Contacts of the helix formed by residues 38 - 44 (chain A) in PDB entry 6MZL
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 2.9 13.1 + - + +
37A SER* 1.3 71.3 - - - +
39A ALA* 1.3 61.8 + - - +
40A GLY 3.2 3.8 - - - +
41A PHE* 3.2 47.5 + - + +
42A LEU* 3.5 11.1 - - - +
46A ILE* 4.0 3.4 - - + -
48A GLY* 3.7 28.3 - - - +
78A ILE* 3.5 16.1 - - + +
81A LEU* 3.9 25.4 - - + +
82A THR* 3.2 25.4 - - - +
197T PHE* 5.3 3.8 - - + -
212T LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 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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37A SER* 3.4 6.6 + - - +
38A LEU* 1.3 77.1 - - - +
40A GLY* 1.3 61.3 + - - +
42A LEU* 3.2 23.9 - - - +
43A PHE* 3.8 1.9 + - - +
66A LEU* 3.3 37.8 - - + +
69A LEU* 4.8 2.9 - - + -
70A GLY* 4.3 10.5 - - - +
74A LEU* 4.8 6.9 - - + +
78A ILE* 3.5 23.7 - - + +
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Residues in contact with GLY 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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37A SER 4.9 0.2 + - - -
38A LEU 3.2 0.8 - - - -
39A ALA* 1.3 76.8 - - - +
41A PHE* 1.3 58.6 + - - +
42A LEU 3.3 0.4 - - - -
43A PHE* 2.9 17.9 + - - +
44A GLY* 2.9 14.0 + - - +
46A ILE* 3.6 34.3 - - - +
52A LEU* 5.5 0.4 - - - +
66A LEU* 3.7 22.6 - - - +
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Residues in contact with PHE 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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38A LEU* 3.2 43.3 + - + +
40A GLY* 1.3 74.3 - - - +
42A LEU* 1.3 54.2 + - - +
46A ILE* 3.3 20.4 - - + +
48A GLY 5.1 0.7 - - - -
81A LEU* 3.5 17.3 - - + -
167T ASN* 2.6 28.8 + - - -
169T VAL* 3.3 14.5 - - + +
210T THR* 4.5 2.5 - - + -
212T LEU* 3.6 25.1 - - + -
220T VAL* 3.5 46.2 - - + -
221T CYS 3.7 4.3 - - - -
222T THR* 3.1 42.6 - - + +
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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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38A LEU 3.5 12.6 - - - +
39A ALA* 3.2 28.5 - - - +
41A PHE* 1.3 79.3 - - - +
43A PHE* 1.3 58.7 + - + +
74A LEU* 3.8 26.9 - - + -
77A LEU* 3.8 22.0 - - + -
78A ILE* 4.7 5.4 - - + -
81A LEU* 3.4 10.3 - - + +
167T ASN* 2.7 19.9 + - - +
169T VAL* 3.8 10.0 - - - +
257T ASN* 3.3 20.9 - - - +
259T VAL* 3.2 19.4 + - + +
313T THR* 3.3 25.8 - - + +
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Residues in contact with PHE 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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39A ALA 4.0 10.1 - - - +
40A GLY* 2.9 14.0 + - - +
42A LEU* 1.3 82.1 - - + +
44A GLY* 1.3 57.6 + - - +
52A LEU* 3.9 20.9 - - + -
58A LEU* 3.6 34.0 - - + +
62A CYS* 3.6 35.4 - - + -
66A LEU* 4.1 13.9 - - + -
69A LEU* 5.7 3.6 - - + -
166T GLN* 4.8 7.4 - - - +
167T ASN* 3.9 4.5 - - - +
259T VAL* 4.3 19.5 - - + +
303T LEU* 5.0 11.0 - - + -
311T VAL* 3.7 29.6 - - + -
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Residues in contact with GLY 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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40A GLY 2.9 8.0 + - - +
43A PHE* 1.3 79.8 - - - +
45A ASN* 1.3 71.4 + - - +
46A ILE 3.7 1.1 - - - -
52A LEU* 4.1 10.6 - - - +
53A GLU 3.0 14.9 - - - +
166T GLN 4.6 4.7 - - - -
167T ASN* 3.1 25.1 - - - +
223T GLY* 5.3 0.4 - - - -
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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