Contacts of the helix formed by residues 41 - 58 (chain A) in PDB entry 2K40
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ARG* 4.6 13.2 + - - -
35A ALA* 4.5 0.7 - - - -
40A LEU* 1.3 77.4 - - - +
42A LEU* 1.3 66.1 + - - +
43A ASP* 4.4 10.5 - - + +
44A ARG* 2.8 76.9 + - + +
45A ILE* 3.3 13.4 + - - +
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Residues in contact with LEU 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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28A ILE* 3.9 30.5 - - + +
31A LEU* 3.6 34.3 - - + +
32A GLU* 4.3 12.6 - - + +
35A ALA* 4.2 12.2 - - + +
40A LEU 4.2 1.0 + - - -
41A GLU* 1.3 70.3 - - - +
43A ASP* 1.3 55.1 + - + +
45A ILE* 3.1 10.3 + - - +
46A GLN* 2.8 50.5 + - + +
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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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1A GLY 5.5 3.1 + - - -
2A ARG 5.8 0.7 + - - -
3A ARG* 4.1 27.4 + - - +
41A GLU* 3.1 10.3 + - + +
42A LEU* 1.3 79.2 - - + +
44A ARG* 1.3 57.6 + - - +
46A GLN* 3.3 6.7 + - - +
47A ILE* 2.9 54.8 + - - +
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Residues in contact with ARG 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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3A ARG* 3.6 32.7 - - + +
6A THR* 4.0 35.3 + - + +
8A PHE* 4.4 9.6 - - + -
39A ASN 5.6 1.0 + - - -
40A LEU* 4.0 25.8 - - + +
41A GLU* 2.8 59.2 + - + +
43A ASP* 1.3 77.6 - - - +
45A ILE* 1.3 57.3 + - - +
47A ILE* 3.6 7.7 + - - +
48A TRP* 2.9 26.3 + - - +
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Residues in contact with ILE 45 (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 PHE* 5.5 0.7 - - - -
16A LEU* 3.5 33.9 - - + -
31A LEU* 3.7 15.9 - - + +
34A LEU* 3.7 15.3 - - + -
35A ALA* 3.4 36.8 - - + +
38A LEU* 4.7 1.1 - - + -
40A LEU* 4.0 22.4 - - + -
41A GLU 3.4 13.0 - - - +
42A LEU* 3.1 4.4 + - - +
44A ARG* 1.3 72.8 - - - +
46A GLN* 1.3 59.4 + - - +
48A TRP* 3.2 4.7 + - + +
49A PHE* 2.8 50.8 + - + -
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Residues in contact with GLN 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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25A TYR* 3.5 24.3 + - - -
28A ILE* 5.6 5.1 - - - +
31A LEU* 4.0 28.4 - - + +
42A LEU* 2.8 31.7 + - + +
43A ASP* 3.5 9.2 - - - +
45A ILE* 1.3 70.2 - - - +
47A ILE* 1.3 61.7 + - + +
49A PHE* 3.3 4.0 + - - +
50A GLN* 2.9 59.7 + - - +
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Residues in contact with ILE 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 ARG* 4.5 18.4 - - + +
4A PRO 3.9 21.3 - - - +
5A ARG* 4.4 0.4 - - - -
6A THR* 4.2 13.7 - - - +
43A ASP* 2.9 53.8 + - - +
44A ARG* 3.8 7.2 - - - +
46A GLN* 1.3 74.2 - - + +
48A TRP* 1.3 56.3 + - - +
50A GLN* 4.8 4.0 - - - +
51A ASN* 2.8 53.3 + - - +
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Residues in contact with TRP 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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6A THR* 4.9 11.9 - - - +
8A PHE* 3.6 24.9 - + + -
13A ILE* 3.2 27.9 - - + +
16A LEU* 3.3 51.4 - - + -
17A GLU* 3.5 5.8 - - - -
20A PHE* 4.0 3.8 - - + -
44A ARG 2.9 15.0 + - - +
45A ILE* 3.2 11.0 + - - +
47A ILE* 1.3 76.8 - - - +
49A PHE* 1.3 104.4 + + - +
51A ASN* 3.7 3.8 - - - +
52A ARG* 2.9 82.0 + - + +
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Residues in contact with PHE 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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16A LEU* 4.3 4.9 - - + -
19A VAL* 4.0 20.0 - - + -
20A PHE* 3.8 27.3 - + + -
23A ASN 4.0 6.1 - - - -
24A CYS 4.5 2.2 - - - -
25A TYR* 4.6 16.7 - - + -
26A PRO* 3.6 35.0 - - + -
