Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 1QNK
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 GLU 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A CYS* 2.8 41.8 - - + +
10A GLN* 4.0 13.2 - - + +
11A CYS* 3.6 31.2 - - + +
14A THR* 6.2 0.4 - - - -
29A LYS* 2.5 52.0 + - + +
30A SER 3.0 9.9 - - - +
31A PRO* 3.7 1.1 - - - +
35A CYS* 4.0 2.2 - - - +
37A GLN 2.6 19.8 - - - +
38A THR* 1.3 76.5 - - - +
40A VAL* 1.3 62.2 - - - +
41A ILE* 2.9 22.5 + - + +
52A LEU 5.5 0.2 - - - -
54A PRO* 4.7 1.6 - - - -
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Residues in contact with VAL 40 (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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11A CYS* 3.4 4.0 - - - -
26A VAL* 4.5 3.6 - - + -
27A LYS 3.3 10.3 - - - +
28A VAL* 4.0 20.2 - - + +
38A THR* 4.0 8.7 - - + -
39A GLU* 1.3 69.4 - - - +
41A ILE* 1.3 62.0 + - - +
51A CYS* 3.3 4.9 - - - -
52A LEU* 2.9 56.9 + - + +
54A PRO* 4.0 27.0 - - + +
59A VAL* 5.0 0.7 - - + -
63A ILE* 3.5 32.3 - - + -
67B LEU* 5.0 6.5 - - + -
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Residues in contact with ILE 41 (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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10A GLN* 3.5 38.6 - - + +
11A CYS* 3.2 24.5 - - - -
27A LYS* 2.5 69.1 + - + +
29A LYS* 4.6 2.0 - - + -
39A GLU 2.9 18.6 - - - +
40A VAL* 1.3 71.6 - - - +
42A ALA* 1.3 56.4 - - - +
43A THR* 4.2 0.9 + - - -
49A LYS* 4.4 36.3 - - + +
50A ALA 4.4 1.3 - - - -
51A CYS* 3.9 12.1 - - - -
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Residues in contact with ALA 42 (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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23A ILE* 3.8 22.9 - - + -
25A SER 3.1 15.7 - - - +
26A VAL* 4.0 13.2 - - + +
40A VAL 4.1 0.6 - - - -
41A ILE* 1.3 75.8 - - - +
43A THR* 1.3 62.2 + - - +
49A LYS* 3.2 6.3 - - - +
50A ALA* 2.8 43.2 + - - +
52A LEU* 4.1 13.0 - - + -
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Residues in contact with THR 43 (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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23A ILE* 3.4 6.0 - - - -
24A GLN* 2.6 33.0 + - + +
25A SER* 2.6 38.0 + - - +
27A LYS* 5.8 2.4 - - - +
41A ILE 4.2 1.6 + - - -
42A ALA* 1.3 71.7 - - - +
44A LEU* 1.3 67.5 + - - +
47A GLY* 5.2 5.4 - - - +
48A GLN 3.6 7.4 - - - +
49A LYS* 3.3 25.8 - - + -
27B LYS* 6.0 0.7 - - - -
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Residues in contact with LEU 44 (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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22A ASN* 2.8 62.6 - - + +
23A ILE* 4.5 2.5 - - + +
24A GLN* 3.9 3.3 - - - +
42A ALA 3.9 0.4 + - - -
43A THR* 1.3 85.6 - - - +
45A LYS* 1.3 62.3 + - - +
46A ASN* 2.9 16.8 - - + +
47A GLY* 3.1 14.7 + - - -
48A GLN* 2.5 57.3 + - + +
49A LYS* 4.0 8.5 - - - +
50A ALA* 5.1 9.9 - - + -
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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