Contacts of the helix formed by residues 33 - 49 (chain A) in PDB entry 2MZD
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 LEU 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A CYS* 3.1 11.2 + - - +
32A SER* 1.3 72.0 - - - +
34A PRO* 1.3 56.7 - - + +
35A SER* 2.9 30.7 - - - +
36A CYS* 2.6 60.2 + - + +
37A GLN 2.8 9.4 + - - -
20B PHE 5.2 0.9 - - - +
21B THR* 5.7 2.0 - - - +
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Residues in contact with PRO 34 (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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32A SER* 3.2 16.2 - - - +
33A LEU* 1.3 88.6 - - + +
35A SER* 1.3 58.3 + - - +
37A GLN* 3.2 31.8 - - + +
38A LYS* 2.8 29.2 + - - +
41A ARG* 5.7 0.7 + - - -
24B PRO* 5.6 8.5 - - + -
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Residues in contact with SER 35 (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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19A SER* 6.2 0.2 - - - -
33A LEU* 2.9 17.2 - - - +
34A PRO* 1.3 79.3 - - - +
36A CYS* 1.4 61.3 + - - +
38A LYS* 3.6 21.3 + - - +
39A MET* 3.2 11.8 + - - +
19B TRP 2.9 18.5 - - - +
20B PHE 3.0 26.8 - - - +
21B THR* 4.0 6.6 - - - +
22B GLU 4.0 14.7 + - - -
24B PRO* 4.0 10.4 - - - +
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Residues in contact with CYS 36 (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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19A SER* 5.5 6.5 - - - -
22A HIS* 3.3 40.8 - - + -
23A ALA* 3.6 6.1 - - + +
31A CYS* 4.0 13.2 - - - -
33A LEU* 2.6 55.0 + - + +
35A SER* 1.4 69.8 - - - +
37A GLN* 1.4 51.6 + - - +
39A MET* 3.2 4.2 + - - -
40A LYS* 2.9 41.6 + - - +
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Residues in contact with GLN 37 (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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29A ALA 2.8 28.6 + - - +
30A ASN* 3.7 13.5 + - - +
31A CYS* 3.3 25.2 + - + +
32A SER* 4.8 2.0 - - - +
33A LEU 2.8 5.5 + - - -
34A PRO* 3.2 36.2 - - + +
36A CYS* 1.4 71.3 - - - +
38A LYS* 1.2 60.7 + - - +
40A LYS* 3.0 12.3 - - - +
41A ARG* 2.7 64.9 + - + +
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Residues in contact with LYS 38 (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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34A PRO 2.8 15.0 + - - +
35A SER* 3.3 21.7 + - - +
37A GLN* 1.2 79.6 - - - +
39A MET* 1.3 50.3 + - - +
41A ARG* 3.0 13.7 + - - +
42A VAL* 2.7 33.1 + - - +
18B GLN 3.8 1.6 - - - -
19B TRP* 2.9 63.8 - - + +
22B GLU* 2.7 39.0 + - - +
24B PRO* 4.6 7.3 - - - +
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Residues in contact with MET 39 (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 ALA 3.3 24.5 - - - +
19A SER* 3.4 17.5 - - - +
20A LEU* 3.2 28.0 - - + -
23A ALA* 3.3 18.4 - - + -
35A SER 3.2 5.1 + - - +
36A CYS* 3.2 4.0 + - - +
38A LYS* 1.3 78.3 - - - +
40A LYS* 1.2 58.0 + - - +
42A VAL* 2.9 9.2 + - + +
43A VAL* 2.7 35.3 + - - +
16B ILE* 3.3 40.6 - - + +
19B TRP* 3.4 5.2 - - + +
20B PHE* 3.3 23.1 - - - -
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Residues in contact with LYS 40 (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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23A ALA* 2.9 28.5 - - - +
26A CYS* 3.0 50.2 - - - +
28A ASN 2.6 32.1 + - - +
29A ALA* 4.9 4.9 - - - -
31A CYS* 3.2 13.7 - - - +
36A CYS* 2.9 20.8 - - - +
37A GLN* 3.0 13.5 - - - +
39A MET* 1.2 77.0 - - - +
41A ARG* 1.3 51.0 + - + +
42A VAL 3.0 0.4 - - - -
43A VAL* 3.0 7.0 + - - +
44A GLN* 2.6 44.2 + - + +
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Residues in contact with ARG 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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29A ALA 5.0 2.8 + - - -
