Contacts of the strand formed by residues 51 - 58 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24R SER* 3.0 30.0 + - - -
59R GLY* 3.6 9.4 - - - -
60R CYS* 2.0 57.9 - - + -
32S LEU* 4.4 10.3 - - - +
33S VAL 3.0 24.0 - - - +
34S ASP* 3.8 7.4 - - + +
35S ILE* 3.9 1.6 - - - -
49S PRO* 3.4 5.4 - - - +
50S SER* 1.3 80.5 - - - +
52S VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R VAL* 4.0 4.0 - - + -
24R SER* 4.1 0.4 - - - -
31S THR 3.5 0.2 - - - +
32S LEU* 3.3 6.9 - - - -
33S VAL* 2.8 37.2 + - + +
35S ILE* 3.6 25.1 - - + +
49S PRO* 4.9 0.4 - - + -
51S CYS* 1.3 81.0 - - - +
53S PRO* 1.3 70.9 - - + +
54S LEU* 3.6 34.7 + - + -
78S MET* 3.6 12.8 - - - -
80S ILE* 3.9 18.2 - - + -
96S PHE* 4.1 14.4 - - + -
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Residues in contact with PRO 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R VAL* 4.5 9.9 - - + +
23R ARG* 3.9 40.4 + - + +
24R SER* 4.2 10.5 - - - -
30S GLU* 3.7 22.9 - - - +
31S THR 3.6 0.2 - - - +
32S LEU* 3.4 23.3 - - + -
52S VAL* 1.3 88.1 - - + +
54S LEU* 1.3 59.4 + - - +
78S MET* 3.1 31.4 - - + +
98S GLN* 4.7 1.7 - - - +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S GLU* 4.3 4.0 - - - +
31S THR* 2.6 47.7 + - - +
33S VAL* 3.5 31.2 - - + -
38S GLU* 4.7 0.9 - - - +
52S VAL* 3.6 15.5 - - + +
53S PRO* 1.3 81.8 - - - +
55S MET* 1.3 61.4 + - - +
56S ARG* 3.3 22.7 + - - +
76S ILE* 3.7 10.5 - - + -
78S MET* 3.7 15.9 - - + -
96S PHE* 3.4 34.5 - - + -
97S LEU 4.0 13.0 - - - +
98S GLN* 4.0 4.0 - - + -
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Residues in contact with MET 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S PRO* 3.9 24.2 - - + +
29S ILE* 3.8 1.8 - - - -
30S GLU* 3.7 29.4 - - - +
54S LEU* 1.3 71.8 - - - +
56S ARG* 1.3 72.8 + - - +
98S GLN* 3.2 26.9 + - + +
99S HIS 2.8 33.0 + - - +
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Residues in contact with ARG 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S PRO* 3.1 4.1 - - - +
29S ILE* 2.6 41.2 + - - +
31S THR* 3.4 26.7 - - + +
33S VAL* 4.2 10.8 - - + +
37S GLN* 4.7 5.9 - - - +
38S GLU* 3.1 37.0 + - - -
54S LEU* 3.3 16.6 + - - +
55S MET* 1.3 96.2 - - - +
57S CYS* 1.3 67.1 - - - +
97S LEU* 2.7 37.8 + - - +
99S HIS* 3.7 29.8 + - + -
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Residues in contact with CYS 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S HIS 3.5 0.2 - - - -
29S ILE* 4.8 0.2 - - - -
31S THR* 4.9 1.6 + - - -
56S ARG* 1.3 80.3 - - - +
58S GLY* 1.3 58.0 + - - +
68S CYS* 3.8 21.7 - - - +
69S VAL 3.5 0.2 - - - -
70S PRO* 3.2 35.7 - - + -
99S HIS* 3.0 22.6 + - + +
101S LYS 3.8 0.2 - - - -
102S CYS* 2.0 50.0 - - - -
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Residues in contact with GLY 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R LEU* 3.9 5.6 - - - -
26S CYS* 3.2 2.7 - - - -
27S HIS* 2.7 35.9 + - - +
29S ILE* 4.2 12.1 - - - -
56S ARG 3.5 0.2 + - - -
57S CYS* 1.3 76.1 - - - +
59S GLY* 1.3 62.9 + - - -
68S CYS* 3.9 5.2 - - - -
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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