Contacts of the strand formed by residues 113 - 119 (chain Y) in PDB entry 5A0Q
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 PRO 113 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8Y GLN* 2.6 27.6 + - + +
9Y GLY 3.8 18.6 - - - +
10Y PRO 4.4 7.9 - - - +
12Y TYR 3.6 7.2 - - - +
13Y VAL* 3.2 24.9 - - + -
106Y GLY 3.9 4.7 - - - +
107Y TYR* 3.5 39.7 - - + +
111Y GLU 4.9 1.0 - - - +
112Y GLY* 1.3 86.2 - - - +
114Y ALA* 1.3 55.0 + - - +
126Y LYS* 4.7 2.8 + - - -
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Residues in contact with ALA 114 (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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8Y GLN* 3.4 9.9 - - - +
13Y VAL* 3.8 2.7 - - - +
77Y PRO* 4.2 9.1 - - + +
104Y LEU 4.1 1.6 - - - +
105Y ALA 3.8 0.3 - - - -
106Y GLY* 2.7 38.4 + - - +
111Y GLU* 5.1 5.8 - - - +
112Y GLY 3.6 6.1 + - - +
113Y PRO* 1.3 76.7 - - - +
115Y LEU* 1.3 59.8 + - - +
116Y TYR* 3.5 30.7 - - + +
126Y LYS* 4.3 9.6 - - - +
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Residues in contact with LEU 115 (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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6Y GLY* 3.5 39.9 - - - +
7Y ILE* 3.5 5.6 - - - +
8Y GLN* 2.3 59.4 + - + +
13Y VAL* 3.9 13.5 - - + -
103Y LEU* 4.2 17.5 - - + -
104Y LEU 3.7 4.9 - - - -
105Y ALA* 4.3 8.1 - - + -
114Y ALA* 1.3 73.7 - - - +
116Y TYR* 1.3 68.2 + - - +
126Y LYS* 3.9 3.5 - - - +
127Y ALA* 3.0 43.3 + - + +
128Y PRO 3.8 0.4 - - - +
129Y PHE* 4.5 0.9 - - - -
130Y ALA 4.3 7.2 - - - +
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Residues in contact with TYR 116 (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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77Y PRO 4.3 2.7 - - - -
78Y THR* 2.3 49.4 - - + +
81Y ALA* 4.3 7.0 - - + -
82Y ASN* 6.3 0.4 - - - -
102Y LEU 3.8 0.3 - - - +
103Y LEU* 3.3 10.9 - - - -
104Y LEU* 3.0 38.4 + - + +
111Y GLU* 4.5 0.5 + - - -
114Y ALA* 3.5 29.1 - - + +
115Y LEU* 1.3 78.1 - - - +
117Y TYR* 1.3 62.1 + - - +
118Y MET* 4.1 8.2 - - + +
124Y LEU* 3.5 38.1 - - + -
125Y ALA 3.5 1.8 - - - +
126Y LYS* 3.5 41.1 - - + +
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Residues in contact with TYR 117 (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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27X PHE* 4.7 7.2 - + - -
29X ILE* 3.6 35.4 - - + +
34X VAL* 4.0 35.9 - - + -
101Y ASN* 4.1 12.5 + - - -
103Y LEU* 3.9 2.9 - - - +
116Y TYR* 1.3 74.0 - - - +
118Y MET* 1.4 63.3 + - - +
119Y ASP* 3.8 27.0 + - + -
123Y ALA 4.1 7.9 - - - -
124Y LEU* 3.8 0.3 - - - +
125Y ALA* 3.1 37.1 + - + +
127Y ALA* 4.1 8.7 - - + +
130Y ALA* 4.3 15.7 - - + -
131Y ALA 3.7 20.4 - - - -
132Y HIS* 3.4 27.4 - + - -
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Residues in contact with MET 118 (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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81Y ALA* 3.5 33.4 - - + +
84Y THR* 3.6 24.2 - - + -
85Y ARG* 5.3 4.5 - - + -
88Y LEU* 5.1 9.2 - - + -
100Y VAL 4.3 0.7 - - - +
101Y ASN* 2.6 23.7 - - - +
102Y LEU* 3.0 40.1 + - + +
104Y LEU* 3.3 33.2 - - + -
116Y TYR* 4.1 4.3 - - + +
117Y TYR* 1.4 82.3 - - - +
119Y ASP* 1.3 63.4 + - - +
122Y ALA* 6.0 0.7 - - - -
123Y ALA 4.2 4.3 - - - +
124Y LEU* 3.6 19.7 - - + +
132Y HIS* 3.8 0.2 - - - -
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Residues in contact with ASP 119 (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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27X PHE* 6.0 1.0 - - - -
29X ILE* 3.1 31.5 - - - +
88Y LEU* 3.8 9.4 - - - +
100Y VAL 4.1 0.2 - - - -
101Y ASN* 3.6 7.9 - - - +
117Y TYR* 3.8 18.3 + - + -
118Y MET* 1.3 76.7 - - - +
120Y TYR* 1.3 84.6 + - - +
121Y LEU* 4.2 16.7 - - + +
122Y ALA* 2.9 21.6 + - - +
123Y ALA* 3.7 33.5 + - + +
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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