Contacts of the helix formed by residues 43 - 61 (chain D) in PDB entry 2ZQK
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 LYS 43 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B SER* 3.2 35.9 - - - +
160B VAL* 4.5 8.0 - - + +
174B GLY* 4.4 19.6 + - - -
24D ASP 3.1 27.0 + - - -
25D ASN* 3.1 17.3 + - - +
26D GLN 4.1 10.5 + - - +
27D LYS* 3.9 7.4 - - + +
42D LEU* 1.3 73.8 - - - +
44D ASP* 1.3 67.7 + - - +
45D ASP* 3.1 15.5 - - - +
46D VAL* 2.8 29.7 - - + +
47D VAL* 3.1 4.2 + - - +
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLN 5.5 0.7 - - - -
157B ARG 3.7 10.3 - - - +
158B SER 2.7 23.3 + - - +
159B GLY* 3.1 12.0 - - - -
27D LYS* 3.2 13.3 + - - -
42D LEU 3.5 2.3 + - - -
43D LYS* 1.3 74.3 - - - +
45D ASP* 1.3 58.5 + - - +
47D VAL* 2.9 5.8 + - - +
48D ALA* 2.8 29.3 + - - +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 4.8 0.5 - - - +
157B ARG* 3.0 29.0 + - + +
158B SER* 2.6 18.8 + - - -
43D LYS* 3.1 22.5 - - - +
44D ASP* 1.3 77.2 - - - +
46D VAL* 1.3 65.2 + - - +
48D ALA* 3.4 8.4 + - - +
49D ASN* 3.1 28.1 + - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ALA* 4.7 10.8 - - + -
25D ASN* 4.0 30.1 - - + +
42D LEU* 3.8 14.4 - - + -
43D LYS* 2.8 44.2 - - + +
45D ASP* 1.3 87.1 + - - +
47D VAL* 1.3 60.1 + - + +
49D ASN* 3.7 7.1 - - + +
50D ILE* 3.2 29.8 + - + +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.4 47.3 - - + +
43D LYS 3.5 5.2 - - - +
44D ASP* 2.9 9.2 + - - +
46D VAL* 1.3 74.6 - - - +
48D ALA* 1.3 54.5 + - - +
49D ASN 3.0 4.3 - - - -
50D ILE* 3.1 6.6 + - + +
51D GLU* 2.5 55.3 + - + +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASP 2.8 15.4 + - - +
45D ASP* 3.7 10.3 - - - +
47D VAL* 1.3 77.8 - - - +
49D ASN* 1.3 60.3 + - - +
51D GLU* 3.9 8.2 - - - +
52D GLU* 3.3 25.1 + - - +
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Residues in contact with ASN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP 3.1 16.5 + - - +
46D VAL* 3.7 9.0 + - + +
47D VAL 3.0 0.4 - - - -
48D ALA* 1.3 76.5 - - - +
50D ILE* 1.3 71.8 + - - +
52D GLU* 2.8 36.7 - - - +
53D GLN* 2.9 36.6 + - - +
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 4.7 13.0 + - - +
15D LEU* 3.7 54.5 - - + +
16D THR* 4.2 17.9 - - - +
19D ALA* 5.4 5.6 - - + -
42D LEU* 6.3 2.7 - - + -
46D VAL* 3.2 24.4 + - + +
47D VAL* 3.1 7.2 + - + +
49D ASN* 1.3 84.0 - - - +
51D GLU* 1.3 62.3 + - - +
53D GLN* 3.8 11.6 - - - +
54D ALA* 3.1 24.4 + - - +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLU* 4.5 8.0 - - - +
12D ARG* 3.0 40.8 + - - +
47D VAL* 2.5 36.9 + - + +
48D ALA* 4.0 8.5 - - - +
50D ILE* 1.3 75.3 - - - +
52D GLU* 1.3 58.2 + - - +
54D ALA* 4.4 2.2 - - - +
