Contacts of the helix formed by residues 60 - 68 (chain A) in PDB entry 1F89
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.1 7.3 + - - +
59A TYR* 1.3 78.9 - - - +
61A THR* 1.3 61.4 + - - +
62A ASP* 3.0 24.8 + - - -
63A GLN* 3.1 21.4 + - - +
64A PHE* 2.7 28.8 + - - -
231A SER* 5.0 7.9 + - - -
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Residues in contact with THR 61 (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 SER* 1.3 73.7 + - - +
62A ASP* 1.3 63.6 + - - +
63A GLN 3.1 1.7 + - - -
64A PHE* 3.5 20.0 + - + +
65A ARG* 4.5 1.7 + - - +
143A HIS* 3.9 19.4 - - + +
144A GLU* 4.0 37.6 + - + +
147A THR* 3.0 42.3 - - - +
148A LEU* 5.7 4.3 - - + -
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Residues in contact with ASP 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 SER* 3.0 17.9 + - - -
61A THR* 1.3 82.4 + - - +
63A GLN* 1.3 77.5 + - - +
65A ARG* 5.1 4.0 - - - +
66A LYS* 4.9 4.0 + - - +
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Residues in contact with GLN 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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23A PRO* 5.8 2.6 - - - +
58A PRO* 4.2 30.1 - - + +
60A SER* 3.1 13.1 + - - +
62A ASP* 1.3 94.3 + - - +
64A PHE* 1.3 66.4 - - - +
65A ARG 3.3 2.5 - - - -
66A LYS* 2.9 30.8 + - - +
67A TYR* 2.8 47.7 + - + -
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Residues in contact with PHE 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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54A CYS* 4.0 19.1 - - - -
58A PRO 4.5 4.5 + - - -
59A TYR* 4.5 11.9 - + - -
60A SER* 2.7 49.0 + - - -
61A THR* 3.5 19.0 + - + +
63A GLN* 1.3 75.8 - - - +
65A ARG* 1.3 54.8 + - - +
67A TYR 3.1 0.9 + - - -
68A SER* 2.7 39.6 + - - -
100A PRO* 3.8 25.6 - - + +
109A ILE* 4.2 4.9 - - + -
110A TYR 4.8 1.1 - - - -
111A ASN* 3.5 29.6 - - + -
148A LEU* 3.5 42.6 - - + -
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Residues in contact with ARG 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 THR 4.5 4.0 + - - +
62A ASP 5.4 3.8 - - - +
63A GLN 3.3 0.6 - - - -
64A PHE* 1.3 77.3 - - - +
66A LYS* 1.3 65.0 + - - +
68A SER* 2.7 23.7 + - - -
69A GLU 4.4 0.7 + - - -
102A LEU* 3.6 15.9 - - - +
107A ASP* 2.6 50.3 + - - -
108A LYS* 5.0 0.8 - - - +
109A ILE* 3.7 39.7 - - + +
147A THR* 4.9 4.9 + - + -
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Residues in contact with LYS 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 ASP 4.9 2.0 + - - +
63A GLN* 2.9 35.5 + - - +
65A ARG* 1.3 80.4 - - - +
67A TYR* 1.3 68.0 + - + -
69A GLU* 3.3 28.8 - - - +
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Residues in contact with TYR 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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22A SER 4.5 1.1 - - - -
23A PRO* 2.5 44.8 + - - +
25A LYS* 3.6 35.0 + - + -
56A ASN* 4.6 2.9 - - - +
57A SER* 3.3 34.5 - - - +
58A PRO* 3.5 20.0 - - + -
63A GLN* 2.8 49.1 + - - +
64A PHE 3.5 0.9 - - - +
66A LYS* 1.3 87.7 - - + +
68A SER* 1.3 57.6 + - - +
69A GLU* 2.8 21.2 + - - +
70A VAL* 4.7 0.2 - - - +
100A PRO* 4.0 12.4 - - + +
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Residues in contact with SER 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 PHE 2.7 19.1 + - - -
65A ARG 2.7 18.7 + - - -
67A TYR* 1.3 70.5 - - - +
69A GLU* 1.3 49.6 + - - +
70A VAL 2.2 38.5 + - - +
100A PRO* 3.4 21.0 - - - +
101A GLU 3.9 9.0 - - - -
102A LEU* 3.5 33.1 + - - +
109A ILE* 3.7 13.4 - - - +
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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