Contacts of the helix formed by residues 60 - 65 (chain H) in PDB entry 1S9C
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 60 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.9 22.2 - + - -
22H TYR* 3.6 42.4 - + + -
26H GLU* 3.7 24.7 - - + -
27H ALA* 4.3 3.4 - - - -
30H TYR* 3.7 36.2 - + + -
56H CYS* 3.3 23.8 - - - -
57H LEU 2.8 18.5 + - - +
59H THR* 1.3 79.4 + - - +
61H GLY* 1.3 56.2 + - - +
62H VAL 3.0 0.2 - - - -
63H ILE* 2.9 38.7 + - + +
64H ILE* 3.3 22.0 + - + -
100H LEU* 4.2 1.6 - - + -
191H SER* 6.1 0.2 - - - -
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Residues in contact with GLY 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H PRO 3.1 8.2 + - - -
59H THR 2.9 1.8 - - - -
60H PHE* 1.3 80.2 - - - +
62H VAL* 1.3 61.5 + - - +
63H ILE 3.1 0.2 - - - -
64H ILE* 3.2 21.2 + - - +
65H GLY 3.2 2.6 + - - -
94H LEU* 4.1 10.1 - - - -
96H LEU* 4.9 0.4 - - - -
100H LEU* 3.4 17.1 - - - +
138H CYS* 4.4 5.5 - - - -
140H ASN* 3.0 21.8 + - - -
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Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 5.2 1.8 - - - +
59H THR* 2.9 17.9 + - - +
61H GLY* 1.3 78.1 - - - +
63H ILE* 1.3 59.6 + - + +
66H GLN* 2.8 29.6 + - - +
92H GLN* 3.7 16.2 - - - +
94H LEU* 3.7 17.9 - - + -
140H ASN* 3.3 11.9 - - - +
142H PHE* 3.7 4.4 - - + -
188H TYR* 5.5 2.2 - - - +
217H LEU* 3.4 41.5 - - + -
220H PHE* 3.7 25.6 - - + -
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 4.1 21.2 - - + +
30H TYR* 3.2 41.7 - - + -
60H PHE* 2.9 28.9 + - + +
62H VAL* 1.3 79.9 - - + +
64H ILE* 1.3 65.5 + - - +
66H GLN* 3.3 28.1 + - - +
67H LYS* 3.6 6.9 + - - +
188H TYR* 4.5 8.3 - - + +
191H SER* 3.2 39.9 - - - +
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Residues in contact with ILE 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 3.8 8.5 - - - -
20H TYR* 4.0 30.5 - - + +
22H TYR* 3.8 12.8 - - + -
60H PHE* 3.8 18.6 - - + +
61H GLY* 3.2 15.7 + - - +
63H ILE* 1.3 81.2 - - - +
65H GLY* 1.3 58.5 + - - +
66H GLN 3.6 0.2 + - - -
67H LYS* 4.1 1.7 + - - +
100H LEU* 3.9 24.5 - - + -
106H LEU* 3.4 34.1 - - + -
108H CYS* 3.7 18.0 - - - -
130H SER* 3.4 24.0 - - - +
138H CYS* 4.5 2.2 - - - -
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Residues in contact with GLY 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H PHE* 4.1 7.2 - - - -
61H GLY 3.2 8.5 + - - -
64H ILE* 1.3 79.1 - - - +
66H GLN* 1.3 61.6 + - - +
67H LYS 3.4 1.9 - - - +
128H VAL* 3.4 42.0 - - - +
130H SER* 4.5 1.6 - - - -
140H ASN* 3.7 12.3 - - - +
142H PHE* 3.5 10.0 - - - -
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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