Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 4Z3K
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 ASN 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A SER* 4.3 2.0 - - - -
14A ARG* 6.4 0.2 - - - +
38A ALA* 3.5 0.8 - - - +
39A ARG* 1.3 73.1 - - - +
41A ASP* 1.3 63.4 + - - +
42A GLU* 3.1 12.3 + - - +
43A ALA* 2.7 40.1 + - + +
44A LEU* 3.2 25.9 + - - +
801A NAP 3.1 17.8 + - - +
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Residues in contact with ASP 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 ARG 3.1 6.7 + - - +
40A ASN* 1.3 70.2 + - - +
42A GLU* 1.3 66.0 + - - +
44A LEU* 3.1 6.6 + - - +
45A ARG* 2.9 45.8 + - - +
62A ARG* 2.8 27.3 + - - -
64A PRO* 3.7 32.1 - - + +
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Residues in contact with GLU 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 ASN* 3.1 8.6 + - - +
41A ASP* 1.3 79.7 - - - +
43A ALA* 1.3 62.1 + - - +
45A ARG* 3.1 16.5 + - + +
46A GLN* 3.0 26.1 + - + +
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Residues in contact with ALA 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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13A SER* 3.7 25.4 - - - +
14A ARG* 5.9 1.6 - - + -
18A ARG* 3.4 24.6 + - - +
40A ASN* 2.7 27.4 + - + +
41A ASP 3.3 0.2 - - - -
42A GLU* 1.3 72.0 - - - +
44A LEU* 1.3 57.3 + - - +
46A GLN* 3.5 4.3 + - - -
47A LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 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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12A ALA* 4.0 27.8 - - + -
13A SER* 4.3 5.2 - - - +
36A LEU* 3.7 31.4 - - + +
37A SER 4.1 0.4 - - - -
38A ALA* 3.9 29.4 - - + +
40A ASN 3.2 16.9 + - - +
41A ASP* 3.1 7.9 + - - +
43A ALA* 1.3 78.8 - - - +
45A ARG* 1.3 56.8 + - - +
47A LEU* 3.4 6.4 + - + +
48A GLU* 2.9 23.9 + - - +
62A ARG* 3.5 23.0 - - + +
63A VAL 4.0 3.4 - - - +
64A PRO* 3.9 27.1 - - + -
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Residues in contact with ARG 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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41A ASP* 2.9 37.6 + - - +
42A GLU* 3.5 17.9 - - + +
44A LEU* 1.3 73.0 - - - +
46A GLN* 1.3 64.6 + - - +
48A GLU* 3.4 4.0 + - - +
49A ALA* 3.1 23.0 + - - +
62A ARG* 3.2 45.1 - - - +
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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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18A ARG* 3.2 21.9 + - - +
42A GLU* 3.0 17.9 + - - +
43A ALA* 3.7 4.9 - - - +
45A ARG* 1.3 73.0 - - - +
47A LEU* 1.3 63.4 - - - +
49A ALA* 3.2 9.9 + - + +
50A GLU* 3.1 44.3 + - + +
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Residues in contact with LEU 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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12A ALA* 3.5 32.3 - - + +
18A ARG* 3.9 27.8 - - - +
21A ALA* 3.8 31.4 - - + -
22A PRO* 4.0 13.2 - - + -
36A LEU* 3.9 22.4 - - + -
43A ALA 3.0 18.6 + - - +
44A LEU* 3.7 7.2 - - + +
46A GLN* 1.3 74.3 - - - +
48A GLU* 1.3 65.0 + - - +
50A GLU* 3.1 23.0 + - + +
51A LEU* 3.3 22.7 + - + +
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Residues in contact with GLU 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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36A LEU* 4.8 1.3 - - + +
44A LEU 2.9 17.3 + - - +
45A ARG* 3.6 5.7 - - - +
46A GLN 3.3 0.4 - - - -
47A LEU* 1.3 77.1 - - - +
49A ALA* 1.3 63.1 + - - +
51A LEU* 3.0 27.2 + - - +
52A GLY 4.1 2.3 + - - -
53A ALA* 4.9 9.4 + - + +
60A VAL* 3.6 41.7 - - + +
62A ARG* 2.8 32.5 + - - +
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Residues in contact with ALA 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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45A ARG 3.1 12.7 + - - +
46A GLN* 3.2 12.5 + - + +
48A GLU* 1.3 76.2 - - - +
50A GLU* 1.3 63.5 + - + +
51A LEU 3.2 1.4 + - - -
52A GLY* 3.6 8.7 + - - -
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Residues in contact with GLU 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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18A ARG* 3.1 27.1 + - - -
22A PRO* 5.5 8.2 - - + +
46A GLN* 3.1 32.0 + - + +
47A LEU* 3.1 17.5 + - + +
49A ALA* 1.3 75.4 - - + +
51A LEU* 1.3 62.2 + - + +
52A GLY 3.4 0.8 + - - -
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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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21A ALA* 4.2 2.2 - - + +
22A PRO* 3.6 38.1 - - + -
25A ALA* 3.9 19.8 - - + +
34A LEU* 4.0 23.8 - - + -
36A LEU* 4.1 18.4 - - + -
47A LEU* 3.3 24.5 - - + +
48A GLU* 3.0 15.6 + - - +
50A GLU* 1.3 79.6 - - - +
52A GLY* 1.3 66.5 + - - +
53A ALA* 4.3 8.6 - - + +
56A SER* 4.4 5.2 + - - -
58A LEU* 5.0 2.6 - - + +
60A VAL* 4.2 11.2 - - + -
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Residues in contact with GLY 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 GLU 4.1 1.0 + - - -
49A ALA 3.6 8.9 + - - -
50A GLU 3.4 3.6 + - - -
51A LEU* 1.3 78.9 - - - +
53A ALA* 1.3 65.3 + - - +
54A GLU 3.4 2.9 - - - -
55A ARG* 3.5 10.5 + - - +
56A SER* 3.2 21.0 + - - -
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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