Contacts of the helix formed by residues 59 - 65 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B TYR* 2.8 33.9 + - - -
34B VAL* 5.5 0.2 - - - +
57B LEU* 3.3 4.4 - - - +
58B PRO* 1.3 72.5 - - - +
60B PHE* 1.3 55.7 + - - +
61B GLY 2.9 6.1 - - - -
62B VAL* 2.9 26.3 + - - +
63B ILE 4.1 0.3 + - - -
94B LEU* 3.7 9.2 - - + -
220B PHE* 3.6 27.6 - - + -
221B GLY* 4.0 9.6 + - - -
224B ALA* 3.4 30.2 - - + +
225B ARG* 5.5 0.5 + - - +
239B PHE* 4.4 11.4 - - + -
242B VAL* 4.7 3.6 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B TYR* 4.0 17.0 - + - -
22B TYR* 3.6 47.1 - + + -
26B GLU* 3.8 26.2 - - + -
27B ALA* 4.3 2.5 - - - -
30B TYR* 3.7 35.8 - + + -
56B CYS* 3.3 25.1 - - - -
57B LEU 2.9 19.6 + - - +
58B PRO 2.8 1.0 + - - -
59B THR* 1.3 79.4 + - - +
61B GLY* 1.3 56.7 + - - +
63B ILE* 2.9 42.0 + - + +
64B ILE* 3.3 19.1 + - + -
100B LEU* 4.1 1.8 - - + -
191B SER* 5.6 0.2 - - - -
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PRO 3.1 8.2 + - - -
59B THR 2.9 2.0 - - - -
60B PHE* 1.3 77.1 - - - +
62B VAL* 1.3 63.9 + - - +
64B ILE* 3.2 21.4 + - - +
65B GLY 3.2 2.6 + - - -
94B LEU* 4.0 12.3 - - - -
96B LEU* 4.9 0.2 - - - -
100B LEU* 3.4 15.9 - - - +
138B CYS* 4.3 4.9 - - - -
140B ASN* 3.0 21.9 + - - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 5.3 2.2 - - + +
59B THR* 2.9 16.7 + - - +
61B GLY* 1.3 77.9 - - - +
63B ILE* 1.3 59.9 + - + +
65B GLY 3.8 0.9 + - - -
66B GLN* 2.9 29.7 + - - +
92B GLN* 3.9 17.3 - - - +
94B LEU* 3.7 15.7 - - + -
140B ASN* 3.5 11.7 - - - +
142B PHE* 4.0 3.7 - - + -
188B TYR* 5.5 1.8 - - - +
217B LEU* 3.3 42.2 - - + -
220B PHE* 3.6 28.3 - - + -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B TYR* 3.8 30.3 - - + +
30B TYR* 3.2 42.2 - - + -
60B PHE* 2.9 23.5 + - + +
62B VAL* 1.3 79.7 - - + +
64B ILE* 1.3 65.1 + - - +
66B GLN* 3.3 28.7 + - - +
67B LYS 4.1 3.3 + - - -
188B TYR* 4.5 9.0 - - + +
191B SER* 3.2 39.7 - - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 3.7 16.8 - - - -
20B TYR* 4.0 31.3 - - + +
22B TYR* 3.8 12.1 - - + -
60B PHE* 3.3 19.0 + - + +
61B GLY* 3.2 15.8 + - - +
63B ILE* 1.3 79.5 - - - +
65B GLY* 1.3 58.8 + - - +
66B GLN 3.5 0.3 + - - -
67B LYS 4.1 1.4 + - - -
100B LEU* 4.0 23.8 - - + -
106B LEU* 3.4 28.5 - - + -
108B CYS* 3.9 8.7 - - - -
130B SER* 3.5 28.9 - - - +
138B CYS* 4.5 3.4 - - - -
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 4.1 8.6 - - - -
61B GLY 3.2 8.1 + - - -
64B ILE* 1.3 77.0 - - - +
66B GLN* 1.3 61.3 + - - +
67B LYS 3.3 4.9 + - - +
68B SER* 4.5 3.8 + - - -
126B MET* 5.9 0.3 - - - +
128B VAL* 3.9 24.7 - - - +
130B SER* 4.4 4.0 - - - -
140B ASN* 3.8 14.8 - - - +
142B PHE* 3.5 19.4 - - - -
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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