Contacts of the helix formed by residues 86 - 96 (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 SER 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA* 5.6 8.7 - - - +
83C SER* 3.0 20.9 + - - +
84C LEU 3.4 0.6 - - - -
85C VAL* 1.3 81.3 - - - +
87C PRO* 1.3 65.2 - - - +
88C ALA* 3.0 8.0 + - - +
89C SER* 2.6 48.3 + - - -
90C PHE 3.2 2.4 + - - -
129C LEU* 5.5 0.2 - - - -
137C ILE* 5.0 0.4 - - - -
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Residues in contact with PRO 87 (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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85C VAL* 3.8 7.9 - - - +
86C SER* 1.3 84.9 - - - +
88C ALA* 1.3 56.5 + - - +
90C PHE* 3.2 3.9 + - + +
91C GLU* 2.8 30.7 + - - +
129C LEU* 4.5 11.2 - - + -
134C LEU* 4.2 33.2 - - + -
135C THR 3.4 26.2 - - - +
137C ILE* 3.9 24.0 - - + -
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 5.5 0.7 - - - +
86C SER* 2.9 8.2 + - - +
87C PRO* 1.3 78.1 - - - +
89C SER* 1.3 57.2 + - - +
91C GLU* 2.8 24.0 + - - +
92C ASN* 2.9 19.5 + - - +
134C LEU* 6.1 0.8 - - - +
62D GLU* 3.6 42.8 - - + +
63D ASP* 4.8 9.6 - - - +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 3.1 29.2 + - - +
13C ALA* 6.1 2.0 - - - -
14C VAL* 4.3 8.3 - - - -
81C CYS 5.1 0.9 - - - +
82C PHE* 3.9 7.1 - - - +
83C SER 3.1 28.9 + - - -
86C SER* 2.6 30.8 + - - -
88C ALA* 1.3 78.6 - - - +
90C PHE* 1.3 65.7 + - - +
92C ASN* 3.2 12.1 + - - +
93C VAL* 3.3 14.2 + - - +
97C TRP* 4.9 1.7 - - - -
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Residues in contact with PHE 90 (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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82C PHE* 3.3 46.9 - + + -
86C SER 3.2 2.2 + - - +
87C PRO 3.3 10.3 - - - +
89C SER* 1.3 83.3 + - - +
91C GLU* 1.3 65.4 + - + +
93C VAL* 3.1 21.2 + - + +
94C ARG* 5.2 4.7 - - - -
137C ILE* 3.3 45.8 - - + -
141C GLN* 3.6 16.2 - - + -
142C GLY* 3.9 8.5 - - - -
145C MET* 3.3 47.5 - - + +
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Residues in contact with GLU 91 (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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87C PRO 2.8 16.5 + - - +
88C ALA* 2.8 10.3 + - - +
90C PHE* 1.3 77.3 - - + +
92C ASN* 1.3 58.8 + - - +
93C VAL 3.2 0.7 + - - -
94C ARG* 2.7 43.2 + - - +
95C ALA* 2.9 32.3 + - + +
62D GLU* 5.6 4.3 - - - +
65D ASP* 5.8 3.8 - - - +
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Residues in contact with ASN 92 (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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11C ASP* 3.4 28.2 - - - +
88C ALA 2.9 9.8 + - - +
89C SER 3.2 9.6 + - - +
91C GLU* 1.3 75.8 - - - +
93C VAL* 1.3 59.5 + - - +
95C ALA* 4.1 10.3 - - - +
96C LYS* 2.7 45.0 + - + +
97C TRP* 2.9 16.6 + - - +
62D GLU* 2.9 35.6 + - - +
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Residues in contact with VAL 93 (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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80C ILE* 3.8 27.1 - - + -
81C CYS 4.7 2.5 - - - +
82C PHE* 3.9 26.0 - - + -
89C SER 3.3 11.9 + - - +
90C PHE* 3.1 18.4 + - - +
92C ASN* 1.3 77.6 - - - +
94C ARG* 1.3 61.4 + - - +
97C TRP* 3.7 10.4 + - + -
98C TYR* 2.9 33.0 + - + +
112C LEU* 3.8 10.8 - - + -
145C MET* 4.0 19.3 - - + -
149C ILE* 4.5 11.0 - - + -
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Residues in contact with ARG 94 (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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90C PHE* 5.2 5.1 - - - -
91C GLU* 2.7 46.3 + - - +
93C VAL* 1.3 80.9 - - - +
95C ALA* 1.3 61.4 + - - +
98C TYR* 4.9 5.6 - - + -
99C PRO* 3.3 19.9 - - - +
145C MET* 3.5 32.7 - - + +
148C GLU* 3.1 40.4 + - - +
149C ILE* 4.9 3.4 - - + -
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Residues in contact with ALA 95 (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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91C GLU* 2.9 29.4 + - + +
92C ASN* 4.1 13.9 - - - +
94C ARG* 1.3 81.1 - - - +
96C LYS* 1.3 57.4 + - - +
99C PRO* 3.8 10.7 - - - +
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Residues in contact with LYS 96 (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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11C ASP* 5.4 0.7 - - - +
60C GLY 4.2 6.9 + - - -
61C GLN 4.2 6.1 + - - -
62C GLU* 4.0 21.6 - - - +
65C ASP* 3.2 29.6 + - - -
68C ARG* 3.9 12.5 - - - +
92C ASN* 2.7 33.6 + - + +
95C ALA* 1.3 76.4 - - - +
97C TRP* 1.3 88.1 + - + +
98C TYR 3.7 1.1 - - - -
99C PRO* 3.6 4.6 - - - +
100C GLU* 3.2 25.2 + - + +
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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