Contacts of the helix formed by residues 24 - 36 (chain A) in PDB entry 2KMA
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 MET 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A SER* 2.5 16.9 + - - +
23A THR* 1.3 79.3 - - - +
25A VAL* 1.3 67.6 + - - +
26A TYR* 3.1 32.5 - - + -
27A ASP 2.8 14.9 + - - -
28A ALA* 3.0 9.8 + - - -
64A ALA 3.3 21.5 - - - +
65A GLY* 3.6 21.8 - - - +
66A LYS* 3.1 25.4 - - - +
67A ALA* 4.0 8.7 - - + +
68A LEU* 4.3 2.3 - - - +
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Residues in contact with VAL 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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24A MET* 1.3 71.7 - - - +
26A TYR* 1.3 58.1 + - - +
28A ALA* 3.1 1.5 + - - +
29A CYS* 2.8 38.1 + - + +
48A GLY* 5.4 2.9 - - - -
49A LEU* 3.7 32.1 - - + +
62A LEU* 3.2 31.0 - - + +
63A GLU 3.0 26.2 - - - +
64A ALA* 3.7 10.8 - - + +
66A LYS* 3.4 20.8 + - - -
68A LEU* 4.7 3.4 - - + +
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Residues in contact with TYR 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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23A THR 5.2 1.3 - - - -
24A MET* 2.9 39.5 + - + +
25A VAL* 1.3 78.7 - - - +
27A ASP* 1.3 60.8 + - + +
29A CYS* 3.0 25.4 - - - -
30A ARG* 3.1 49.0 + - - +
64A ALA* 3.7 30.2 - - + +
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Residues in contact with ASP 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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20A GLU* 4.0 11.1 - - - +
23A THR* 3.0 34.0 - - - +
24A MET* 2.8 5.4 + - + -
26A TYR* 1.3 79.4 - - + +
28A ALA* 1.3 63.1 + - - +
30A ARG* 2.9 59.7 + - - +
31A MET* 3.2 34.5 - - - +
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Residues in contact with ALA 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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19A PHE* 3.6 25.5 - - + -
23A THR* 3.5 18.8 - - + +
24A MET 3.0 6.5 + - - +
25A VAL* 3.1 8.3 + - - +
27A ASP* 1.3 77.8 - - - +
29A CYS* 1.3 57.8 + - - +
31A MET* 3.1 2.9 + - - -
32A ILE* 2.9 34.3 + - - +
49A LEU* 3.6 23.1 - - + -
68A LEU* 4.7 4.3 - - + -
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Residues in contact with CYS 29 (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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25A VAL* 2.8 28.1 + - + +
26A TYR* 3.0 33.7 - - - -
28A ALA* 1.3 74.4 - - - +
30A ARG* 1.3 60.8 + - - +
32A ILE* 3.5 10.9 - - - +
33A ARG* 3.2 34.3 + - - +
44A PRO 5.8 1.1 - - - +
47A PHE 4.8 8.3 - - - +
48A GLY* 5.7 0.7 - - - -
49A LEU* 5.2 2.7 - - + -
81A TYR* 4.0 20.9 + - + +
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Residues in contact with ARG 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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26A TYR* 3.1 45.9 + - - +
27A ASP* 2.9 48.8 + - - +
28A ALA 3.1 1.0 - - - -
29A CYS* 1.3 84.0 - - - +
31A MET* 1.3 66.2 + - + +
33A ARG* 3.8 25.7 + - - +
34A GLU* 3.2 21.2 + - - +
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Residues in contact with MET 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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-1A PHE* 6.2 4.5 - - - -
17A MET* 4.5 3.8 - - + -
18A GLN 5.4 1.1 - - - +
19A PHE* 3.4 35.0 - - + -
20A GLU* 5.4 4.3 - - - +
23A THR* 3.9 3.1 - - + +
27A ASP* 3.2 44.0 - - - +
28A ALA* 3.1 2.8 + - - +
30A ARG* 1.3 84.4 - - + +
32A ILE* 1.3 61.6 + - - +
34A GLU* 2.9 23.8 + - - +
35A ARG* 2.9 51.9 + - - +
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Residues in contact with ILE 32 (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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8A ILE* 3.5 44.0 - - + -
10A ILE* 4.9 0.2 - - + -
17A MET* 4.2 10.7 - - + +
19A PHE* 4.3 10.8 - - + -
28A ALA 2.9 21.1 + - - +
29A CYS* 3.5 6.7 - - - +
31A MET* 1.3 76.6 - - - +
33A ARG* 1.3 60.6 + - - +
35A ARG* 4.6 1.1 - - - -
36A ILE* 2.8 55.5 + - + +
39A ALA* 4.2 4.3 - - + -
49A LEU* 5.2 2.7 - - + -
81A TYR* 3.5 45.1 - - + -
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Residues in contact with ARG 33 (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 CYS* 3.2 21.8 + - - +
30A ARG* 3.8 27.0 - - - +
31A MET 3.2 0.6 - - - -
32A ILE* 1.3 81.8 - - - +
34A GLU* 1.3 64.4 + - - +
36A ILE 3.4 4.1 - - - +
37A PRO* 4.7 1.2 - - - +
39A ALA* 4.0 3.1 - - - -
40A LEU* 3.1 40.6 - - + +
44A PRO* 3.5 41.3 - - - +
81A TYR* 4.5 8.0 + - - +
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Residues in contact with GLU 34 (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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30A ARG 3.2 14.6 + - - +
31A MET* 2.9 13.2 + - - +
33A ARG* 1.3 81.6 - - - +
35A ARG* 1.3 97.5 + - - +
36A ILE 4.8 0.7 - - - -
37A PRO* 5.0 2.6 - - - +
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Residues in contact with ARG 35 (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 PHE* 5.9 5.9 - - - -
17A MET* 3.7 36.1 - - - +
18A GLN 5.0 5.7 + - - -
31A MET* 2.9 47.6 - - - +
34A GLU* 1.3 110.3 + - - +
36A ILE* 1.3 63.8 + - + +
37A PRO* 3.2 12.8 - - - +
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Residues in contact with ILE 36 (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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8A ILE* 4.8 2.0 - - + -
10A ILE* 4.0 9.6 - - + -
15A LYS* 3.5 39.5 - - + -
17A MET* 3.4 32.8 - - + -
32A ILE* 2.8 38.5 + - + +
33A ARG 3.4 9.8 - - - +
35A ARG* 1.3 83.1 - - + +
37A PRO* 1.3 61.7 - - - +
38A GLU* 3.5 22.2 - - + +
39A ALA* 3.2 19.8 + - + +
40A LEU* 3.5 0.9 - - - +
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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