Contacts of the strand formed by residues 31 - 39 (chain F) in PDB entry 3QO3
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 31 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F SER* 4.1 14.7 + - - -
24F ILE 3.5 6.3 - - - +
25F TYR* 3.4 46.0 + - + +
29F GLY 3.7 3.2 + - - +
30F ILE* 1.3 80.1 - - - +
32F LEU* 1.3 73.7 + - - +
33F GLN* 3.8 27.0 + - + +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E THR* 3.5 30.5 - - + +
23F SER* 3.4 3.6 - - - -
24F ILE* 2.7 47.3 + - + +
26F LEU* 4.0 18.8 - - + -
30F ILE* 3.9 19.7 - - + -
31F LYS* 1.3 75.6 - - - +
33F GLN* 1.3 61.4 + - - +
46F LEU* 3.8 15.5 - - + -
52F GLN* 3.8 19.7 - - - +
54F VAL* 3.7 25.4 - - + -
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Residues in contact with GLN 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL 3.4 6.5 - - - +
23F SER* 3.9 17.0 - - - +
31F LYS* 3.8 28.7 + - + +
32F LEU* 1.3 79.5 - - - +
34F GLY* 1.3 59.7 + - - +
46F LEU* 3.8 13.3 - - - +
47F LYS 5.3 1.7 - - - -
48F ASN 5.3 0.9 + - - -
52F GLN* 4.4 6.1 + - - +
65F SER* 4.2 10.7 + - - -
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Residues in contact with GLY 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F PRO* 3.6 5.2 - - - +
22F VAL* 2.8 35.0 + - - +
33F GLN* 1.3 78.7 - - - +
35F GLN* 1.3 62.3 + - - -
46F LEU* 3.6 9.9 - - - +
47F LYS 3.4 11.7 - - - -
48F ASN* 4.9 2.9 - - - -
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Residues in contact with GLN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU 5.7 0.2 - - - +
19F ARG* 3.4 46.8 + - - +
20F VAL 3.5 24.0 - - - +
21F PRO* 4.2 9.6 - - + +
34F GLY* 1.3 76.8 - - - +
36F ILE* 1.3 63.3 + - - +
37F GLU 3.2 0.7 + - - -
46F LEU* 3.4 4.8 - - - -
47F LYS* 2.7 45.4 + - + +
48F ASN* 4.3 17.1 - - - +
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Residues in contact with ILE 36 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F LEU* 4.0 21.1 - - + +
15F LEU* 3.7 37.1 + - + -
16F ARG* 3.3 40.5 - - + +
20F VAL 4.7 2.2 + - - -
22F VAL* 3.9 21.1 - - + +
24F ILE* 5.1 2.2 - - + -
35F GLN* 1.3 73.1 - - - +
37F GLU* 1.3 62.8 + - - +
38F SER* 3.9 16.6 - - - +
39F PHE* 4.3 10.3 - - + -
44F ILE* 4.0 26.0 - - + -
45F LEU 3.6 2.9 - - - -
46F LEU* 4.4 3.6 - - + -
62F VAL* 4.8 3.8 - - + -
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Residues in contact with GLU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 3.1 16.5 - - - +
35F GLN 3.2 3.8 + - - -
36F ILE* 1.3 72.7 - - - +
38F SER* 1.3 65.8 + - - +
45F LEU* 2.7 35.0 + - + +
47F LYS* 3.5 22.8 + - + +
51F SER* 2.7 29.6 + - - -
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.3 25.2 - - - +
16F ARG* 4.0 13.0 - - - +
36F ILE* 3.5 2.2 - - - -
37F GLU* 1.3 85.4 + - - +
39F PHE* 1.3 63.1 + - - +
44F ILE* 3.6 2.3 - - - +
45F LEU* 2.7 51.5 + - - +
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Residues in contact with PHE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLN* 5.0 3.8 + - - +
7E LEU* 3.0 15.8 - - - +
9F ASP* 3.7 35.9 - - - -
12F LEU* 3.6 35.0 - - + -
13F ASN* 3.3 41.1 - - - -
16F ARG* 4.2 8.3 - - - -
36F ILE* 4.3 9.9 - - + -
38F SER* 1.3 82.5 - - - +
40F ASP* 1.3 70.0 + - - +
43F VAL 3.4 12.1 - - - +
44F ILE* 4.0 17.5 - - + -
56F LYS* 4.7 1.3 - - - -
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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