Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 4QNA
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 PHE 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO 2.8 17.8 + - - +
21A GLU* 3.3 28.1 - - - +
23A LEU* 1.3 90.2 - - + +
25A THR* 1.3 60.5 + - - +
26A LYS 4.1 1.0 + - - -
42A ILE 3.2 6.1 - - - +
43A ASP* 3.7 37.2 - - + -
44A ASN* 3.6 5.7 + - - +
45A ARG* 3.9 19.1 - - - -
50A VAL* 4.0 16.4 - - + -
52A ILE* 4.6 11.2 - - + -
86A TYR* 4.3 11.9 - + + -
89A TYR* 3.6 24.2 - + - -
96A TRP* 4.8 3.6 - - + -
98A ILE* 3.4 44.9 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 5.9 0.2 - - - -
24A PHE* 1.3 72.5 - - - +
26A LYS* 1.3 65.7 + - - +
27A LEU* 3.9 20.3 - - + +
41A GLY* 3.0 7.4 - - - -
42A ILE* 2.9 41.5 + - + -
44A ASN* 2.7 28.3 + - - -
52A ILE* 4.1 3.0 - - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 5.7 3.4 - - + +
24A PHE 4.1 2.0 + - - -
25A THR* 1.3 77.2 - - - +
27A LEU* 1.3 71.9 + - - +
39A PHE* 3.6 51.4 - - + -
40A LYS 4.0 2.5 - - - -
52A ILE* 4.1 6.7 - - + -
54A ILE* 4.5 13.4 - - + +
96A TRP* 3.8 37.3 - - + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.9 18.8 - - + +
26A LYS* 1.3 87.4 - - - +
28A GLU* 1.3 77.8 + - - +
39A PHE* 3.5 15.8 - - - -
40A LYS* 2.7 39.2 + - + +
41A GLY* 4.1 5.2 - - - -
42A ILE* 3.7 31.4 - - + -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 1.3 92.9 - - - +
29A LYS* 1.3 69.6 + - - +
30A ILE* 4.4 5.0 - - + +
39A PHE* 3.4 2.4 - - - -
40A LYS* 2.7 64.2 + - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 1.3 79.8 - - - +
30A ILE* 1.3 64.4 + - - +
31A GLY 2.5 31.1 + - - +
32A LYS* 4.0 19.3 - - - +
37A GLU* 3.0 44.4 + - - +
38A VAL 3.4 12.6 - - - +
39A PHE* 3.6 19.9 - - + -
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Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.8 15.5 - - + +
29A LYS* 1.3 79.8 - - - +
31A GLY* 1.3 57.8 + - - +
32A LYS* 2.7 24.7 + - - -
38A VAL* 2.9 21.8 + - + +
39A PHE 3.8 6.7 - - - +
40A LYS* 3.7 37.5 - - + +
51A ALA* 4.4 1.6 - - + -
101A TYR* 3.7 23.3 - - + +
401A X11 3.6 37.9 - - + -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 2.5 28.3 + - - +
30A ILE* 1.3 82.5 - - - +
32A LYS* 1.3 63.9 + - - -
38A VAL* 3.1 36.5 + - - -
401A X11 4.4 8.3 - - - -
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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