Contacts of the helix formed by residues 59 - 65 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G TYR* 2.8 34.4 + - - -
34G VAL* 5.5 0.2 - - - +
57G LEU* 4.7 4.7 - - - +
58G PRO* 1.3 71.3 - - - +
60G PHE* 1.3 55.6 + - - +
61G GLY 2.9 6.5 - - - -
62G VAL* 2.9 26.6 + - - +
63G ILE 4.1 0.2 + - - -
94G LEU* 3.7 11.2 - - + -
220G PHE* 3.6 27.6 - - + -
221G GLY* 4.0 9.1 + - - -
224G ALA* 3.5 30.5 - - + +
239G PHE* 4.6 9.9 - - + -
242G VAL* 4.8 2.0 - - + -
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Residues in contact with PHE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TYR* 3.4 28.5 - + - -
22G TYR* 3.6 41.7 - + + -
26G GLU* 3.8 23.3 - - + -
27G ALA* 4.3 3.1 - - - -
30G TYR* 3.7 35.5 - + + -
56G CYS* 3.3 25.4 - - - -
57G LEU 2.8 18.8 + - - +
59G THR* 1.3 79.1 + - - +
61G GLY* 1.3 57.9 + - - +
63G ILE* 2.9 37.8 + - + +
64G ILE* 3.3 18.8 + - + +
100G LEU* 4.1 2.0 - - + -
191G SER* 5.6 0.2 - - - -
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Residues in contact with GLY 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G PRO 3.2 7.8 + - - -
59G THR 2.9 1.6 - - - -
60G PHE* 1.3 81.0 - - - +
62G VAL* 1.3 60.5 + - - +
64G ILE* 3.2 21.7 + - - +
65G GLY 3.2 2.4 + - - -
94G LEU* 4.0 10.5 - - - -
96G LEU* 4.9 0.2 - - - -
100G LEU* 3.3 15.7 - - - +
138G CYS* 4.3 5.1 - - - -
140G ASN* 2.9 23.5 + - - -
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Residues in contact with VAL 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G TYR* 5.3 2.0 - - - +
59G THR* 2.9 17.2 + - - +
61G GLY* 1.3 77.3 - - - +
63G ILE* 1.3 59.5 + - + +
65G GLY 3.7 0.2 + - - -
66G GLN* 2.9 29.3 + - - +
92G GLN* 3.7 15.9 - - - +
94G LEU* 3.6 16.6 - - + +
140G ASN* 3.3 11.0 - - - +
142G PHE* 3.6 4.8 - - + -
188G TYR* 5.5 1.8 - - - +
217G LEU* 3.3 42.0 - - + -
220G PHE* 3.6 27.8 - - + -
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G TYR* 3.7 34.0 - - + +
30G TYR* 3.1 43.3 - - + -
60G PHE* 2.9 20.9 + - + +
62G VAL* 1.3 79.9 - - + +
64G ILE* 1.3 65.8 + - - +
66G GLN* 3.3 28.4 + - - +
67G LYS 3.9 4.2 + - - -
188G TYR* 4.4 8.5 - - + +
191G SER* 3.1 40.8 - - - +
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 3.8 12.5 - - - -
20G TYR* 3.7 42.9 - - + +
22G TYR* 3.8 12.3 - - + -
60G PHE* 3.3 14.8 + - + +
61G GLY* 3.2 14.8 + - - +
63G ILE* 1.3 80.1 - - - +
65G GLY* 1.3 59.3 + - - +
66G GLN 3.5 0.2 + - - -
67G LYS 4.2 1.0 + - - -
100G LEU* 4.0 24.2 - - + -
106G LEU* 3.5 33.9 - - + -
108G CYS* 3.8 7.2 - - - -
130G SER* 3.5 23.1 - - - +
138G CYS* 4.6 2.5 - - - -
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Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G PHE* 4.2 3.3 - - - -
61G GLY 3.2 8.1 + - - -
64G ILE* 1.3 80.5 - - - +
66G GLN* 1.3 61.2 + - - +
67G LYS 3.4 0.8 + - - -
68G SER* 3.5 18.1 + - - -
69G MET 4.5 0.2 + - - -
128G VAL* 3.6 24.5 - - - +
130G SER* 4.3 4.3 - - - -
140G ASN* 3.9 11.4 - - - +
142G PHE* 3.5 17.4 - - - -
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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