Contacts of the strand formed by residues 78 - 84 (chain C) in PDB entry 1SOT
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 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C VAL 4.0 0.3 - - - +
62C TYR* 3.9 0.7 - - - -
63C ASN* 2.7 41.7 + - - +
76C ILE* 3.8 0.8 - - - +
77C ARG* 1.1 85.5 + - - +
79C LEU* 1.3 74.7 + - - +
96C HIS* 4.5 9.7 + - + +
97C VAL* 3.8 30.4 - - + +
99C ASN 5.6 0.2 + - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASN* 4.8 3.1 - - - +
61C VAL 3.3 6.3 - - - +
62C TYR* 3.8 18.6 - - + -
76C ILE* 3.0 37.2 - - + -
77C ARG 5.3 0.2 - - - -
78C THR* 1.3 87.8 - - - +
80C GLY* 1.3 59.7 + - - +
97C VAL* 3.8 8.0 - - - +
161C PRO* 6.3 0.7 - - + -
162C TYR* 3.3 47.8 - - + +
198C HIS 5.0 3.9 - - - +
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Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN* 3.5 11.4 - - - +
61C VAL* 2.8 30.1 + - - -
79C LEU* 1.3 77.7 - - - +
81C SER* 1.3 64.8 + - - -
97C VAL* 3.8 17.9 - - - -
160C ASN 3.9 1.5 - - - +
161C PRO* 6.2 0.7 - - - -
198C HIS 4.8 8.3 - - - -
199C GLY* 6.1 1.1 - - - -
201C SER 4.2 3.4 - - - -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.5 2.5 - - - -
59C VAL 3.1 9.6 - - - -
61C VAL* 3.8 3.8 - - - -
80C GLY* 1.3 73.4 - - - -
82C GLY* 1.3 55.8 - - - +
93C THR* 2.7 25.4 + - - -
159C GLY* 3.6 1.3 - - - -
160C ASN* 2.6 38.9 + - - -
198C HIS 5.5 0.2 + - - -
199C GLY 3.7 6.6 + - - -
200C ASN 3.9 2.0 - - - -
201C SER 3.2 9.5 + - - -
202C GLY* 3.1 13.1 - - - +
203C GLY* 3.6 25.1 - - - -
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.3 8.7 - - - +
59C VAL* 2.8 43.0 + - - -
61C VAL* 3.9 2.1 - - - +
81C SER* 1.3 77.0 - - - +
83C VAL* 1.3 65.3 + - - -
91C ILE* 4.2 2.7 - - - -
92C ILE 3.2 11.9 - - - -
93C THR* 4.0 5.6 - - - -
202C GLY 3.3 3.1 - - - -
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA 3.7 4.7 - - - +
58C VAL* 4.7 1.6 - - + +
82C GLY* 1.3 78.2 - - - +
84C ILE* 1.3 66.8 + - - +
85C MSE 3.2 21.0 + - - +
91C ILE* 3.1 6.1 - - - +
92C ILE 2.8 37.2 + - - +
141C ILE* 3.6 40.4 - - + -
202C GLY 3.8 2.2 - - - +
203C GLY 3.7 5.4 - - - -
204C ALA* 3.7 33.7 - - + +
212C LEU* 4.7 3.4 - - + -
215C ILE* 3.8 16.2 - - + -
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA* 2.9 18.8 + - - +
59C VAL* 3.7 26.5 - - + -
83C VAL* 1.3 71.3 - - - +
85C MSE 1.3 58.8 + - - +
86C ASP 3.9 19.3 - - - +
90C TYR 3.7 7.9 - - - +
91C ILE* 3.8 19.7 - - + -
108C LEU* 4.0 14.1 - - + -
132C ILE* 4.9 1.3 - - + -
138C LEU* 4.2 19.3 - - + -
139C PRO* 3.2 42.8 - - + +
140C THR* 4.3 2.0 - - - +
141C ILE* 3.2 29.1 + - - +
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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