Contacts of the strand formed by residues 70 - 75 (chain B) in PDB entry 3QO0
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 LEU 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.3 43.7 - - + +
62B TYR* 3.4 39.3 - - + -
66B MET* 3.5 39.5 + - + +
68B GLY* 3.7 3.4 - - - -
69B ARG* 1.3 84.0 + - - +
71B THR* 1.3 67.9 + - - +
83B LEU* 4.0 10.8 - - + -
84B GLN 3.3 0.7 - - - -
85B MET* 3.6 31.4 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B TYR* 3.6 6.3 - - - +
70B LEU* 1.3 78.2 + - - +
72B ILE* 1.3 70.8 + - - +
73B SER* 4.9 6.6 + - - +
82B PHE* 3.5 3.1 - - - +
84B GLN* 2.8 55.4 + - + +
86B ASN* 4.5 6.9 + - - -
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 3.8 18.8 - - + +
49B GLY* 3.5 13.2 - - - +
50B ARG* 3.4 32.1 - - - +
51B ILE* 3.7 33.0 - - + +
60B THR* 3.8 16.8 - - + +
62B TYR* 3.2 30.6 + - + +
71B THR* 1.3 75.9 - - - +
73B SER* 1.3 66.6 + - - +
81B ALA* 5.5 0.4 - - + -
82B PHE 3.1 10.5 - - - +
83B LEU* 3.5 28.0 - - + -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 5.2 2.4 - - - -
51B ILE* 3.9 9.6 - - - -
71B THR* 4.9 8.1 + - - +
72B ILE* 1.3 77.6 - - - +
74B ARG* 1.3 66.9 + - - +
81B ALA* 3.3 5.0 - - - +
82B PHE* 2.8 49.6 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 4.0 26.8 + - - -
30B SER* 3.6 21.8 - - - +
32B SER 4.7 1.2 + - - -
34B VAL* 5.0 3.8 - - - -
51B ILE* 4.0 24.9 - - + +
52B LYS 3.1 19.0 + - - -
53B ARG* 4.0 5.7 - - - +
54B ASN* 4.0 7.3 - - - +
58B ASP* 2.7 38.6 + - - +
73B SER* 1.3 83.4 - - - +
75B ASP* 1.3 60.1 + - - +
76B ASP* 3.0 42.2 + - - +
80B THR 3.3 6.1 - - - +
81B ALA* 4.2 9.0 - - + +
82B PHE* 4.7 2.0 - - - +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 1.3 71.2 - - - +
76B ASP* 1.3 57.3 + - - +
77B SER* 2.5 30.6 + - - -
78B LYS* 3.2 34.5 + - + +
79B ASN 2.8 22.0 + - - -
80B THR 2.7 15.7 + - - +
82B PHE* 3.7 23.5 - - + -
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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