55D LYS* 4.1 17.8 + - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA 3.3 14.7 + - - +
49D ASN* 2.8 35.7 + - - +
51D GLU* 1.3 80.9 - - - +
53D GLN* 1.3 63.1 + - + +
54D ALA 3.4 0.2 - - - -
55D LYS* 3.2 8.0 + - - +
56D ALA* 2.9 28.3 + - - +
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Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D THR* 4.8 1.8 - - - -
15D LEU* 3.3 29.3 - - + +
49D ASN* 2.9 39.1 + - - +
50D ILE* 3.8 10.8 - - - +
52D GLU* 1.3 75.2 - - + +
54D ALA* 1.3 54.8 + - - +
55D LYS 2.7 15.9 + - - -
56D ALA* 2.8 18.1 + - - +
57D ALA* 3.1 16.7 + - - +
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLU* 3.1 36.5 - - - +
11D THR* 3.7 22.6 + - + +
12D ARG* 3.4 37.0 - - - +
15D LEU* 4.9 0.2 - - - +
50D ILE* 3.1 13.3 + - + +
51D GLU 4.6 2.2 - - - +
52D GLU 3.4 0.2 - - - -
53D GLN* 1.3 78.0 - - - +
55D LYS* 1.3 55.3 + - - +
58D GLY* 3.4 10.8 + - - -
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLU* 3.9 30.5 - - - +
51D GLU* 4.1 12.5 + - - +
52D GLU* 3.2 10.6 + - - +
53D GLN 2.7 5.1 + - - -
54D ALA* 1.3 75.5 - - - +
56D ALA* 1.3 66.6 + - - +
57D ALA 3.4 0.4 - - - -
58D GLY* 3.8 0.6 - - - -
59D GLU* 3.0 28.0 + - + +
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU 2.9 16.3 + - - +
53D GLN* 2.8 8.6 + - - +
55D LYS* 1.3 77.4 - - - +
57D ALA* 1.3 51.1 + - + +
59D GLU* 3.6 7.3 - - - +
60D GLU* 2.8 33.3 + - - +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D THR* 5.4 9.9 - - + +
53D GLN 3.1 8.9 + - - +
56D ALA* 1.3 75.5 - - + +
58D GLY* 1.3 57.6 + - - +
59D GLU 3.0 5.4 - - - -
60D GLU* 3.5 18.0 - - + +
61D ALA* 2.9 30.1 + - - +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ALA 4.6 5.7 + - - -
7D THR* 3.5 33.0 + - - +
8D GLU* 4.2 9.6 - - - -
11D THR* 4.7 5.2 + - - -
54D ALA 3.4 22.3 + - - -
55D LYS 3.4 3.3 + - - -
56D ALA 3.3 1.0 - - - -
57D ALA* 1.3 77.5 - - - +
59D GLU* 1.3 58.1 + - - +
61D ALA* 4.2 3.9 - - - +
62D LYS* 4.3 4.9 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LYS* 3.0 20.1 + - + +
56D ALA* 3.7 5.0 - - - +
58D GLY* 1.3 77.5 - - - +
60D GLU* 1.3 59.2 + - - +
61D ALA 2.9 5.8 - - - -
62D LYS* 2.9 54.7 + - - +
63D GLN* 3.3 23.4 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA 2.8 18.7 + - - +
57D ALA* 3.1 18.2 + - - +
59D GLU* 1.3 82.8 - - - +
61D ALA* 1.3 60.4 + - - +
63D GLN* 4.0 6.9 + - + +
64D GLN* 3.3 33.8 + - - +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 4.5 13.0 - - + -
57D ALA 2.9 14.7 + - - +
58D GLY 4.2 7.2 - - - +
59D GLU 2.9 0.2 - - - -
60D GLU* 1.3 79.8 - - - +
62D LYS* 1.3 57.6 + - - +
63D GLN 3.3 0.4 - - - -
64D GLN* 3.3 8.1 + - - +
65D ALA* 3.0 28.5 + - - +
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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