Contacts of the helix formed by residues 61 - 69 (chain B) in PDB entry 2AFU
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 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B THR* 1.3 73.6 - - - +
62B ILE* 1.3 63.0 + - - +
63B SER* 3.1 10.6 + - - -
64B GLU* 2.9 41.0 + - - +
65B MET* 3.1 21.1 + - - +
169B GLU* 3.1 12.5 + - - +
172B ARG* 3.7 8.7 - - - +
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Residues in contact with ILE 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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60B THR* 4.0 1.0 + - - -
61B SER* 1.3 72.2 + - - +
63B SER* 1.3 63.7 + - - +
65B MET* 3.5 28.2 + - + -
66B TRP* 3.0 35.6 + - + +
341B GLU* 3.8 43.7 - - + +
344B ILE* 3.7 18.4 - - + -
345B ASP* 3.3 35.0 + - + +
348B ASN* 3.8 12.6 - - - +
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Residues in contact with SER 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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61B SER* 3.1 10.2 + - - -
62B ILE* 1.3 85.7 - - - +
64B GLU* 1.3 75.5 + - - +
66B TRP* 3.6 6.2 + - - +
67B GLN* 3.1 25.8 + - - +
341B GLU* 5.4 6.3 - - - -
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Residues in contact with GLU 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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61B SER* 2.9 31.5 + - - +
63B SER* 1.3 91.6 + - - +
65B MET* 1.3 60.1 + - - +
67B GLN* 4.7 10.6 + - - +
68B ASN* 2.8 57.9 + - - +
69B ASP* 4.7 0.6 - - - +
94B ARG* 5.5 1.1 - - - +
169B GLU* 5.2 0.2 - - - -
172B ARG* 4.9 16.4 - - - +
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Residues in contact with MET 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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61B SER 3.1 14.6 + - - +
62B ILE* 3.5 23.8 - - + +
64B GLU* 1.3 75.9 - - - +
66B TRP* 1.3 74.0 + - + +
69B ASP* 2.7 38.3 + - + +
70B LEU* 2.7 22.3 + - + -
162B VAL* 5.2 2.0 - - + -
165B ALA* 3.5 48.5 - - + +
166B MET* 3.9 7.9 - - + -
169B GLU* 3.7 17.2 + - + +
344B ILE* 3.9 11.9 - - + -
348B ASN* 3.6 22.0 - - - -
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Residues in contact with TRP 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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62B ILE* 3.0 39.3 + - + +
63B SER* 3.7 7.6 - - - +
65B MET* 1.3 80.0 - - + +
67B GLN* 1.3 57.5 + - - +
70B LEU* 3.7 20.3 - - + +
71B GLN* 3.0 46.5 + - + +
336B GLU* 2.9 38.5 + - + +
339B LEU* 3.6 42.8 - - + -
341B GLU* 3.8 31.4 - - + -
344B ILE* 3.7 20.9 - - + -
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Residues in contact with GLN 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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63B SER 3.1 15.8 + - - +
64B GLU* 4.0 10.8 + - - +
66B TRP* 1.3 83.0 - - - +
68B ASN* 1.3 83.3 + - - +
71B GLN* 3.6 20.2 - - - +
72B PRO* 3.8 12.5 - - - +
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Residues in contact with ASN 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 GLU* 2.8 49.5 + - - +
67B GLN* 1.3 98.1 + - - +
69B ASP* 1.3 58.3 + - - +
72B PRO* 3.7 5.8 - - - +
90B HIS* 3.0 19.8 + - - -
94B ARG* 3.5 36.0 + - - +
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Residues in contact with ASP 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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65B MET* 2.7 28.6 + - + +
68B ASN* 1.3 74.5 - - - +
70B LEU* 1.3 64.6 + - - +
72B PRO* 3.7 0.8 - - - +
73B LEU* 3.6 9.7 - - - +
90B HIS* 2.9 24.7 - - - -
94B ARG* 2.6 42.5 + - - +
165B ALA* 3.9 19.5 - - + -
168B LEU* 3.5 25.9 - - + +
169B GLU* 3.7 19.8 + - - +
172B ARG* 5.4 1.0 - - - +
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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