Contacts of the strand formed by residues 42 - 47 (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 ILE 42 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38Y MET* 3.1 28.4 + - + -
39Y SER* 3.1 30.3 + - - +
41Y LYS* 1.4 83.1 - - - +
43Y LEU* 1.3 62.1 + - - +
44Y LEU* 4.2 5.2 - - + -
64Y VAL* 4.6 7.9 - - + -
74Y GLU* 4.1 4.5 - - + +
75Y LEU* 3.1 42.0 - - + +
76Y SER 4.2 1.1 - - - +
77Y PRO* 4.8 6.3 - - + -
80Y ALA* 3.7 32.3 - - + -
104Y LEU* 3.8 21.3 - - + -
105Y ALA 3.6 2.9 - - - -
188Y ILE* 4.5 0.6 - - - +
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Residues in contact with LEU 43 (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 VAL* 4.1 2.5 - - + -
35Y MET* 4.3 4.9 - - + -
36Y PHE 4.2 2.7 - - - -
37Y LYS* 4.2 14.8 - - + +
41Y LYS 5.3 0.2 - - - -
42Y ILE* 1.3 76.6 - - - +
44Y LEU* 1.4 86.5 + - - +
45Y LEU* 3.4 23.4 - - + +
103Y LEU 3.3 1.7 - - - +
104Y LEU* 4.5 0.2 - - - -
105Y ALA* 2.9 40.8 + - + +
181Y ARG* 3.7 24.9 - - - -
183Y ILE* 3.8 23.8 - - + -
188Y ILE* 3.7 32.8 - - + -
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Residues in contact with LEU 44 (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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36Y PHE* 2.9 45.8 + - + +
38Y MET* 3.8 32.3 - - + +
42Y ILE* 4.4 3.8 + - + -
43Y LEU* 1.4 79.1 - - - +
45Y LEU* 1.4 58.3 + - - +
56Y PHE* 3.8 24.7 - - + -
57Y ALA* 4.6 2.2 - - - -
60Y ILE* 4.8 8.5 - - + -
84Y THR* 4.8 3.6 - - + +
102Y LEU* 2.9 37.5 - - + -
103Y LEU 3.6 4.3 - - - -
104Y LEU* 3.5 30.3 - - + -
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Residues in contact with LEU 45 (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* 3.1 24.0 - - + +
5Y ILE 4.4 0.7 - - - +
15Y VAL* 3.5 31.6 - - + -
16Y ALA 4.2 7.4 - - - +
17Y SER* 3.6 8.5 - - - +
34Y LYS 3.3 16.4 - - - +
35Y MET* 3.6 7.2 - - - -
43Y LEU* 3.4 18.2 - - + +
44Y LEU* 1.4 81.3 - - - +
46Y CYS* 1.3 57.6 + - - +
102Y LEU* 3.0 14.6 - - - +
103Y LEU* 3.1 33.8 + - + +
181Y ARG* 3.3 27.4 - - - +
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Residues in contact with CYS 46 (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* 4.1 0.9 - - - +
34Y LYS* 3.3 20.5 + - - +
36Y PHE* 3.3 28.8 - - + -
45Y LEU* 1.3 69.8 - - - +
47Y VAL* 1.4 66.2 + - - +
48Y GLY 4.0 0.3 + - - -
53Y THR* 3.9 27.0 + - - +
56Y PHE* 5.2 1.8 - - - -
57Y ALA* 5.2 0.2 - - + -
100Y VAL* 3.2 37.5 - - - -
101Y ASN 3.9 1.6 - - - -
102Y LEU* 3.2 26.9 - - + -
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Residues in contact with VAL 47 (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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3Y TYR 4.3 8.3 - - - +
4Y LEU* 3.6 19.6 - - + +
34Y LYS* 3.4 31.6 - - - +
46Y CYS* 1.4 78.7 - - - +
48Y GLY* 1.4 62.6 + - - +
53Y THR* 4.3 0.4 - - - -
101Y ASN* 3.0 49.4 + - + +
132Y HIS* 3.7 16.4 - - + -
133Y GLY* 4.0 14.1 - - - +
134Y TYR* 6.3 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