Contacts of the helix formed by residues 61 - 69 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A THR* 1.3 74.4 + - - +
62A ILE* 1.3 63.8 + - - +
63A SER* 3.4 9.0 + - - -
64A GLU* 2.9 41.5 + - - +
65A MET* 3.0 20.8 + - - +
169A GLU* 3.1 12.0 + - - +
172A ARG* 3.8 7.2 - - - +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 4.8 0.4 + - - -
61A SER* 1.3 71.4 - - - +
63A SER* 1.3 65.6 + - - +
65A MET* 3.4 14.0 + - + +
66A TRP* 2.9 34.7 + - + +
341A GLU* 3.7 43.3 - - + +
344A ILE* 3.9 17.7 - - + -
345A ASP* 3.5 52.4 + - + +
348A ASN* 4.0 9.9 - - - +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 3.4 8.3 + - - -
62A ILE* 1.3 82.8 - - - +
64A GLU* 1.3 70.4 + - - +
66A TRP* 3.4 7.6 + - - +
67A GLN* 3.1 24.9 + - - +
341A GLU* 6.0 1.6 - - - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER* 2.9 38.1 + - - +
63A SER* 1.3 79.2 + - - +
65A MET* 1.3 64.5 + - - +
67A GLN* 5.1 3.0 - - - +
68A ASN* 2.9 52.2 + - - +
69A ASP* 5.4 0.2 - - - -
94A ARG* 6.0 0.4 - - - -
169A GLU* 4.9 4.5 - - - +
172A ARG* 5.0 13.2 - - - +
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A SER 3.0 13.4 + - - +
62A ILE* 3.6 15.9 - - + +
64A GLU* 1.3 75.6 - - - +
66A TRP* 1.3 72.1 + - + +
69A ASP* 2.7 39.1 + - + +
70A LEU* 3.0 26.9 + - + -
162A VAL* 5.3 1.8 - - + +
165A ALA* 3.6 39.0 - - + +
166A MET* 4.0 6.7 - - + -
169A GLU* 3.5 27.5 + - + -
344A ILE* 4.2 17.7 - - + -
348A ASN* 3.6 23.1 - - - -
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Residues in contact with TRP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 2.9 29.5 + - + +
63A SER* 3.5 9.9 - - - +
65A MET* 1.3 82.0 - - + +
67A GLN* 1.3 58.1 + - - +
70A LEU* 3.6 20.5 - - + +
71A GLN* 3.1 46.7 + - + +
336A GLU* 2.8 38.3 + - + -
339A LEU* 3.6 42.2 - - + -
341A GLU* 3.9 32.5 - - + -
344A ILE* 3.7 21.3 - - + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER 3.1 13.7 + - - +
64A GLU* 4.2 3.2 - - - +
66A TRP* 1.3 80.6 - - + +
68A ASN* 1.3 81.1 + - - +
71A GLN* 3.6 18.5 - - - +
72A PRO* 3.5 18.4 - - - +
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 2.9 44.6 + - - +
67A GLN* 1.3 103.6 + - - +
69A ASP* 1.3 59.4 + - - +
72A PRO* 4.1 3.4 - - - +
90A HIS* 3.1 21.1 - - - -
94A ARG* 3.4 38.8 + - - +
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU 5.0 0.2 - - - +
65A MET* 2.7 28.1 + - + +
68A ASN* 1.3 73.0 - - - +
70A LEU* 1.3 60.5 + - - +
71A GLN 3.9 0.2 - - - -
72A PRO* 4.1 0.4 - - - -
73A LEU* 3.6 13.9 - - - +
90A HIS* 2.9 21.4 + - - -
94A ARG* 2.6 48.3 + - - +
165A ALA* 4.0 14.9 - - + +
168A LEU* 3.5 25.3 - - + +
169A GLU* 3.8 22.0 + - - +
172A ARG* 5.2 1.6 - - - +
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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