Contacts of the helix formed by residues 65 - 78 (chain B) in PDB entry 3NUI
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 HIS 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.7 31.8 + - + +
63B PHE 3.9 0.6 - - - +
64B ASP* 1.3 74.8 + - - +
66B LYS* 1.3 58.0 + - - +
67B GLY* 3.3 11.9 + - - -
68B LEU* 3.0 47.8 + - + +
69B ILE* 3.0 30.8 + - - +
291B PHE* 4.3 6.9 - - + -
335B LYS* 5.0 0.4 - - - -
339B VAL* 3.6 37.2 - - + +
343B GLU* 4.3 10.5 + - + -
345B LEU* 5.4 4.0 - - + -
428B ILE* 5.4 5.5 - - - +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 6.1 0.9 - - - +
64B ASP 3.1 8.3 + - - +
65B HIS* 1.3 73.4 - - - +
67B GLY* 1.3 63.7 + - - +
69B ILE* 3.8 8.2 - - + +
70B ASP* 2.6 67.3 + - - +
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Residues in contact with GLY 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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65B HIS* 3.3 14.5 + - - -
66B LYS* 1.3 78.9 - - - +
68B LEU* 1.3 55.7 + - - +
70B ASP* 3.4 4.6 + - - +
71B ALA* 2.9 28.9 + - - +
335B LYS* 3.8 21.3 - - - -
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Residues in contact with LEU 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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61B ALA* 3.8 28.5 - - + -
65B HIS* 3.0 22.0 - - + +
67B GLY* 1.3 73.0 - - - +
69B ILE* 1.3 61.4 + - - +
71B ALA* 3.3 2.3 + - + +
72B ALA* 2.9 30.5 + - - +
288B THR 4.8 2.2 - - - +
289B ALA* 3.9 15.7 - - + -
291B PHE* 3.6 25.3 - - + -
332B ILE* 4.0 15.8 - - + +
335B LYS* 3.6 17.0 - - + -
336B ALA* 3.4 38.1 - - + +
339B VAL* 4.4 8.7 - - + -
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Residues in contact with ILE 69 (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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76A TYR* 3.4 30.0 - - - +
77A GLU* 3.8 24.5 - - - +
80A PRO* 4.2 6.3 - - + -
63B PHE 4.5 0.7 - - - +
64B ASP* 3.7 31.4 - - + +
65B HIS 3.0 21.1 + - - +
66B LYS* 3.8 7.2 - - + +
68B LEU* 1.3 76.7 - - - +
70B ASP* 1.3 61.7 + - - +
72B ALA* 3.2 3.3 + - - +
73B LYS* 2.9 47.9 + - + +
291B PHE* 3.7 17.5 - - + -
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 4.6 4.2 - - - +
66B LYS* 2.6 55.3 + - - +
67B GLY* 3.9 4.7 - - - +
69B ILE* 1.3 82.8 - - - +
71B ALA* 1.3 59.2 + - - +
73B LYS* 3.7 12.8 + - - +
74B ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 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 GLY 2.9 18.7 + - - +
68B LEU* 3.6 4.5 - - + +
70B ASP* 1.3 78.7 - - - +
72B ALA* 1.3 61.5 + - - +
74B ALA* 3.5 7.1 + - - +
75B GLN* 3.3 26.7 + - - +
331B ALA 5.5 2.9 - - - +
332B ILE* 4.9 4.9 - - + -
335B LYS* 3.9 28.7 - - + -
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Residues in contact with ALA 72 (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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76A TYR* 3.7 34.1 - - + -
68B LEU 2.9 17.8 + - - +
69B ILE 3.9 1.3 - - - +
71B ALA* 1.3 74.7 - - - +
73B LYS* 1.3 66.4 + - - +
75B GLN* 3.1 14.4 + - - +
76B TYR* 3.4 16.3 + - - -
291B PHE* 4.4 2.7 - - + -
332B ILE* 3.5 32.5 - - + -
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Residues in contact with LYS 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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73A LYS* 3.4 65.3 - - + +
76A TYR* 4.0 10.5 - - + -
77A GLU* 2.8 33.6 + - - +
69B ILE* 2.9 29.2 + - + +
70B ASP* 3.7 12.7 + - - +
72B ALA* 1.3 77.2 - - - +
74B ALA* 1.3 62.4 + - - +
76B TYR* 3.2 2.5 + - - -
77B GLU* 3.0 23.0 + - - +
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Residues in contact with ALA 74 (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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70B ASP 2.9 18.6 + - - +
71B ALA* 3.8 7.9 - - - +
72B ALA 3.3 0.2 - - - -
73B LYS* 1.3 77.2 - - - +
75B GLN* 1.3 63.4 + - - +
77B GLU* 3.5 9.0 + - - +
78B ARG* 3.3 25.2 + - - +
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Residues in contact with GLN 75 (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 ALA 3.3 16.4 + - - +
72B ALA 3.1 9.7 + - - +
74B ALA* 1.3 78.9 - - - +
76B TYR* 1.3 60.2 - - - +
78B ARG* 3.1 28.0 + - - +
79B PHE* 3.2 6.6 + - - -
80B PRO* 4.2 6.7 - - - +
92B GLN* 3.2 27.5 + - - +
328B VAL* 3.8 37.1 - - + +
331B ALA* 3.3 30.8 - - + +
332B ILE* 4.6 4.5 - - + -
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Residues in contact with TYR 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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69A ILE* 3.3 30.2 - - + +
72A ALA* 3.6 24.5 - - + -
73A LYS* 4.2 15.3 - - + -
76A TYR* 3.6 28.0 - + - -
291A PHE* 2.5 42.6 + + + -
292A PHE* 3.4 17.5 - - - -
332A ILE* 4.3 2.7 - - + -
72B ALA 3.5 12.8 - - - -
73B LYS 3.2 6.9 + - - +
75B GLN* 1.3 77.2 - - - +
77B GLU* 1.3 68.6 + - - +
78B ARG 3.0 2.2 + - - -
79B PHE* 3.2 36.4 + + - +
292B PHE* 3.6 9.9 - - - -
328B VAL* 3.7 19.1 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.1 15.2 - - - +
70A ASP* 4.9 1.6 - - - +
73A LYS* 2.7 35.6 + - - +
73B LYS 3.0 16.2 + - - +
74B ALA* 3.7 10.8 - - - +
76B TYR* 1.3 78.1 - - - +
78B ARG* 1.3 71.7 + - + +
79B PHE 4.0 0.7 + - - -
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Residues in contact with ARG 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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34A THR 4.9 3.0 - - - +
35A HIS* 5.7 1.8 - - + -
74B ALA* 3.3 12.9 + - - +
75B GLN* 3.1 11.4 + - - +
76B TYR 3.0 0.4 - - - -
77B GLU* 1.3 90.8 - - + +
79B PHE* 1.3 66.7 + - - +
80B PRO* 3.4 5.2 - - - +
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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