Contacts of the helix formed by residues 105 - 115 (chain C) 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 HIS 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C SER* 3.4 7.0 - - - -
104C LEU* 1.3 81.5 - - + +
106C GLU* 1.3 62.3 + - + +
107C LEU 3.0 5.7 + - - -
108C GLU* 3.1 24.8 + - - +
109C ASP* 4.1 3.1 + - - +
115N PRO* 5.5 6.6 - - + +
116N LEU* 4.3 36.6 + - + +
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C SER* 4.0 18.7 + - - +
104C LEU 3.3 0.2 - - - -
105C HIS* 1.3 76.0 - - + +
107C LEU* 1.3 53.7 + - - +
108C GLU 3.2 0.4 - - - -
109C ASP* 3.0 20.0 + - + +
110C TYR* 2.6 36.6 + - - +
161N LYS* 3.1 31.3 + - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PHE* 6.1 0.7 - - + -
102C VAL* 5.2 5.2 - - + -
103C SER 4.5 2.8 + - - +
104C LEU* 3.0 48.6 + - + +
106C GLU* 1.3 75.8 - - - +
108C GLU* 1.4 61.9 + - - +
110C TYR* 3.1 7.6 + - + +
111C ILE* 2.9 33.4 + - + +
119N PHE* 4.2 16.8 - - + -
154N LEU* 3.8 27.1 - - + -
157N LEU* 4.8 7.0 - - + +
158N ALA* 4.3 28.5 - - + +
161N LYS* 4.1 19.7 - - + +
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Residues in contact with GLU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU 4.3 0.2 + - - -
105C HIS* 3.1 14.3 + - - +
107C LEU* 1.4 75.9 - - - +
109C ASP* 1.3 65.7 + - - +
111C ILE* 3.1 15.5 + - - +
112C HIS* 3.1 26.2 + - + +
115N PRO* 2.8 45.8 - - - +
116N LEU* 5.5 1.6 - - + -
118N ASP* 4.7 1.6 - - - +
119N PHE* 3.3 33.8 + - + +
122N GLN* 3.7 15.8 + - - +
126N TYR* 4.9 2.0 - - - +
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C HIS 4.1 2.4 + - - +
106C GLU* 3.0 23.1 + - + +
108C GLU* 1.3 81.3 - - - +
110C TYR* 1.3 58.3 + - - +
112C HIS* 3.1 13.5 + - - +
113C ASN* 2.9 36.4 + - - +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ILE* 4.6 2.1 - - - +
106C GLU 2.6 20.5 + - - +
107C LEU* 3.1 8.9 + - + +
109C ASP* 1.3 73.7 - - - +
111C ILE* 1.3 59.1 + - + +
113C ASN* 3.0 21.2 + - + +
114C ILE* 3.0 56.2 + - + +
157N LEU* 3.5 17.7 - - + -
160N GLN* 2.8 22.2 + - + +
161N LYS* 3.4 50.3 - - + -
164N SER* 2.3 41.5 + - - -
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 2.9 18.7 + - + +
108C GLU* 3.1 6.9 + - - +
110C TYR* 1.3 78.5 - - + +
112C HIS* 1.3 61.6 + - + +
114C ILE* 3.0 4.6 + - - +
115C GLU* 2.9 60.3 + - + +
116C PRO* 3.4 4.2 - - + +
119N PHE* 3.5 34.1 - - + -
123N LEU* 5.6 0.7 - - + -
126N TYR* 3.6 28.0 - - + +
157N LEU* 3.7 33.9 - - + -
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Residues in contact with HIS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C GLU* 3.1 31.0 + - + +
109C ASP* 3.1 13.1 + - - +
111C ILE* 1.3 78.1 - - + +
113C ASN* 1.3 62.7 + - - +
114C ILE 3.4 0.2 - - - -
116C PRO* 3.6 22.8 - - + +
117C VAL* 4.9 2.3 - - - +
122N GLN* 5.4 4.4 + - - -
126N TYR* 4.9 15.8 + + - -
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASP* 2.9 27.3 + - - +
110C TYR* 3.0 27.3 + - + +
112C HIS* 1.3 79.0 - - - +
114C ILE* 1.3 67.5 + - + +
117C VAL* 3.3 26.4 - - - +
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ILE* 5.9 6.7 - - + -
47C ALA* 4.7 11.4 - - + -
110C TYR* 3.0 56.3 + - + +
111C ILE* 3.0 6.3 + - - +
113C ASN* 1.3 85.8 - - + +
115C GLU* 1.3 61.2 + - + +
116C PRO 3.4 0.9 - - - -
117C VAL* 2.8 5.4 + - - -
118C THR* 2.7 63.3 + - + +
129N THR* 4.2 5.2 - - - +
157N LEU* 5.0 1.6 - - + -
160N GLN* 3.4 22.4 - - - +
164N SER* 4.8 2.0 - - - +
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ILE* 2.9 30.0 + - + +
114C ILE* 1.3 76.6 - - + +
116C PRO* 1.3 63.1 - - + +
118C THR* 3.9 13.8 - - - +
120C PRO* 5.8 1.6 - - - +
126N TYR* 3.3 28.7 - - - +
127N THR* 3.0 36.7 + - - +
128N PRO* 3.7 2.6 - - - +
129N THR* 4.6 8.5 - - - +
157N LEU* 3.4 32.0 - - + +
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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