Contacts of the strand formed by residues 51 - 58 (chain R) in PDB entry 1QTY
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 CYS 51 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32R LEU* 4.5 10.3 - - - +
33R VAL 3.0 22.2 - - - +
34R ASP* 3.9 9.0 - - - +
35R ILE* 3.8 1.1 - - - -
49R PRO* 3.3 13.5 - - - +
50R SER* 1.3 78.4 - - - +
52R VAL* 1.3 65.5 + - - +
24S SER* 3.2 27.4 - - - -
59S GLY* 3.7 7.9 - - - -
60S CYS* 2.0 58.2 - - + -
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Residues in contact with VAL 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R THR 3.6 0.3 - - - +
32R LEU* 3.4 6.9 - - - -
33R VAL* 2.7 48.6 + - + +
35R ILE* 3.6 20.4 - - + -
49R PRO* 4.7 0.4 - - + -
51R CYS* 1.3 81.2 - - - +
53R PRO* 1.3 67.5 - - + +
54R LEU* 3.6 25.4 + - + -
78R MET* 3.8 9.6 - - - -
80R ILE* 3.8 7.6 - - + -
96R PHE* 3.9 22.9 - - + -
20S VAL* 3.5 24.2 - - + -
24S SER* 4.1 0.7 - - - -
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Residues in contact with PRO 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R GLU* 3.7 22.9 - - - +
31R THR 3.5 6.7 - - - +
32R LEU* 3.6 17.0 - - + -
52R VAL* 1.3 89.8 - - + +
54R LEU* 1.3 60.0 + - - +
78R MET* 3.2 24.1 - - + +
98R GLN* 4.9 1.4 - - - +
15S VAL* 6.5 0.2 - - + -
20S VAL* 4.2 10.3 - - + +
23S ARG* 3.8 42.5 + - + +
24S SER* 4.2 10.1 - - - +
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Residues in contact with LEU 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R GLU* 4.4 3.3 - - - +
31R THR* 2.7 43.7 + - - +
33R VAL* 3.5 34.8 - - + -
38R GLU* 4.6 0.2 - - - +
52R VAL* 3.8 15.0 - - + -
53R PRO* 1.3 80.4 - - - +
55R MET* 1.3 60.7 + - - +
56R ARG* 3.4 29.2 + - - +
76R ILE* 3.8 9.2 - - + -
78R MET* 3.8 17.0 - - + -
96R PHE* 3.3 37.7 - - + -
97R LEU 4.2 4.0 - - - +
98R GLN* 4.2 4.9 - - + -
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Residues in contact with MET 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R PRO* 3.8 26.9 - - + +
29R ILE 3.8 2.5 - - - +
30R GLU* 4.0 26.9 - - - +
54R LEU* 1.3 72.5 - - - +
56R ARG* 1.3 71.9 + - - +
98R GLN* 3.4 29.2 + - - +
99R HIS 2.9 33.6 + - - +
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Residues in contact with ARG 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R PRO* 4.1 3.8 - - - -
29R ILE* 2.8 33.2 + - - +
31R THR* 3.4 26.0 - - + +
33R VAL* 4.4 12.8 - - + +
37R GLN* 4.8 6.3 - - - +
38R GLU* 2.5 39.8 + - - -
54R LEU* 3.4 14.7 + - - +
55R MET* 1.3 94.7 - - - +
57R CYS* 1.3 66.6 + - - +
58R GLY 3.4 0.2 + - - -
97R LEU* 2.7 39.6 + - - +
99R HIS* 3.7 29.8 + - + +
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Residues in contact with CYS 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R THR* 5.0 1.6 + - - -
56R ARG* 1.3 79.5 - - - +
58R GLY* 1.3 58.9 + - - +
68R CYS* 4.0 18.6 - - - +
69R VAL* 3.5 1.8 - - - -
70R PRO* 3.3 31.0 - - + -
99R HIS* 2.9 25.8 + - + +
102R CYS* 2.0 51.4 - - + -
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Residues in contact with GLY 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R CYS* 3.4 2.1 - - - -
27R HIS* 2.9 35.6 + - - +
29R ILE* 4.1 13.5 - - - -
56R ARG 3.4 0.6 + - - -
57R CYS* 1.3 76.9 - - - +
59R GLY* 1.3 61.6 + - - -
68R CYS* 3.8 5.6 - - - -
32S LEU* 4.0 6.5 - - - -
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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