GLU* 1.3 80.9 - - + +
75B VAL* 1.3 59.2 + - - +
77B LEU* 4.1 4.7 - - - +
78B LYS* 3.4 21.7 + - - +
88B LEU* 5.3 3.2 - - + +
91B VAL* 4.1 19.5 - - + -
104B VAL* 4.6 7.4 - - + -
106B LEU* 3.8 29.4 - - + -
356B ILE* 4.0 27.6 - - + +
359B GLU* 3.9 38.7 - - + +
360B VAL* 4.5 6.3 - - + -
363B TRP* 5.9 2.0 - - + -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 2.9 56.7 + - + +
72B ARG* 3.9 3.1 - - - +
74B LEU* 1.3 74.7 - - - +
76B LEU* 1.3 67.3 + - - +
78B LYS* 3.2 42.1 + - - +
79B CYS* 3.3 10.7 + - - -
338B TYR* 3.7 18.6 - - + -
339B ASP 5.6 0.2 - - - +
343B GLU* 3.6 29.4 - - + +
359B GLU* 4.4 4.7 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 2.9 40.7 + - + +
73B GLU* 4.2 2.7 - - - +
75B VAL* 1.3 71.2 - - - +
77B LEU* 1.3 58.7 + - - +
79B CYS* 3.1 22.4 + - - +
80B VAL* 3.6 14.7 + - - +
147B ILE* 3.7 33.3 - - + +
338B TYR* 3.5 39.3 - - + -
365B B96 3.8 42.2 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLU* 3.1 41.5 + - + +
74B LEU* 4.1 3.1 - - - +
76B LEU* 1.3 75.6 - - - +
78B LYS* 1.3 59.3 + - - +
80B VAL* 3.5 20.3 - - + +
86B ILE* 3.6 42.1 - - + +
87B SER* 6.0 1.4 - - - -
88B LEU* 3.6 46.8 + - + +
106B LEU* 4.3 4.3 - - + -
365B B96 3.7 31.4 - - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 5.5 1.0 + - - -
74B LEU 3.4 10.9 + - - +
75B VAL* 3.2 37.7 + - - +
77B LEU* 1.3 75.1 - - - +
79B CYS* 1.3 63.3 + - - +
80B VAL 3.3 3.1 + - - +
335B PRO* 3.5 17.3 - - - +
336B GLN* 4.4 24.0 + - - +
343B GLU* 5.3 3.5 + - - -
359B GLU* 3.3 36.4 + - - +
363B TRP* 5.7 10.3 - - + +
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Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.3 22.9 - - - -
76B LEU 3.1 9.3 + - - +
78B LYS* 1.3 83.6 - - - +
80B VAL* 1.3 56.8 - - - +
145B ALA* 3.8 3.0 - - + +
147B ILE* 4.2 13.5 - - + -
334B PRO* 3.4 15.9 - - - +
335B PRO* 3.3 18.7 - - - +
336B GLN* 3.4 28.4 - - - +
337B ILE 4.3 2.0 - - - -
338B TYR* 3.8 31.9 - - - +
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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