Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 1RK9
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 1.3 79.2 - - - +
41A ALA* 1.3 60.8 + - - +
42A ASP* 3.5 15.1 + - - +
43A ASP* 3.0 13.2 + - - +
44A VAL* 2.9 28.8 + - - +
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Residues in contact with ALA 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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39A LYS 4.1 0.2 + - - -
40A SER* 1.3 74.0 + - - +
42A ASP* 1.3 57.1 + - - +
44A VAL* 3.3 16.8 + - + +
45A LYS* 3.0 25.9 + - - +
100A VAL* 5.2 0.2 - - - +
104A SER* 5.6 3.4 - - - +
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Residues in contact with ASP 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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40A SER* 3.3 10.1 + - - +
41A ALA* 1.3 78.5 - - - +
43A ASP* 1.3 56.4 + - - +
45A LYS* 3.2 36.2 + - - +
46A LYS* 2.6 57.7 + - - +
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Residues in contact with ASP 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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6A LEU* 3.2 52.8 - - - +
7A LEU* 3.4 10.7 - - - +
39A LYS* 3.4 17.3 - - + +
40A SER* 3.0 27.0 + - - +
42A ASP* 1.3 72.7 - - - +
44A VAL* 1.3 58.8 + - - +
45A LYS 3.1 1.3 - - - -
46A LYS* 2.9 26.8 + - - +
47A VAL* 2.9 16.6 + - - +
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Residues in contact with VAL 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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31A PHE* 4.8 6.3 - - + -
36A LEU* 3.9 34.1 - - + +
37A LYS* 5.2 1.3 - - - +
39A LYS* 5.6 0.6 - - + +
40A SER 2.9 14.1 + - - +
41A ALA* 3.3 17.5 - - + +
43A ASP* 1.3 73.4 - - - +
45A LYS* 1.3 58.2 + - - +
47A VAL* 3.4 9.1 - - + +
48A PHE* 3.2 19.1 + - - +
100A VAL* 3.4 25.2 - - + +
101A ASP* 5.8 0.2 - - - -
104A SER* 3.6 37.9 - - - +
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Residues in contact with LYS 45 (chain A).
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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41A ALA 3.0 10.1 + - - +
42A ASP* 3.2 36.5 + - - +
44A VAL* 1.3 77.1 - - - +
46A LYS* 1.3 60.8 + - + +
47A VAL 3.3 0.3 + - - -
48A PHE* 3.4 4.7 + - - +
49A HIS* 3.0 28.4 + - - +
100A VAL* 3.9 24.0 - - + -
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Residues in contact with LYS 46 (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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1A MET* 4.0 26.7 + - + +
3A MET* 4.0 4.3 - - - +
6A LEU* 3.5 31.2 - - + -
42A ASP* 2.6 49.9 + - - +
43A ASP* 2.9 11.2 + - - +
45A LYS* 1.3 75.0 - - + +
47A VAL* 1.3 66.1 + - - +
49A HIS* 3.5 10.9 + - + +
50A MET* 3.3 18.2 + - - +
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Residues in contact with VAL 47 (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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3A MET* 3.8 11.4 - - + -
6A LEU* 6.0 0.9 - - + -
7A LEU* 3.7 22.2 - - + -
31A PHE* 5.3 1.1 - - + -
36A LEU* 3.3 47.3 - - + -
43A ASP* 2.9 18.5 + - - +
44A VAL* 3.4 11.4 - - + +
45A LYS 3.2 0.2 - - - -
46A LYS* 1.3 71.0 - - + +
48A PHE* 1.3 58.6 + - - +
50A MET* 2.8 26.2 + - - +
51A LEU* 3.2 15.0 - - + +
71A PHE* 3.9 20.9 - - + -
103A PHE* 5.1 7.2 - - + -
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Residues in contact with PHE 48 (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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44A VAL 3.2 9.0 + - - +
45A LYS 3.7 8.1 - - - +
47A VAL* 1.3 78.1 - - - +
49A HIS* 1.3 62.1 + + - +
50A MET 3.1 1.7 + - - -
51A LEU* 3.1 10.4 + - - +
52A ASP* 3.0 34.2 + - + +
57A GLY* 3.3 39.5 - - - -
58A PHE* 3.8 2.9 - - - -
59A ILE* 3.6 27.1 - - + -
98A ILE* 3.1 38.6 - - + -
99A GLY* 3.8 6.7 - - - -
100A VAL* 3.8 36.3 - - + -
103A PHE* 4.6 9.0 - + + -
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Residues in contact with HIS 49 (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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1A MET* 5.8 6.8 - - + -
45A LYS 3.0 17.3 + - - +
46A LYS* 3.6 14.4 - - + +
47A VAL 3.1 0.4 + - - -
48A PHE* 1.3 81.3 - + - +
50A MET* 1.3 58.1 + - - +
52A ASP* 4.0 10.2 + - - +
55A LYS* 2.8 67.3 + - + +
57A GLY* 6.1 2.5 - - - -
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Residues in contact with MET 50 (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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1A MET* 3.1 34.1 - - - +
2A SER* 5.1 0.9 - - - -
3A MET* 3.9 21.5 - - + +
46A LYS 3.3 9.0 + - - +
47A VAL 2.8 17.1 + - - +
49A HIS* 1.3 71.7 - - - +
51A LEU* 1.3 62.5 + - - +
52A ASP* 3.6 1.1 - - - -
53A LYS* 4.3 11.8 + - - +
55A LYS* 5.0 1.7 + - - +
69A LYS 5.3 3.1 - - - +
70A GLY* 3.0 47.2 - - - +
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Residues in contact with LEU 51 (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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3A MET* 4.7 0.4 - - - -
47A VAL* 3.2 20.0 - - + +
48A PHE* 3.1 6.2 + - - +
50A MET* 1.3 79.8 - - + +
52A ASP* 1.3 50.9 + - - +
53A LYS* 2.8 28.6 + - - +
59A ILE* 3.5 22.5 - - + +
63A GLU* 4.0 11.4 - - - +
67A ILE* 3.4 51.6 - - + +
70A GLY* 4.6 0.2 - - - -
71A PHE* 3.7 32.8 - - + +
103A PHE* 3.3 34.3 - - + -
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Residues in contact with ASP 52 (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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48A PHE* 3.0 22.9 + - + +
49A HIS* 4.5 9.7 - - - -
50A MET 4.7 0.4 - - - -
51A LEU* 1.3 71.5 - - - +
53A LYS* 1.3 63.5 + - - +
54A ASP* 3.2 4.7 - - - -
55A LYS* 3.0 46.9 + - - +
57A GLY* 2.8 27.9 + - - -
58A PHE 3.0 25.6 + - - +
59A ILE* 4.2 7.1 - - + +
63A GLU* 3.3 5.6 - - - -
112A CA 3.0 19.2 - - - -
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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