Contacts of the strand formed by residues 101 - 107 (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 ASN 101 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4Y LEU* 3.9 1.2 - - - +
47Y VAL* 3.0 44.1 + - + +
48Y GLY* 4.9 0.4 - - - -
99Y HIS 4.3 0.2 - - - -
100Y VAL* 1.3 72.8 - - - +
102Y LEU* 1.3 59.2 + - - +
117Y TYR* 4.1 14.8 + - - -
118Y MET 2.6 29.7 - - - +
119Y ASP* 3.6 11.8 - - - -
120Y TYR* 4.9 7.4 - - + +
132Y HIS* 2.5 44.2 + - - +
133Y GLY 4.1 5.0 + - - +
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Residues in contact with LEU 102 (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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4Y LEU* 4.7 0.2 - - - -
36Y PHE* 4.9 0.2 - - + -
44Y LEU* 2.9 54.3 - - + -
45Y LEU 3.0 14.4 - - - +
46Y CYS* 3.2 33.9 - - + -
56Y PHE* 4.6 5.8 - - + -
57Y ALA* 5.4 0.2 - - + -
84Y THR* 5.8 0.2 - - - +
88Y LEU* 6.2 1.3 - - + -
100Y VAL* 3.9 6.0 - - + -
101Y ASN* 1.3 76.3 + - - +
103Y LEU* 1.3 89.2 + - - +
104Y LEU* 3.5 4.9 - - - +
116Y TYR 3.8 0.2 - - - +
118Y MET* 3.0 51.9 + - + +
132Y HIS* 3.1 7.3 - - - -
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Residues in contact with LEU 103 (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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4Y LEU* 4.9 0.4 - - + -
5Y ILE 4.0 7.9 - - - +
6Y GLY* 3.8 18.6 - - - +
15Y VAL* 3.6 31.4 - - + -
43Y LEU 3.3 5.7 - - - +
45Y LEU* 3.1 40.3 + - + +
102Y LEU* 1.3 79.6 - - - +
104Y LEU* 1.4 58.3 + - - +
105Y ALA* 3.4 2.0 + - + +
115Y LEU* 4.2 15.3 - - + -
116Y TYR 3.3 21.5 - - - +
130Y ALA* 3.8 21.1 - - + -
132Y HIS* 3.4 26.4 + - + +
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Residues in contact with LEU 104 (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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42Y ILE* 3.8 14.8 - - + -
43Y LEU 3.7 3.1 - - - +
44Y LEU* 3.5 26.7 - - + +
60Y ILE* 6.0 0.9 - - + -
77Y PRO* 3.1 32.1 - - + +
80Y ALA* 3.8 15.9 - - + +
81Y ALA* 3.7 24.5 - - + +
84Y THR* 4.0 7.0 - - + -
102Y LEU* 3.5 5.4 - - + +
103Y LEU* 1.4 67.1 - - - +
105Y ALA* 1.3 67.5 + - - +
106Y GLY 4.0 0.3 + - - -
115Y LEU* 3.7 2.0 - - - -
116Y TYR* 3.0 31.7 + - + +
118Y MET* 3.3 20.6 - - + +
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Residues in contact with ALA 105 (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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13Y VAL* 4.1 5.4 - - + -
15Y VAL* 3.6 31.6 - - + -
42Y ILE* 3.6 2.6 - - - -
43Y LEU* 2.9 41.8 + - + +
45Y LEU* 6.0 0.2 - - + -
103Y LEU* 3.4 3.9 + - + +
104Y LEU* 1.3 79.2 - - - +
106Y GLY* 1.3 57.9 + - - +
114Y ALA 4.0 4.0 - - - -
115Y LEU* 4.3 5.4 - - + +
183Y ILE* 3.8 17.7 - - + -
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Residues in contact with GLY 106 (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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13Y VAL* 3.4 11.7 - - - +
41Y LYS 3.2 15.9 - - - -
42Y ILE* 4.5 0.2 - - - -
77Y PRO* 3.4 18.8 - - - -
105Y ALA* 1.3 78.9 - - - +
107Y TYR* 1.3 60.0 + - - -
114Y ALA 2.7 28.2 + - - +
183Y ILE* 4.5 6.0 - - - +
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Residues in contact with TYR 107 (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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10Y PRO 5.3 0.2 + - - -
11Y ASP* 3.6 21.9 + - - -
12Y TYR* 4.4 3.6 - - - -
13Y VAL* 4.6 1.3 - - + -
41Y LYS* 3.3 34.8 + - + +
77Y PRO* 3.3 4.7 - - - +
106Y GLY* 1.3 73.7 - - - +
108Y ASP* 1.3 84.6 + - - +
109Y GLU* 3.1 32.1 + - - -
112Y GLY* 5.3 0.2 - - - -
113Y PRO* 3.5 45.0 - - + +
183Y ILE* 3.7 19.1 - - + -
184Y ASP* 4.1 13.7 - - - -
185Y LYS* 3.0 44.3 + - + +
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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