Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 2K42
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 ASP 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLN 4.1 1.8 - - - -
41A ALA 3.2 1.9 + - - +
42A GLN* 3.0 15.5 + - - +
44A THR* 1.3 80.0 - - - +
46A ALA* 1.3 61.7 + - - +
47A GLU* 3.8 19.4 + - - +
48A THR* 3.5 18.8 + - - +
49A SER* 2.6 34.8 + - - -
93B GLN* 4.3 6.8 - - + +
99B ALA* 3.2 10.2 - - + +
100B GLU* 3.0 26.2 + - - +
101B HIS* 2.7 30.3 + - + +
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Residues in contact with ALA 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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16A PRO 4.8 2.7 - - - +
17A GLN* 3.1 27.8 + - + +
44A THR 4.1 0.4 + - - -
45A ASP* 1.3 77.7 + - - +
47A GLU* 1.3 66.7 + - + +
49A SER* 3.3 1.6 + - - -
50A LYS* 3.0 28.9 + - - +
100B GLU* 3.2 36.0 + - + +
101B HIS* 4.9 2.0 + - - +
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Residues in contact with GLU 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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45A ASP* 3.8 13.0 + - - +
46A ALA* 1.3 78.8 - - + +
48A THR* 1.3 72.3 + - - +
50A LYS* 3.8 8.2 - - - +
51A LEU* 3.2 33.2 + - + +
91B GLY* 3.3 25.0 - - - +
92B ILE* 4.1 15.0 - - + -
93B GLN* 4.3 13.3 + - - +
100B GLU* 5.7 3.8 + - - +
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Residues in contact with THR 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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38A ILE* 4.2 2.5 - - + -
42A GLN* 3.3 37.2 - - + +
45A ASP* 3.5 17.8 + - - +
46A ALA 3.2 0.4 - - - -
47A GLU* 1.3 81.2 - - - +
49A SER* 1.3 57.8 + - - +
51A LEU* 3.2 3.3 + - - +
52A ILE* 3.0 42.4 + - + +
87B LEU* 3.8 4.0 - - + +
92B ILE* 3.1 40.7 - - + +
93B GLN 3.6 9.7 + - - -
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Residues in contact with SER 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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14A TRP* 2.9 27.8 + - - -
15A ASP 4.5 0.3 + - - -
16A PRO 5.3 0.3 + - - -
19A GLY* 3.0 8.2 + - - -
20A PHE* 3.6 11.1 - - - -
43A LEU 3.2 27.1 - - - -
45A ASP 2.6 19.6 + - - -
46A ALA* 3.3 2.9 + - - -
48A THR* 1.3 76.3 - - - +
50A LYS* 1.3 62.4 + - - +
52A ILE* 3.0 12.2 + - - +
53A TYR* 2.9 26.3 + - - +
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Residues in contact with LYS 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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14A TRP* 3.6 25.5 - - + -
16A PRO* 3.7 21.6 + - - +
46A ALA 3.0 16.9 + - - +
47A GLU* 3.8 9.0 - - - +
49A SER* 1.3 82.2 + - - +
51A LEU* 1.3 60.5 + - + +
53A TYR* 3.4 6.2 + - - +
54A ASP* 3.1 23.6 + - - +
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Residues in contact with LEU 51 (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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47A GLU* 3.2 20.6 + - + +
48A THR 3.8 2.9 - - - +
50A LYS* 1.3 82.8 - - + +
52A ILE* 1.3 60.8 + - - +
54A ASP* 3.6 19.9 - - + +
55A PHE 2.8 22.3 + - - -
86B HIS* 3.2 16.8 - - + +
87B LEU* 4.1 11.4 - - + -
90B HIS* 3.7 43.1 - - + +
92B ILE* 3.3 26.9 - - + -
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Residues in contact with ILE 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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20A PHE* 3.5 12.6 - - + -
33A PHE* 3.4 30.1 - - + -
38A ILE* 3.4 45.8 - - + -
43A LEU* 3.7 12.6 - - + -
48A THR* 3.0 27.4 + - + +
49A SER* 3.0 13.7 + - - +
