Contacts of the strand formed by residues 51 - 56 (chain I) in PDB entry 3QSU
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 LYS 51 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I ASN* 3.6 4.7 - - - -
48I SER 3.0 22.7 + - - +
49I GLN* 4.1 7.0 + - + +
50I GLY* 1.3 85.5 + - - +
52I GLN* 1.3 61.3 + - - +
53I HIS* 2.9 26.5 + - + +
64K THR* 4.3 8.7 - - + +
65K VAL 3.5 18.6 - - - +
66K GLU* 2.9 45.7 + - - +
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Residues in contact with GLN 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I GLU* 4.8 5.2 - - - +
45I SER* 3.5 25.1 + - - +
47I ASN* 3.5 17.0 + - - +
51I LYS* 1.3 72.6 - - - +
53I HIS* 1.3 62.1 + - - +
54I LEU* 4.0 28.9 - - - +
11K ALA* 5.1 7.3 - - - +
15K PHE* 5.0 14.0 - - - -
63K TYR 5.6 0.4 + - - -
64K THR* 2.8 28.2 + - - -
65K VAL* 4.3 6.8 + - + +
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Residues in contact with HIS 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I MET* 3.5 27.2 - - + -
44I VAL 3.3 1.9 - - - +
45I SER* 3.3 4.0 - - - -
46I LEU* 2.8 48.3 + - + +
48I SER* 3.4 28.9 + - - -
51I LYS* 2.9 35.7 + - + -
52I GLN* 1.3 77.3 - - - +
54I LEU* 1.3 60.6 + - - +
55I ILE* 3.8 9.7 + - + +
78I ZN 2.1 35.2 - - - -
25K PHE* 5.9 2.0 - + - -
62K THR* 4.0 14.8 - - + -
63K TYR 3.5 4.5 - - - -
64K THR* 4.1 13.2 + - - -
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Residues in contact with LEU 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL* 4.0 15.5 - - + -
44I VAL 3.7 3.6 - - - +
45I SER* 4.7 4.3 - - - +
52I GLN* 4.0 21.0 - - - +
53I HIS* 1.3 73.3 - - - +
55I ILE* 1.3 59.9 + - - +
56I TYR* 4.2 0.3 + - - -
7K ILE* 3.6 31.6 - - + -
8K GLN* 4.6 13.0 - - + -
11K ALA* 3.9 23.1 - - + -
12K LEU* 4.4 7.4 - - + -
15K PHE* 5.2 2.7 - - + -
61K SER 4.1 0.2 - - - +
62K THR* 3.2 4.1 - - - -
63K TYR* 2.8 75.7 + - + +
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Residues in contact with ILE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I VAL* 4.6 11.2 - - + -
26I PHE* 3.6 36.1 - - + -
32I MET* 5.1 0.4 - - - -
43I VAL* 3.1 8.1 - - - -
44I VAL* 2.9 42.2 + - + +
46I LEU* 3.6 40.2 - - + -
53I HIS* 4.1 7.6 - - + +
54I LEU* 1.3 76.8 - - - +
56I TYR* 1.3 74.2 + - - +
59I ALA* 4.6 0.4 - - + -
60I ILE* 3.6 17.9 - - + -
61K SER 3.4 7.0 - - - +
62K THR* 4.0 14.1 - - + +
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Residues in contact with TYR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I TYR* 3.6 9.6 - - + -
43I VAL* 3.7 15.5 - - + -
55I ILE* 1.3 76.1 - - - +
57I LYS* 1.3 67.2 + - - +
58I HIS* 3.3 33.7 - + + +
59I ALA* 2.9 19.1 + - - +
60I ILE 3.6 2.6 + - - -
79I ZN 4.6 3.8 - - - -
8K GLN* 2.5 40.7 + - - +
57K LYS* 3.5 21.5 - - + +
60K ILE* 3.5 36.1 - - + +
61K SER 3.1 9.7 + - - +
63K TYR* 2.8 45.4 + + - -
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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