Contacts of the helix formed by residues 59 - 65 (chain I) 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 THR 59 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30I TYR* 2.7 34.2 + - - -
57I LEU* 3.3 4.4 - - - +
58I PRO* 1.3 72.6 - - + +
60I PHE* 1.3 60.4 + - - +
61I GLY 2.9 6.3 - - - -
62I VAL* 2.9 21.1 + - - +
63I ILE 4.1 0.3 + - - -
94I LEU* 3.7 12.1 - - + -
220I PHE* 3.9 26.7 - - + -
221I GLY* 4.0 9.2 + - - -
224I ALA* 3.4 30.9 - - + +
225I ARG 5.7 0.2 + - - -
239I PHE* 4.4 11.9 - - + -
242I VAL* 4.8 1.6 - - + -
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Residues in contact with PHE 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I TYR* 4.0 22.2 - + - -
22I TYR* 3.7 41.7 - + + -
26I GLU* 3.7 25.6 - - + -
27I ALA* 4.4 3.6 - - - -
30I TYR* 3.7 35.5 - + + -
56I CYS* 3.3 23.6 - - - -
57I LEU 2.8 19.5 + - - +
59I THR* 1.3 79.0 + - - +
61I GLY* 1.3 57.6 + - - +
62I VAL 3.0 0.2 - - - -
63I ILE* 2.9 37.3 + - + +
64I ILE* 3.3 22.9 + - + -
100I LEU* 4.2 2.0 - - + -
191I SER* 5.6 0.2 - - - -
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Residues in contact with GLY 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58I PRO 3.1 8.4 + - - -
59I THR 2.9 1.8 - - - -
60I PHE* 1.3 78.2 - - - +
62I VAL* 1.3 62.7 + - - +
64I ILE* 3.2 20.9 + - - +
65I GLY 3.3 2.6 + - - -
94I LEU* 4.1 9.2 - - - -
100I LEU* 3.3 17.8 - - - +
138I CYS* 4.4 5.5 - - - -
140I ASN* 2.9 23.8 + - - -
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I TYR* 5.2 2.0 - - + +
59I THR 2.9 17.9 + - - +
61I GLY* 1.3 77.4 - - - +
63I ILE* 1.3 59.5 + - + +
65I GLY 3.7 0.2 + - - -
66I GLN* 2.9 28.6 + - - +
92I GLN* 3.7 14.8 - - - +
94I LEU* 3.6 20.8 - - + +
140I ASN* 3.3 11.2 - - - +
142I PHE* 3.6 5.4 - - + -
188I TYR* 5.4 2.7 - - - +
217I LEU* 3.4 40.8 - - + -
220I PHE* 3.6 24.9 - - + -
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Residues in contact with ILE 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I TYR* 3.7 32.7 - - + +
30I TYR* 3.2 35.4 - - + -
60I PHE* 2.9 23.6 + - + +
62I VAL* 1.3 79.5 - - + +
64I ILE* 1.3 65.2 + - - +
66I GLN* 3.3 27.7 + - - +
67I LYS* 4.0 4.5 + - - +
188I TYR* 4.6 7.6 - - - +
191I SER* 3.1 46.4 - - - +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I PHE* 3.8 6.4 - - - -
20I TYR* 3.7 38.7 - - + +
22I TYR* 3.8 13.0 - - + +
60I PHE* 3.3 18.6 + - + +
61I GLY* 3.2 15.7 + - - +
63I ILE* 1.3 80.1 - - - +
65I GLY* 1.3 59.2 + - - +
66I GLN 3.5 0.2 + - - -
67I LYS 4.2 1.0 + - - -
100I LEU* 4.0 24.0 - - + -
106I LEU* 3.5 36.1 - - + -
108I CYS* 3.7 12.5 - - - -
130I SER* 3.6 21.1 - - - +
138I CYS* 4.6 2.2 - - - -
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Residues in contact with GLY 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I PHE* 4.0 4.2 - - - -
61I GLY 3.3 7.9 + - - -
64I ILE* 1.3 77.0 - - - +
66I GLN* 1.3 62.4 + - - +
67I LYS 3.4 1.8 - - - -
68I SER* 3.3 18.5 + - - -
128I VAL* 3.6 24.3 - - - +
130I SER* 4.2 5.2 - - - -
140I ASN* 3.8 11.8 - - - +
142I PHE* 3.6 16.7 - - - -
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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