Contacts of the helix formed by residues 88 - 99 (chain Y) in PDB entry 1YQV
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 ILE 88 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3Y PHE* 3.6 32.0 - - + -
8Y LEU* 4.2 9.9 - - + -
11Y ALA* 3.8 36.8 - - + -
12Y MET* 4.1 14.8 - - + +
14Y ARG* 5.6 1.7 - - - +
15Y HIS* 3.9 13.0 - - + +
40Y THR* 4.8 3.6 - - + -
55Y ILE* 4.6 18.4 - - + -
85Y SER 5.0 0.7 - - - -
86Y SER 3.9 0.2 + - - -
87Y ASP* 1.3 73.6 + - - +
89Y THR* 1.3 66.9 + - - +
90Y ALA 3.4 0.9 - - - -
91Y SER* 3.1 10.3 + - - +
92Y VAL* 2.9 41.4 + - + +
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Residues in contact with THR 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y HIS* 3.1 27.3 + - + +
87Y ASP* 2.5 28.9 + - - -
88Y ILE* 1.3 77.1 - - - +
90Y ALA* 1.3 65.2 + - - +
92Y VAL* 3.2 1.7 + - - +
93Y ASN* 3.0 40.3 + - - +
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Residues in contact with ALA 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Y ILE* 5.0 9.3 - - + +
82Y ALA* 3.4 31.6 - - + +
83Y LEU* 3.5 16.8 - - + +
85Y SER* 6.3 0.2 - - - -
87Y ASP 4.6 3.6 + - - +
88Y ILE 3.4 0.8 - - - -
89Y THR* 1.3 80.2 - - - +
91Y SER* 1.3 63.3 + - - +
93Y ASN* 3.4 7.7 + - - +
94Y CYS* 3.1 19.2 + - - +
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Residues in contact with SER 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Y TYR 5.1 0.2 + - - -
54Y GLY* 5.0 0.9 - - - -
55Y ILE* 4.2 26.6 + - - +
56Y LEU* 4.4 8.1 + - - +
58Y ILE* 3.9 12.4 - - - +
83Y LEU* 3.4 36.9 + - - +
88Y ILE* 3.1 12.9 + - - -
90Y ALA* 1.3 78.0 - - - +
92Y VAL* 1.3 58.9 + - - +
94Y CYS* 3.4 2.6 + - - +
95Y ALA* 2.8 31.6 + - - +
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Residues in contact with VAL 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Y MET* 5.3 1.3 - - + -
15Y HIS* 3.9 27.8 - - + +
17Y LEU* 3.9 23.8 - - + -
56Y LEU* 5.2 3.8 - - + -
88Y ILE* 2.9 47.2 + - + +
89Y THR 3.7 4.7 - - - +
91Y SER* 1.3 76.9 - - - +
93Y ASN* 1.3 65.1 + - - +
95Y ALA* 3.1 7.1 + - - +
96Y LYS* 2.9 47.8 + - - +
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Residues in contact with ASN 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y HIS* 6.0 1.6 - - - -
89Y THR* 3.0 37.6 + - - +
90Y ALA* 3.8 7.5 - - - +
92Y VAL* 1.3 77.7 - - - +
94Y CYS* 1.3 60.7 + - - +
96Y LYS* 3.3 26.4 + - - +
97Y LYS* 3.4 30.5 + - - +
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Residues in contact with CYS 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Y ILE* 3.7 40.4 - - + -
63Y TRP* 3.9 0.9 - - - -
76Y CYS* 2.0 52.9 - - + -
78Y ILE* 5.1 2.0 - - + -
83Y LEU* 4.6 6.7 - - + -
90Y ALA 3.1 15.1 + - - +
93Y ASN* 1.3 76.0 - - - +
95Y ALA* 1.3 60.5 + - - +
97Y LYS* 3.0 8.8 + - - +
98Y ILE* 2.9 35.1 + - - +
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Residues in contact with ALA 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y LEU* 5.4 2.7 - - + -
28Y TRP* 4.2 10.9 - - + -
56Y LEU* 3.7 24.9 - - + -
58Y ILE* 5.5 0.7 - - + -
91Y SER 2.8 19.4 + - - +
92Y VAL* 3.1 6.9 + - - +
94Y CYS* 1.3 77.4 - - - +
96Y LYS* 1.3 60.5 + - + +
98Y ILE* 3.3 3.0 + - - +
99Y VAL* 3.0 24.3 + - - +
108Y TRP* 3.5 26.5 - - + -
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Residues in contact with LYS 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y HIS 2.8 29.1 + - - -
16Y GLY* 4.2 4.5 + - - -
17Y LEU* 4.1 14.1 - - + -
20Y TYR* 3.5 53.4 + - + +
28Y TRP* 5.4 0.2 - - - -
92Y VAL* 2.9 30.3 + - + +
93Y ASN* 3.6 18.9 + - - +
94Y CYS 3.2 0.6 - - - -
95Y ALA* 1.3 76.9 - - - +
97Y LYS* 1.3 60.1 + - + +
99Y VAL* 3.3 8.2 - - - +
100Y SER* 3.0 22.2 + - - -
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Residues in contact with LYS 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Y TRP* 4.7 6.1 - - + -
75Y LEU 4.2 7.9 - - - +
76Y CYS* 4.1 38.9 + - - +
93Y ASN* 3.4 30.3 + - - +
94Y CYS* 3.0 8.2 + - - +
96Y LYS* 1.3 78.0 - - + +
98Y ILE* 1.3 66.1 + - - +
100Y SER* 3.0 16.1 + - - -
101Y ASP* 3.4 9.2 + - - +
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Residues in contact with ILE 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58Y ILE* 4.1 16.6 - - + -
63Y TRP* 3.5 50.0 - - + +
94Y CYS* 2.9 35.6 + - - +
95Y ALA 3.3 6.0 + - - +
97Y LYS* 1.3 76.2 - - - +
99Y VAL* 1.3 57.5 + - - +
101Y ASP* 3.0 24.6 + - - +
103Y ASN 5.5 0.2 + - - -
104Y GLY 4.3 4.5 + - - +
107Y ALA* 3.4 30.0 - - + +
108Y TRP* 3.6 28.3 - - + +
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Residues in contact with VAL 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Y TYR* 3.8 25.8 - - + -
21Y ARG* 3.4 18.9 + - + -
23Y TYR* 3.6 34.8 - - + -
28Y TRP* 3.9 9.4 - - + -
95Y ALA 3.0 15.3 + - - +
96Y LYS* 3.3 18.6 - - - +
98Y ILE* 1.3 76.7 - - - +
100Y SER* 1.3 57.0 + - - +
101Y ASP 3.4 1.1 - - - -
102Y GLY 4.7 0.2 + - - -
104Y GLY* 3.5 32.1 + - - -
105Y MET* 3.8 11.4 - - + -
108Y TRP* 4.2 3.8 - - + -
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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