Contacts of the helix formed by residues 64 - 72 (chain B) in PDB entry 3NER
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 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B GLY 3.6 1.7 + - - -
63B HIS* 1.3 77.6 - - - +
65B SER* 1.3 65.2 + - - +
66B ASP* 3.3 10.2 + - - +
67B ALA* 2.9 15.4 + - - +
68B ARG* 3.1 21.6 + - - +
201B HEM 2.7 36.3 + - - -
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Residues in contact with SER 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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48A GLU* 2.7 41.8 + - - +
64B SER* 1.3 74.4 - - - +
66B ASP* 1.3 63.9 + - - +
68B ARG* 3.2 7.9 + - - +
69B GLU* 3.0 26.8 + - - +
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Residues in contact with ASP 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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64B SER* 3.3 9.4 + - - +
65B SER* 1.3 73.9 - - - +
67B ALA* 1.3 66.8 + - - +
69B GLU* 3.2 7.8 + - - +
70B MET* 2.9 44.6 + - - +
201B HEM 4.9 4.4 - - - +
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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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58B PHE* 5.1 1.8 - - - -
63B HIS* 3.7 22.0 - - + -
64B SER* 2.9 21.5 + - - +
66B ASP* 1.3 77.6 + - - +
68B ARG* 1.3 56.6 + - - +
70B MET* 3.2 6.3 + - - +
71B LEU* 3.0 23.7 + - - +
201B HEM 3.5 51.1 + - + +
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Residues in contact with ARG 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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44A GLU* 3.7 23.3 - - - +
45A VAL* 4.0 22.5 - - - +
48A GLU* 2.5 43.4 + - - +
58B PHE* 4.1 24.3 - - + -
59B GLU* 5.1 10.9 + - - -
63B HIS* 3.0 32.6 + - - +
64B SER 3.1 8.4 + - - +
65B SER* 3.6 14.1 + - - +
66B ASP 3.2 0.2 - - - -
67B ALA* 1.3 75.5 - - - +
69B GLU* 1.3 68.3 + - + +
71B LEU* 3.3 23.1 + - + +
72B LYS* 3.7 10.9 + - - +
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Residues in contact with GLU 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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49A GLN* 5.5 2.1 - - - +
56A GLU* 6.1 1.4 - - - -
57A SER* 5.0 4.9 + - - -
65B SER* 3.0 15.9 + - - +
66B ASP* 3.6 12.1 - - - +
68B ARG* 1.3 78.3 - - - +
70B MET* 1.3 62.6 + - - +
72B LYS* 3.1 59.8 + - - +
73B GLN* 4.1 4.7 + - - +
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Residues in contact with MET 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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35B PHE* 3.8 28.5 - - - -
40B PRO* 6.1 0.2 - - - -
66B ASP* 2.9 36.7 + - - +
67B ALA 3.3 7.4 - - - +
68B ARG 3.2 0.2 - - - -
69B GLU* 1.3 74.7 - - - +
71B LEU* 1.3 65.7 + - - +
73B GLN* 3.0 41.8 + - - +
74B TYR* 3.4 18.8 - - + +
201B HEM 3.8 28.3 - - + -
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Residues in contact with LEU 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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25B ILE* 4.0 15.9 - - + -
26B HIS* 5.9 2.2 - - + -
30B TYR* 3.3 57.8 - - + +
58B PHE* 3.8 28.0 - - + -
67B ALA 3.0 12.2 + - - +
68B ARG* 3.4 17.3 - - + +
69B GLU 3.2 0.2 - - - -
70B MET* 1.3 76.1 - - - +
72B LYS* 1.3 63.0 + - + +
74B TYR* 2.9 16.0 + - - +
201B HEM 3.1 43.5 - - + -
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Residues in contact with LYS 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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56A GLU* 5.5 2.0 - - - +
57A SER* 4.4 16.1 + - - +
60A ASP* 2.8 29.9 + - - +
61A VAL* 6.4 1.6 - - - -
30B TYR* 4.7 0.9 - - - -
68B ARG 4.0 7.9 - - - +
69B GLU* 3.1 45.5 + - - +
71B LEU* 1.3 79.4 - - + +
73B GLN* 1.3 61.8 + - + +
74B TYR 3.2 0.7 + - - -
75B TYR* 3.3 16.4 + - - +
302B SO4 3.4 43.7 + - - +
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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