Contacts of the helix formed by residues 59 - 65 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30K TYR* 2.8 34.5 + - - -
34K VAL* 5.6 0.2 - - - +
57K LEU* 4.7 3.8 - - - +
58K PRO* 1.3 71.5 - - - +
60K PHE* 1.3 60.4 + - - +
61K GLY 2.9 6.1 - - - -
62K VAL* 2.9 20.7 + - - +
63K ILE 4.1 0.3 + - - -
94K LEU* 3.5 11.2 - - + -
220K PHE* 3.6 27.8 - - + -
221K GLY* 4.0 8.5 + - - -
224K ALA* 3.6 29.2 - - + +
225K ARG 5.7 0.2 + - - -
239K PHE* 4.5 11.7 - - + -
242K VAL* 4.7 1.8 - - + -
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Residues in contact with PHE 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K TYR* 3.9 22.7 - + - -
22K TYR* 3.6 43.3 - + + -
26K GLU* 3.8 26.0 - - + -
27K ALA* 4.2 3.4 - - - -
30K TYR* 3.7 36.3 - + + -
56K CYS* 3.4 23.8 - - - -
57K LEU 2.8 19.3 + - - +
59K THR* 1.3 80.0 + - - +
61K GLY* 1.3 57.7 + - - +
63K ILE* 2.9 41.5 + - + +
64K ILE* 3.3 18.7 + - + +
100K LEU* 4.1 1.8 - - + -
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Residues in contact with GLY 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K PRO 3.1 8.5 + - - -
59K THR 2.9 2.2 - - - -
60K PHE* 1.3 77.5 - - - +
62K VAL* 1.3 61.7 + - - +
64K ILE* 3.1 21.8 + - - +
65K GLY 3.2 2.6 + - - -
94K LEU* 4.1 10.3 - - - -
96K LEU* 5.0 0.2 - - - -
100K LEU* 3.4 14.8 - - - +
138K CYS* 4.6 6.2 - - - -
140K ASN* 2.9 23.9 + - - -
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Residues in contact with VAL 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K TYR* 5.3 2.5 - - - +
59K THR* 2.9 17.5 + - - +
61K GLY* 1.3 77.5 - - - +
63K ILE* 1.3 61.0 + - + +
66K GLN* 2.8 29.6 + - - +
92K GLN* 3.7 20.2 - - - +
94K LEU* 3.7 18.1 - - + +
140K ASN* 3.2 11.9 - - - +
142K PHE* 3.5 5.6 - - + -
188K TYR* 5.5 1.1 - - - +
217K LEU* 3.3 37.5 - - + -
220K PHE* 3.8 24.9 - - + -
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Residues in contact with ILE 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K TYR* 3.6 29.5 - - + +
30K TYR* 3.1 35.7 - - + -
60K PHE* 2.9 22.0 + - + +
62K VAL* 1.3 79.1 - - + +
64K ILE* 1.3 65.4 + - - +
66K GLN* 3.4 24.9 + - - +
67K LYS* 3.5 11.6 + - - +
188K TYR* 4.6 8.5 - - + +
191K SER* 3.1 46.9 - - - +
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Residues in contact with ILE 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE* 3.8 9.2 - - - -
20K TYR* 3.7 34.3 - - + +
22K TYR* 3.8 11.2 - - + -
60K PHE* 3.8 20.6 - - + +
61K GLY* 3.1 12.2 + - - +
63K ILE* 1.3 81.2 - - - +
65K GLY* 1.3 59.9 + - - +
67K LYS* 3.9 1.6 - - - +
100K LEU* 4.1 21.3 - - + -
106K LEU* 3.3 35.4 - - + -
108K CYS* 3.5 20.2 - - - -
130K SER* 3.7 20.4 - - - +
138K CYS* 4.7 2.7 - - - -
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Residues in contact with GLY 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE* 4.0 10.2 - - - -
61K GLY 3.2 8.1 + - - -
64K ILE* 1.3 76.7 - - - +
66K GLN* 1.3 62.5 + - - +
67K LYS 3.4 1.3 - - - -
68K SER 4.1 5.9 - - - +
108K CYS* 4.6 0.2 - - - -
126K MET* 4.9 0.9 - - - +
128K VAL* 3.8 30.2 - - - +
130K SER* 4.4 4.3 - - - -
140K ASN* 3.9 10.9 - - - +
142K PHE* 3.6 16.8 - - - -
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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