Contacts of the helix formed by residues 61 - 69 (chain B) in PDB entry 1NUE
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 PHE 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LYS* 3.9 32.8 - - + -
52B TYR* 3.4 35.4 - - + -
53B ILE* 5.8 0.2 - - + -
55B LEU* 3.3 29.2 - - + +
56B LYS* 3.8 29.4 - - + +
58B ARG 3.1 17.8 + - - +
60B PHE* 1.3 85.0 - - - +
62B PRO* 1.4 72.7 - - + +
64B LEU* 3.1 8.5 + - + +
65B VAL* 3.0 45.9 + - + +
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Residues in contact with PRO 62 (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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56B LYS 5.5 0.7 - - - +
58B ARG 4.1 2.9 - - - +
59B PRO 3.5 14.8 - - - +
60B PHE 3.8 0.2 - - - -
61B PHE* 1.4 101.4 - - + +
63B GLY* 1.3 59.6 + - - +
65B VAL* 3.5 5.6 + - + +
66B LYS* 3.0 35.2 + - + +
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Residues in contact with GLY 63 (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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59B PRO 5.2 0.2 + - - -
60B PHE* 3.2 7.7 + - - +
62B PRO* 1.3 77.6 - - - +
64B LEU* 1.3 59.1 + - - +
66B LYS* 3.5 6.4 + - - +
67B TYR* 3.0 29.6 + - - +
160B GDP 5.9 2.0 - - - -
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Residues in contact with LEU 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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52B TYR* 3.8 42.2 - - + +
55B LEU* 4.2 4.5 - - + -
60B PHE* 2.9 33.6 + - + +
61B PHE* 3.1 11.4 + - + +
63B GLY* 1.3 74.1 - - - +
65B VAL* 1.3 64.9 + - - +
67B TYR* 3.4 14.7 + - + +
68B MET* 3.0 44.8 + - + +
160B GDP 3.7 46.1 + - - +
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Residues in contact with VAL 65 (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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45B GLU* 3.7 43.5 - - + +
48B LEU* 3.8 12.8 - - + +
49B LYS* 4.1 19.3 - - + +
52B TYR* 5.5 1.6 - - + -
61B PHE* 3.0 54.4 + - + +
62B PRO* 4.0 5.6 - - + +
64B LEU* 1.3 79.2 - - + +
66B LYS* 1.3 63.1 + - + +
68B MET* 3.5 3.5 + - - -
69B ASN* 3.1 22.9 + - - +
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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
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45B GLU* 3.0 39.0 + - - +
49B LYS* 6.1 0.2 - - - +
62B PRO* 3.0 23.7 + - + +
63B GLY* 3.7 6.7 - - - +
65B VAL* 1.3 74.6 - - - +
67B TYR* 1.3 67.6 + - - +
69B ASN* 3.1 7.8 + - - +
70B SER* 2.9 22.1 + - - -
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Residues in contact with TYR 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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12B LYS* 3.2 23.9 - - + +
13B PRO* 3.6 14.1 - - + +
14B ASP* 2.5 39.7 + - + -
63B GLY 3.0 16.6 + - - +
64B LEU* 3.9 22.0 - - + -
66B LYS* 1.3 73.9 - - - +
68B MET* 1.3 78.8 + - + +
70B SER* 2.3 40.7 + - - -
113B GLY* 3.4 20.9 - - - -
114B ARG* 3.5 38.8 - - - +
115B ASN 3.8 7.3 + - - -
160B GDP 4.7 3.1 - - - -
149C TRP* 4.6 4.3 - + - -
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Residues in contact with MET 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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10B ALA* 5.5 6.7 - - + -
12B LYS* 3.7 38.6 - - + -
13B PRO* 3.6 22.5 - - - +
43B ALA 4.9 3.5 + - - +
48B LEU* 3.5 35.0 - - + +
51B HIS* 5.5 2.5 - - + +
52B TYR* 4.1 25.8 - - + +
64B LEU* 3.0 37.0 + - + +
65B VAL* 3.9 1.6 - - - +
67B TYR* 1.3 81.3 - - + +
69B ASN* 1.3 57.8 + - - +
71B GLY 3.7 5.9 - - - +
73B VAL* 4.3 21.5 - - + +
118B HIS* 5.6 1.3 - - + -
133B TRP* 5.5 4.7 - - + -
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Residues in contact with ASN 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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42B ARG* 3.2 28.8 + - - +
43B ALA 2.8 25.6 + - - -
44B SER* 4.0 2.4 - - - +
45B GLU* 3.8 34.1 - - + +
48B LEU* 3.7 10.1 - - + -
65B VAL 3.1 16.3 + - - +
66B LYS* 3.1 6.0 + - - +
67B TYR 3.1 0.8 - - - -
68B MET* 1.3 75.0 - - - +
70B SER* 1.3 65.2 + - - +
71B GLY 3.2 3.8 + - - -
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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