Contacts of the helix formed by residues 74 - 82 (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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ALA* 4.8 7.6 - - + +
42A LEU* 3.8 30.5 - - + +
69A LEU* 3.3 60.3 - - + +
72A LEU* 3.9 13.7 - - + -
73A GLY* 1.3 77.1 - - - +
75A GLY* 1.3 57.1 + - - +
76A SER 3.2 1.1 - - - -
77A LEU* 3.1 17.2 + - + +
78A ILE* 2.9 35.3 + - + +
292T ILE* 6.1 0.2 - - + -
294T ARG* 5.8 0.4 - - - +
301T VAL* 5.4 13.2 - - + -
303T LEU* 5.9 2.5 - - + -
313T THR* 4.9 10.3 - - + -
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Residues in contact with GLY 75 (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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70A GLY 4.1 12.0 + - - -
71A ALA 5.1 1.1 + - - -
73A GLY* 3.1 4.0 - - - +
74A LEU* 1.3 78.1 - - - +
76A SER* 1.3 57.4 + - - +
78A ILE* 3.4 17.1 - - - +
79A THR* 2.9 35.9 + - - +
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Residues in contact with SER 76 (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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73A GLY* 3.2 16.8 + - - -
75A GLY* 1.3 76.0 - - - +
77A LEU* 1.3 78.0 + - - +
79A THR* 2.6 23.7 + - - -
80A GLU* 2.9 18.4 + - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.8 22.2 - - + -
73A GLY 4.8 5.2 - - - +
74A LEU* 3.1 15.5 + - + +
76A SER* 1.3 91.4 + - - +
78A ILE* 1.3 60.5 + - - +
80A GLU* 3.3 11.3 - - + +
81A LEU* 2.9 34.4 + - - +
257T ASN* 3.3 29.2 - - - +
301T VAL* 5.4 11.7 - - + -
313T THR* 4.1 5.2 - - + +
314T GLY* 4.0 22.2 - - - -
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Residues in contact with ILE 78 (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 PHE 3.3 28.3 - - - +
37A SER* 4.3 6.3 - - - -
38A LEU* 3.5 12.6 - - + +
39A ALA* 3.5 41.5 - - + +
42A LEU* 4.7 1.8 - - + -
70A GLY* 4.3 14.6 - - - +
74A LEU 2.9 20.3 + - - +
75A GLY* 3.4 17.9 - - - +
76A SER 3.2 0.2 - - - -
77A LEU* 1.3 76.8 - - - +
79A THR* 1.3 59.6 + - + +
81A LEU* 3.0 7.7 + - - +
82A THR* 2.9 29.2 + - - -
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Residues in contact with THR 79 (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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75A GLY 2.9 17.2 + - - +
76A SER* 2.6 25.5 + - - -
78A ILE* 1.3 74.2 - - + +
80A GLU* 1.3 61.9 + - - +
82A THR* 3.0 23.8 - - - +
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Residues in contact with GLU 80 (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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76A SER 2.9 19.1 + - - +
77A LEU* 3.3 19.7 - - + +
78A ILE 3.2 0.2 - - - -
79A THR* 1.3 79.5 + - - +
81A LEU* 1.3 67.0 + - + +
82A THR 3.5 3.5 + - - -
171T THR* 5.6 4.5 - - - +
256T GLN* 4.0 23.4 - - + +
316T LYS* 4.4 12.5 + - - +
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Residues in contact with LEU 81 (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* 3.9 21.6 - - + +
41A PHE* 3.5 17.5 - - + -
42A LEU* 3.4 41.1 - - + +
77A LEU 2.9 20.5 + - - +
78A ILE* 3.0 6.6 + - - +
80A GLU* 1.3 83.3 - - + +
82A THR* 1.3 58.9 + - - +
169T VAL* 3.8 17.5 - - + -
171T THR* 5.3 2.0 - - - +
220T VAL* 3.6 29.8 - - - +
256T GLN* 5.0 7.4 - - + +
257T ASN* 3.6 30.1 - - + +
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Residues in contact with THR 82 (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 PHE* 3.9 37.2 + - + +
38A LEU* 3.2 25.2 - - - +
78A ILE* 2.9 12.5 + - - -
79A THR* 3.0 21.5 - - - +
80A GLU 4.2 3.1 - - - -
81A LEU* 1.3 79.8 - - - +
197T PHE* 5.7 2.4 - - + -
214T PHE* 4.1 31.2 - - + -
220T VAL* 6.0 0.7 - - - -
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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