Contacts of the helix formed by residues 40 - 50 (chain D) in PDB entry 1Z6Z
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D SER* 4.3 2.2 - - - -
14D ARG* 6.0 4.6 - - - +
38D ALA* 3.4 1.2 - - - +
39D ARG* 1.3 73.5 - - - +
41D ASP* 1.3 63.2 + - - +
42D GLU* 3.2 21.1 + - - +
43D ALA* 3.3 24.0 + - + +
44D LEU* 3.2 25.0 + - - +
804D NAP 3.1 17.9 + - - +
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Residues in contact with ASP 41 (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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39D ARG 3.1 6.9 + - - +
40D ASN* 1.3 69.3 + - - +
42D GLU* 1.3 60.8 + - - +
44D LEU* 3.1 7.4 + - - +
45D ARG* 2.9 39.8 + - - +
62D ARG* 2.9 29.8 + - - -
64D PRO* 3.4 32.0 - - + +
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Residues in contact with GLU 42 (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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40D ASN* 3.2 10.4 + - - +
41D ASP* 1.3 78.2 - - - +
43D ALA* 1.3 56.9 + - - +
45D ARG* 3.4 27.8 + - - +
46D GLN* 3.0 30.4 + - + +
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Residues in contact with ALA 43 (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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13D SER* 3.7 28.3 - - - +
14D ARG* 5.8 1.6 - - + -
18D ARG* 3.6 11.5 + - - +
40D ASN* 3.3 28.9 + - - +
41D ASP 3.3 0.6 - - - -
42D GLU* 1.3 77.1 - - - +
44D LEU* 1.3 59.5 + - - +
46D GLN* 3.5 6.4 + - - +
47D LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 44 (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 ALA* 4.0 19.1 - - + -
13D SER* 4.3 4.7 - - - +
36D LEU* 4.0 22.2 - - + +
37D SER 4.0 8.7 - - - -
38D ALA* 3.9 43.1 - - + +
40D ASN 3.2 17.5 + - - +
41D ASP* 3.1 10.2 + - - +
43D ALA* 1.3 74.6 - - - +
45D ARG* 1.3 58.8 + - - +
47D LEU* 3.3 7.9 + - + +
48D GLU* 2.9 24.9 + - - +
62D ARG* 3.5 21.6 - - + +
63D VAL 4.1 3.4 - - - +
64D PRO* 4.0 24.0 - - + -
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Residues in contact with ARG 45 (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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41D ASP* 2.9 32.9 + - - +
42D GLU* 3.7 24.2 + - - +
44D LEU* 1.3 72.9 - - - +
46D GLN* 1.3 66.5 + - - +
48D GLU* 3.4 4.1 + - - +
49D ALA* 3.2 23.0 + - - +
62D ARG* 3.4 35.9 - - - +
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Residues in contact with GLN 46 (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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18D ARG* 3.1 29.8 + - - +
42D GLU* 3.0 23.6 + - - +
43D ALA* 3.7 7.7 - - - +
44D LEU 3.3 0.2 - - - -
45D ARG* 1.3 77.1 - - - +
47D LEU* 1.3 61.7 + - - +
49D ALA* 3.7 7.1 + - + +
50D GLU* 3.4 19.1 + - - +
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Residues in contact with LEU 47 (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 ALA* 3.4 32.8 - - + +
18D ARG* 4.0 25.1 - - - +
21D ALA* 3.8 26.5 - - + -
22D PRO* 4.2 16.4 - - + -
36D LEU* 3.8 26.0 - - + -
43D ALA 3.0 18.4 + - - +
44D LEU* 3.6 7.9 - - + +
45D ARG 3.2 0.2 - - - -
46D GLN* 1.3 74.1 - - - +
48D GLU* 1.3 65.7 + - - +
50D GLU* 2.9 25.1 + - + +
51D LEU* 3.5 17.1 - - + +
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Residues in contact with GLU 48 (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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36D LEU* 4.9 1.3 - - + +
44D LEU 2.9 16.7 + - - +
45D ARG* 3.4 5.4 + - - +
47D LEU* 1.3 77.2 - - - +
49D ALA* 1.3 62.4 + - - +
51D LEU* 3.2 27.4 + - - +
60D VAL* 3.8 42.0 - - + +
62D ARG* 2.7 38.6 + - - +
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Residues in contact with ALA 49 (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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45D ARG 3.2 16.3 + - - +
46D GLN* 3.7 8.5 - - - +
47D LEU 3.2 0.2 - - - -
48D GLU* 1.3 71.7 - - - +
50D GLU* 1.3 58.2 + - - +
51D LEU 3.0 14.3 + - - -
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Residues in contact with GLU 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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18D ARG* 5.5 4.9 - - - +
22D PRO* 5.5 6.7 - - + +
46D GLN 3.4 9.6 + - - +
47D LEU* 2.9 20.6 + - + +
49D ALA* 1.3 76.6 - - - +
51D LEU* 1.3 62.7 + - + +
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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