Contacts of the strand formed by residues 43 - 48 (chain K) in PDB entry 1KQ2
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 VAL 43 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K ASP* 2.8 54.9 + - - +
42K TYR* 1.3 77.6 - - - +
44K VAL* 1.3 73.1 + - - +
54K LEU* 3.7 31.0 - - + -
55K ILE 3.2 11.2 - - - +
56K TYR* 3.9 21.3 - - + -
57K LYS* 3.6 0.9 - - - -
7M ILE* 3.9 8.3 - - + -
8M GLN* 3.8 35.9 - - + +
63M TYR* 5.9 0.4 - - + -
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Residues in contact with VAL 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K LEU* 4.2 6.5 - - + -
24K VAL* 6.4 0.7 - - + -
36K ILE* 4.3 22.7 - - + -
38K GLU 3.7 9.0 - - - +
39K TYR* 4.0 12.1 - - + +
43K VAL* 1.3 84.2 - - - +
45K SER* 1.3 71.5 + - - +
46K LEU* 3.7 7.1 + - + +
53K HIS 3.7 0.9 - - - +
54K LEU* 4.4 2.9 - - - -
55K ILE* 2.8 38.7 + - + +
57K LYS* 4.0 15.3 - - + -
60K ILE* 4.6 10.3 - - + -
63K TYR* 3.6 24.7 - - + +
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Residues in contact with SER 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K ILE* 3.6 4.3 - - - -
37K GLU* 3.0 23.2 + - - +
38K GLU* 2.9 39.7 + - - +
44K VAL* 1.3 73.1 - - - +
46K LEU* 1.3 59.1 + - - +
52K GLN* 2.7 35.4 + - - +
53K HIS 3.6 5.1 + - - -
54K LEU* 4.4 13.2 - - - +
7M ILE* 4.5 5.3 - - - +
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Residues in contact with LEU 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K VAL* 3.9 9.9 - - + -
24K VAL* 3.7 25.1 - - + -
32K MET* 4.0 31.2 - - + -
34K GLY* 3.9 24.0 - - - +
35K VAL 3.4 11.9 - - - +
36K ILE* 4.2 7.6 - - + -
44K VAL* 3.7 3.8 + - + -
45K SER* 1.3 74.9 + - - +
47K ASN* 1.3 63.0 + - - +
48K SER* 3.5 24.7 + - - -
52K GLN* 3.7 2.7 - - - -
53K HIS* 2.8 37.1 + - + +
55K ILE* 3.9 17.7 - - + -
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Residues in contact with ASN 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K GLY* 3.3 2.5 - - - -
35K VAL* 2.7 46.2 + - + +
37K GLU* 3.6 29.1 + - + +
46K LEU* 1.3 71.6 - - - +
48K SER* 1.3 62.4 + - - +
49K GLN 4.4 0.2 + - - -
50K GLY* 3.4 34.1 + - - -
51K LYS 3.7 5.2 - - - -
52K GLN* 3.4 20.3 + - - +
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Residues in contact with SER 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K MET* 4.6 5.7 - - - +
33K LYS 2.7 29.8 + - - -
34K GLY* 4.3 0.7 - - - -
46K LEU* 3.5 12.9 + - - -
47K ASN* 1.3 75.2 + - - +
49K GLN* 1.3 90.7 + - - +
50K GLY 2.9 4.0 - - - -
51K LYS* 2.8 23.0 + - - +
53K HIS* 3.6 19.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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