Contacts of the strand formed by residues 77 - 83 (chain C) in PDB entry 2YIN
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 VAL 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ILE* 4.2 7.6 - - + -
5C LYS 3.5 0.2 + - - -
6C CYS* 3.4 24.5 - - + -
7C VAL 3.1 12.8 + - - -
53C LEU* 5.8 0.4 - - + -
75C THR* 3.0 18.9 - - - +
76C ASP* 1.3 78.4 - - - +
78C PHE* 1.3 75.0 + - - +
79C LEU* 5.0 0.4 - - + -
108C THR* 3.8 5.4 - - - -
109C PRO* 3.8 15.7 - - + +
111C ILE* 4.5 11.4 - - + -
172C ALA* 3.8 28.5 - - + +
175C ALA* 4.8 2.2 - - + -
176C VAL* 3.6 21.8 - - + -
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Residues in contact with PHE 78 (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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7C VAL* 3.4 37.5 - - + -
9C VAL* 4.7 4.9 - - + -
72C TYR* 4.0 23.8 - + - -
75C THR* 3.6 26.2 - - + -
77C VAL* 1.3 79.6 - - - +
79C LEU* 1.3 65.1 + - - +
80C ILE* 4.0 1.8 - - + -
101C VAL* 3.7 35.0 - - + -
105C CYS* 3.8 34.3 - - + -
108C THR* 3.7 17.7 - - + -
109C PRO 3.0 11.1 + - - +
110C ILE* 3.5 12.8 - - + -
111C ILE 2.9 26.0 + - - -
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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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6C CYS* 3.6 23.8 - - - -
7C VAL 2.8 12.1 + - - +
8C VAL* 3.5 22.3 - - + +
9C VAL* 2.9 31.8 + - - +
19C LEU* 6.4 1.1 - - + -
20C LEU* 5.3 0.4 - - + -
77C VAL* 5.0 0.4 - - + -
78C PHE* 1.3 75.0 - - - +
80C ILE* 1.3 62.4 + - - +
81C CYS* 4.8 2.5 - - - -
111C ILE* 3.6 31.4 - - + -
113C VAL* 4.1 15.7 - - + -
168C VAL* 4.1 13.0 - - + -
169C PHE* 4.0 27.4 - - + -
172C ALA* 4.3 14.4 - - + -
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Residues in contact with ILE 80 (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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9C VAL* 3.3 24.0 - - + +
78C PHE* 4.0 2.8 - - + -
79C LEU* 1.3 73.1 - - - +
81C CYS* 1.3 57.3 + - - +
93C VAL* 3.8 20.6 - - + -
97C TRP* 4.2 9.0 - - + -
98C TYR* 4.2 25.6 - - + +
101C VAL* 4.3 9.9 - - + -
110C ILE* 3.8 35.0 - - + -
111C ILE 2.8 13.6 + - - +
112C LEU* 3.1 27.0 - - + +
113C VAL* 2.5 34.0 + - - -
149C ILE* 5.1 2.0 - - + -
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Residues in contact with CYS 81 (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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8C VAL* 4.6 16.6 - - - -
9C VAL 2.9 12.7 + - - +
10C GLY* 3.6 19.5 - - - -
11C ASP 4.4 0.3 + - - -
14C VAL* 3.8 21.8 - - + +
16C LYS* 5.0 6.3 - - + -
19C LEU* 4.6 10.1 - - - -
79C LEU* 4.8 3.4 - - - -
80C ILE* 1.3 81.5 - - - +
82C PHE* 1.3 64.7 + - - +
89C SER* 5.1 1.2 - - - +
93C VAL* 4.7 2.8 - - - +
97C TRP* 4.9 2.1 - - - -
113C VAL* 2.9 44.9 - - - +
115C THR* 4.0 4.3 - - - +
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Residues in contact with PHE 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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14C VAL* 3.7 7.2 - - - -
81C CYS* 1.3 78.1 - - - +
83C SER* 1.3 74.7 + - - +
84C LEU* 3.5 35.2 - - + -
89C SER* 3.5 17.9 - - - +
90C PHE* 3.3 48.0 - + + +
93C VAL* 3.9 10.5 - - + -
112C LEU* 3.1 35.4 - - + -
113C VAL 2.9 14.3 + - - +
114C GLY* 3.7 5.8 - - - -
115C THR* 2.9 27.0 + - - -
137C ILE* 4.1 3.1 - - + -
154C TYR* 3.8 9.0 - + - -
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Residues in contact with SER 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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13C ALA 4.9 4.0 - - - -
14C VAL* 3.9 19.7 - - - +
82C PHE* 1.3 81.3 - - - +
84C LEU* 1.3 64.4 + - - +
85C VAL* 3.2 27.5 + - - +
86C SER* 3.0 31.0 + - - +
89C SER* 3.1 10.6 + - - -
115C THR* 4.1 8.7 - - - -
116C LYS* 3.6 13.6 + - - +
137C ILE* 4.3 1.0 - - - +
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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