Contacts of the helix formed by residues 114 - 122 (chain O) 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 THR 114 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113O SER* 1.3 84.4 + - - +
115O PRO* 1.3 70.9 - - - +
116O LEU* 3.2 4.0 + - - -
117O VAL* 3.3 22.1 - - - +
118O ASP* 3.0 19.6 + - - +
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Residues in contact with PRO 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K PRO* 4.7 6.6 - - + +
113O SER* 4.1 12.6 - - - +
114O THR* 1.3 85.5 - - - +
116O LEU* 1.3 62.2 + - + +
118O ASP* 3.6 14.8 - - + +
119O PHE* 2.9 27.2 + - - +
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Residues in contact with LEU 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K VAL* 5.2 11.4 - - + -
104K VAL* 3.8 47.6 - - + +
105K ASP* 4.3 16.4 - - - +
107K LEU* 5.7 0.2 - - + -
108K PRO* 5.3 3.4 - - + -
114O THR* 3.2 2.3 - - - -
115O PRO* 1.3 79.4 - - + +
117O VAL* 1.3 62.5 + - - +
119O PHE* 3.1 20.4 + - + +
120O LEU* 2.9 38.8 + - + +
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Residues in contact with VAL 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O THR* 3.3 30.9 - - + +
116O LEU* 1.3 75.4 - - - +
118O ASP* 1.3 67.6 + - - +
120O LEU* 3.2 21.7 + - + +
121O MET* 2.9 43.6 + - + +
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Residues in contact with ASP 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O SER* 2.9 29.8 + - - +
114O THR* 3.0 16.2 + - - +
115O PRO* 3.6 13.3 - - + +
116O LEU 3.2 0.2 - - - -
117O VAL* 1.3 77.9 - - - +
119O PHE* 1.3 58.8 + - - +
121O MET* 3.2 10.2 + - - +
122O GLN* 2.9 33.6 + - - +
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Residues in contact with PHE 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K LEU* 3.6 46.2 - - + -
108K PRO* 3.6 21.8 - - + -
111K ALA* 5.0 0.4 - - + -
115O PRO 2.9 15.3 + - - +
116O LEU* 3.1 18.8 + - + +
118O ASP* 1.3 75.0 - - - +
120O LEU* 1.3 65.0 + - + +
122O GLN* 3.3 15.0 - - - +
123O LEU* 3.0 51.4 + - + +
126O TYR* 3.2 39.5 - + - -
154O LEU* 4.0 17.5 - - + -
157O LEU* 5.1 9.4 - - + -
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Residues in contact with LEU 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K LEU* 4.2 31.6 - - + +
91K SER* 5.0 7.9 - - - +
94K VAL* 4.5 25.6 - - + -
116O LEU* 2.9 25.7 + - + +
117O VAL* 3.3 31.9 - - + +
119O PHE* 1.3 86.2 - - + +
121O MET* 1.3 67.1 + - + +
123O LEU* 3.3 37.2 - - + +
150O ARG* 4.7 4.9 + - - -
154O LEU* 5.1 6.1 - - + -
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Residues in contact with MET 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931E ASP 5.3 8.1 - - - +
933E ARG* 5.4 11.0 - - + -
934E TYR* 5.1 16.8 - - + +
90K LEU* 5.2 4.3 - - + -
117O VAL* 2.9 34.5 + - + +
118O ASP* 3.2 13.2 + - - +
120O LEU* 1.3 85.3 - - + +
122O GLN* 1.3 58.5 + - - +
123O LEU 3.1 4.3 + - - -
124O GLU* 3.2 29.1 + - - +
150O ARG* 4.5 7.1 + - - +
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Residues in contact with GLN 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K PRO* 4.7 6.3 - - - +
118O ASP* 2.9 17.0 + - - +
119O PHE* 3.3 29.2 - - - +
121O MET* 1.3 72.3 - - - +
123O LEU* 1.3 59.7 + - - +
124O GLU* 3.0 4.5 - - - +
125O ASP* 2.8 39.5 + - + +
126O TYR* 2.6 40.2 + - + -
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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