51A LEU* 1.3 75.6 - - - +
53A TYR* 1.3 60.1 + - - +
55A PHE* 3.0 9.1 - - - +
56A ILE* 2.9 29.2 + - + +
83B LEU* 4.2 7.6 - - + -
87B LEU* 4.0 10.3 - - + -
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Residues in contact with TYR 53 (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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2A HIS* 5.6 1.3 - + - -
8A HIS* 3.8 13.5 + + + -
9A VAL 4.3 3.6 - - - -
10A SER* 2.8 45.3 + - - -
12A VAL* 3.8 21.8 - - + -
14A TRP* 4.4 30.1 - + + -
20A PHE* 4.3 4.9 - - + -
49A SER 2.9 11.5 + - - +
50A LYS 3.7 9.6 - - - +
52A ILE* 1.3 76.2 - - - +
54A ASP* 1.3 61.5 + - + +
56A ILE* 3.0 17.4 + - + +
57A GLU* 2.8 65.0 + - + +
62A LEU* 5.9 2.0 - - + -
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Residues in contact with ASP 54 (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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50A LYS 3.1 11.3 + - - +
51A LEU* 3.6 18.5 - - + +
52A ILE 3.3 0.2 - - - -
53A TYR* 1.3 81.4 - - + +
55A PHE* 1.3 56.4 + - - +
57A GLU* 3.3 12.8 + - - +
58A ASP* 2.9 32.0 + - - +
86B HIS* 2.7 32.2 + - - -
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Residues in contact with PHE 55 (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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32A LEU* 4.0 7.9 - - + -
51A LEU 2.8 16.9 + - - +
52A ILE* 3.0 17.0 - - - +
54A ASP* 1.3 75.4 + - - +
56A ILE* 1.3 74.0 + - + -
58A ASP* 3.0 15.6 + - + +
59A GLN* 2.7 35.5 + - - -
65A VAL* 4.4 3.8 - - + -
79B VAL* 3.3 37.9 - - + -
82B ARG* 3.2 42.4 - - + -
83B LEU* 3.4 40.2 - - + -
86B HIS* 3.5 20.6 - + + -
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Residues in contact with ILE 56 (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 HIS* 5.7 1.1 - - + -
12A VAL* 4.9 1.8 - - + -
20A PHE* 4.4 10.3 - - + -
29A LEU* 4.0 24.2 - - + -
32A LEU* 5.4 0.4 - - + -
33A PHE* 4.0 17.9 - - + -
52A ILE* 2.9 22.1 + - + +
53A TYR* 3.0 14.6 + - + +
55A PHE* 1.3 90.3 - - + +
57A GLU* 1.3 60.8 + - - +
58A ASP 3.4 0.5 + - - -
59A GLN 3.5 5.0 + - - -
61A GLY* 3.1 47.0 + - - +
62A LEU* 3.6 22.0 - - + -
65A VAL* 3.7 16.3 - - + +
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Residues in contact with GLU 57 (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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1A GLY 5.4 2.0 - - - +
2A HIS* 2.7 39.3 + - - -
8A HIS* 3.0 25.8 - - + +
53A TYR* 2.8 50.1 + - + +
54A ASP* 3.8 11.2 - - - +
56A ILE* 1.3 75.8 - - - +
58A ASP* 1.3 66.2 + - - +
60A GLY* 3.1 12.6 + - - -
61A GLY* 4.2 7.4 - - - +
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Residues in contact with ASP 58 (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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54A ASP* 2.9 18.2 + - - +
55A PHE* 3.0 16.1 + - - +
57A GLU* 1.3 78.3 - - - +
59A GLN* 1.3 71.3 + - - +
60A GLY 3.2 1.3 + - - -
86B HIS* 5.4 7.9 - - + +
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Residues in contact with GLN 59 (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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55A PHE* 2.7 40.0 + - - +
56A ILE 3.5 0.6 + - - -
57A GLU 3.3 0.4 - - - -
58A ASP* 1.3 90.1 - - - +
60A GLY* 1.3 56.9 + - - +
61A GLY 3.6 1.3 - - - -
64A ALA* 3.2 16.1 - - + +
65A VAL* 3.5 29.3 - - + +
68A GLU* 3.5 32.1 - - - +
71A ARG* 5.7 1.7 + - - +
82B ARG* 3.5 28.8 - - - +
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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