31A LEU* 3.8 15.3 - - + -
34A LEU* 4.0 12.3 - - + -
45A ILE* 2.8 47.0 + - + +
46A GLN* 4.0 4.7 - - - +
48A TRP* 1.3 98.4 - + - +
50A GLN* 1.3 56.9 + - - +
52A ARG* 3.1 6.1 - - - +
53A ARG* 3.0 30.3 + - - +
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Residues in contact with GLN 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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25A TYR* 3.4 24.9 + - + +
46A GLN* 2.9 49.7 + - - +
47A ILE* 4.4 4.7 - - - +
49A PHE* 1.3 68.1 - - - +
51A ASN* 1.3 58.7 + - - +
53A ARG* 3.5 6.0 + - - +
54A ALA* 2.9 30.6 + - - +
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Residues in contact with ASN 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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5A ARG* 3.7 35.2 - - + +
47A ILE* 2.8 49.3 + - - +
48A TRP* 3.8 4.3 - - - +
50A GLN* 1.3 75.1 - - - +
52A ARG* 1.3 57.1 + - - +
54A ALA* 3.7 7.8 - - - +
55A LYS* 2.9 43.4 + - + +
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Residues in contact with ARG 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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13A ILE* 4.3 7.9 - - - +
17A GLU* 2.7 45.5 + - - +
20A PHE* 3.7 34.5 - - + -
48A TRP* 2.9 60.2 + - + +
49A PHE* 3.1 13.5 - - - +
50A GLN 3.2 0.2 - - - -
51A ASN* 1.3 75.2 - - - +
53A ARG* 1.3 57.4 + - - +
55A LYS* 3.3 24.1 + - - +
56A LEU* 3.0 28.6 + - - +
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Residues in contact with ARG 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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20A PHE* 4.3 7.4 - - + -
24A CYS* 2.9 51.7 + - - +
25A TYR* 3.7 25.5 - - - +
49A PHE 3.0 12.0 + - - +
50A GLN* 4.0 5.8 - - - +
52A ARG* 1.3 75.3 - - - +
54A ALA* 1.3 64.0 + - - +
56A LEU* 3.2 14.8 + - + +
57A LYS* 2.9 27.6 + - - +
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Residues in contact with ALA 54 (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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50A GLN 2.9 22.0 + - - +
51A ASN* 3.7 10.8 - - - +
53A ARG* 1.3 72.2 - - - +
55A LYS* 1.3 55.7 + - + +
57A LYS* 3.4 7.4 + - - +
58A ARG* 3.0 25.3 + - - -
61A ARG* 4.6 20.0 - - - +
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Residues in contact with LYS 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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5A ARG* 5.9 7.9 - - + +
51A ASN* 2.9 32.7 + - + +
52A ARG* 3.3 22.4 + - - +
54A ALA* 1.3 70.6 - - + +
56A LEU* 1.3 62.8 + - - +
58A ARG* 3.2 23.4 + - - +
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Residues in contact with LEU 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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20A PHE* 4.4 23.1 - - + -
24A CYS* 5.3 8.3 - - + -
52A ARG 3.0 16.6 + - - +
53A ARG* 3.6 13.7 - - + +
55A LYS* 1.3 75.5 - - - +
57A LYS* 1.3 61.8 + - - +
58A ARG* 4.3 3.3 - - - +
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Residues in contact with LYS 57 (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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53A ARG* 2.9 19.3 + - - +
54A ALA* 3.6 8.1 - - - +
56A LEU* 1.3 74.1 - - - +
58A ARG* 1.3 58.6 + - - +
59A SER* 2.9 28.2 + - - +
60A HIS* 3.4 25.6 - - - +
61A ARG* 4.2 13.2 - - + +
62A GLU* 2.7 44.5 + - - +
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Residues in contact with ARG 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 ALA 3.0 14.3 + - - -
55A LYS* 3.2 16.8 + - - +
56A LEU 4.3 3.1 - - - +
57A LYS* 1.3 75.0 - - - +
59A SER* 1.3 62.6 + - - +
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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