Contacts of the strand formed by residues 79 - 86 (chain C) in PDB entry 2I62
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 PHE 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C PHE* 3.8 19.7 - + - -
55C VAL* 3.6 21.3 - - + -
56C LYS* 3.4 35.7 - - - -
57C GLY* 3.3 22.2 - - - -
58C GLU 4.2 0.2 - - - +
59C LEU 4.0 8.5 - - - -
60C LEU* 3.8 32.5 - - + -
75C ALA 2.8 16.7 + - - +
76C CYS* 3.7 19.8 - - - +
78C SER* 1.3 80.4 - - - +
80C THR* 1.3 65.9 + - - +
81C GLU 3.3 7.0 + - - +
82C ILE* 4.2 9.4 - - + +
135C ALA* 4.3 2.6 - - - +
159C ASP* 4.1 7.9 - - + -
160C CYS* 3.5 27.6 - - + -
193C PHE* 5.3 0.4 - + - -
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Residues in contact with THR 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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220A GLU* 3.9 24.5 - - + +
221A THR* 5.3 6.1 - - - +
201B LYS* 2.6 35.5 + - - +
251B GLU* 2.7 43.2 - - - +
57C GLY 4.1 2.2 + - - +
58C GLU* 3.5 12.6 + - - +
76C CYS 5.4 1.3 - - - +
78C SER 5.7 1.8 - - - +
79C PHE* 1.3 73.5 - - - +
81C GLU* 1.3 64.2 + - - +
82C ILE 4.3 0.4 - - - -
135C ALA* 3.8 9.2 - - - -
137C LYS* 3.6 4.2 - - - -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS* 3.7 36.5 - - + +
216B PRO* 4.0 26.0 - - - +
218B GLY 4.7 5.2 + - - -
58C GLU* 2.9 27.0 + - - +
59C LEU* 3.8 21.1 - - + +
60C LEU* 2.8 31.9 + - - +
79C PHE* 4.2 1.0 - - - +
80C THR* 1.3 84.6 - - - +
82C ILE* 1.3 60.9 - - - +
135C ALA 3.7 2.7 - - - -
137C LYS* 4.0 16.6 - - + +
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Residues in contact with ILE 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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60C LEU* 3.2 25.8 - - + -
72C LEU* 4.2 15.5 - - + -
75C ALA* 4.7 5.8 - - + -
76C CYS* 3.9 35.7 - - + +
79C PHE* 4.2 7.9 - - + +
81C GLU* 1.3 78.9 - - - +
83C ILE* 1.3 73.8 + - - +
84C VAL* 4.0 18.8 - - + -
132C LEU* 4.0 11.9 - - + -
135C ALA* 2.8 22.7 + - + +
136C ILE* 3.2 12.4 - - + +
137C LYS* 2.8 30.8 + - - +
138C GLN 4.0 0.2 + - - -
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Residues in contact with ILE 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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59C LEU* 4.0 20.6 - - + -
60C LEU 2.9 10.5 + - - +
61C ILE* 4.3 16.8 - - + -
62C ASP* 2.8 30.1 + - - +
82C ILE* 1.3 77.8 - - - +
84C VAL* 1.3 71.7 + - - +
85C SER* 4.8 2.2 - - - -
137C LYS* 5.1 4.3 - - + -
138C GLN* 3.7 25.6 - - + +
140C LEU* 3.8 25.1 - - + -
150C LEU* 5.1 0.9 - - + -
155C LEU* 3.2 45.3 - - + -
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Residues in contact with VAL 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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62C ASP* 3.8 9.0 - - + +
65C SER* 4.1 5.8 - - - +
69C ILE* 5.9 0.2 - - + -
72C LEU* 3.5 31.9 - - + -
82C ILE* 4.0 8.7 - - + -
83C ILE* 1.3 79.2 - - - +
85C SER* 1.3 64.8 + - - +
92C LEU* 5.0 0.2 - - - -
95C LEU* 3.4 34.3 - - + -
136C ILE* 4.0 14.8 - - + -
138C GLN 3.2 5.2 + - - +
139C VAL* 3.4 26.0 - - + -
140C LEU 2.9 22.7 + - - -
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Residues in contact with SER 85 (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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61C ILE* 5.3 0.4 - - - -
62C ASP 2.7 20.9 + - - -
63C ILE* 3.4 11.8 - - - +
64C GLY 3.0 2.9 + - - -
65C SER* 2.8 34.1 + - - -
83C ILE* 4.8 3.1 - - - -
84C VAL* 1.3 78.8 - - - +
86C ASP* 1.3 56.7 + - - +
92C LEU* 4.2 2.2 - - - -
140C LEU* 3.0 15.5 - - - -
142C CYS* 3.2 23.2 - - - -
150C LEU* 3.9 13.9 - - - -
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Residues in contact with ASP 86 (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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64C GLY* 3.3 13.3 - - - -
65C SER* 4.0 1.6 - - - +
66C GLY* 2.9 24.0 + - - +
85C SER* 1.3 75.5 - - - +
87C TYR* 1.3 66.2 + - - +
88C THR* 3.0 13.7 + - - +
91C ASN* 3.0 15.0 + - + +
92C LEU* 3.7 21.3 - - + +
140C LEU 3.1 6.3 + - - +
141C LYS* 3.3 8.8 - - - -
142C CYS* 2.9 25.0 + - - -
4003C SAH 2.6 41.9 + - - -
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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