30A ASN* 5.8 0.4 + - - -
34A PRO 5.7 0.4 + - - -
37A GLN* 2.7 58.6 + - - +
38A LYS* 3.1 11.7 - - - +
40A LYS* 1.3 71.2 - - + +
42A VAL* 1.3 57.7 + - - +
44A GLN* 3.6 10.3 - - + -
45A HIS* 2.6 32.6 + - - +
19B TRP* 6.1 0.9 - - + -
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Residues in contact with VAL 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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38A LYS 2.7 7.7 + - - +
39A MET* 2.9 16.4 + - + +
41A ARG* 1.3 78.3 - - + +
43A VAL* 1.3 55.1 + - - +
45A HIS* 3.6 4.1 - - + +
46A THR* 2.6 38.1 + - - -
59A ILE* 3.2 36.8 - - + -
63A LEU* 3.7 10.5 - - + -
16B ILE* 3.6 30.1 - - + -
19B TRP* 3.5 25.1 - - + -
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Residues in contact with VAL 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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20A LEU* 3.6 35.9 - - + +
24A ALA* 4.7 8.5 - - - +
39A MET 2.7 17.8 + - - +
40A LYS* 3.0 11.0 - - - +
42A VAL* 1.3 71.9 - - - +
44A GLN* 1.3 67.6 + - + +
46A THR* 3.1 3.6 - - - -
47A LYS* 2.8 46.8 + - + +
63A LEU* 3.6 8.7 - - + -
82A PRO* 3.4 38.1 - - + -
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Residues in contact with GLN 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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23A ALA 5.9 0.2 - - - +
40A LYS* 2.6 30.9 + - + +
41A ARG* 3.7 10.8 - - + -
43A VAL* 1.3 85.6 - - + +
45A HIS* 1.4 62.1 + - - +
47A LYS* 3.8 16.3 + - - +
48A GLY* 3.1 19.4 + - - -
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Residues in contact with HIS 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 ARG 2.6 22.9 + - - +
42A VAL* 3.1 13.4 + - + +
44A GLN* 1.4 71.4 - - - +
46A THR* 1.3 68.7 + - - +
48A GLY 3.7 0.7 - - - -
49A CYS* 2.9 52.5 + - - +
57A CYS* 4.1 21.1 - - - -
59A ILE* 3.6 22.6 - - + +
60A CYS* 4.7 0.2 - - - -
19B TRP* 6.3 3.1 - + - -
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Residues in contact with THR 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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42A VAL 2.6 22.9 + - - -
43A VAL 3.1 7.6 - - - +
45A HIS* 1.3 74.5 - - - +
47A LYS* 1.3 60.0 + - + +
49A CYS 2.7 24.9 + - - +
52A LYS* 2.8 29.4 - - - +
59A ILE* 3.8 2.1 - - - +
60A CYS* 3.0 50.1 + - + +
63A LEU* 3.1 16.5 - - + +
82A PRO* 5.4 1.8 - - + -
83A PHE* 4.8 8.3 - - + -
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Residues in contact with LYS 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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43A VAL* 2.8 39.4 + - + +
44A GLN* 4.2 17.4 + - - +
45A HIS 3.3 0.2 - - - -
46A THR* 1.3 79.0 - - + +
48A GLY* 1.3 58.8 + - - +
49A CYS 3.0 10.1 - - - +
50A LYS* 4.5 10.0 - - - -
52A LYS* 3.6 16.6 + - - +
82A PRO* 4.5 18.9 - - + +
83A PHE* 5.9 2.7 - - - -
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Residues in contact with GLY 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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44A GLN 3.1 17.0 + - - -
45A HIS 3.7 1.3 - - - -
47A LYS* 1.3 77.5 - - - +
49A CYS* 1.3 60.5 + - - +
50A LYS 4.2 0.3 + - - -
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Residues in contact with CYS 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 HIS* 2.9 50.5 + - - +
46A THR* 2.7 17.6 + - - +
47A LYS 3.1 9.4 - - - +
48A GLY* 1.3 83.3 - - - +
50A LYS* 1.3 63.1 + - - +
51A ARG* 4.4 4.5 - - + +
52A LYS* 3.0 22.0 - - + +
57A CYS* 5.5 4.3 - - + -
60A CYS* 4.8 1.1 - - - -
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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