Contacts of the helix formed by residues 112 - 124 (chain Q) 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 GLU 112 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895D HIS* 5.2 3.1 - - + -
898D VAL* 3.3 20.0 - - - +
106Q ARG* 2.6 45.1 + - - +
108Q SER* 5.5 2.2 + - - -
110Q THR* 3.6 19.4 + - + +
111Q LEU* 1.3 90.0 - - - +
113Q VAL* 1.3 68.1 + - + +
114Q LYS* 3.3 19.2 + - - +
115Q ASP 3.9 2.1 + - - -
116Q VAL* 3.7 9.5 + - - +
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Residues in contact with VAL 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895D HIS* 5.9 0.7 - - + -
898D VAL* 3.8 28.0 - - + -
901D TYR* 6.1 0.9 - - + -
112Q GLU* 1.3 77.3 - - + +
114Q LYS* 1.3 71.5 + - + +
116Q VAL* 3.5 3.4 + - - +
117Q GLN* 2.9 41.4 + - + +
128Q ILE* 4.1 26.0 - - + -
63S GLU* 4.7 6.1 - - - +
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Residues in contact with LYS 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L HIS* 4.4 25.9 - - + +
62L LYS* 5.6 11.7 - - - +
106Q ARG* 3.6 14.8 - - - +
112Q GLU* 3.3 31.7 + - - +
113Q VAL* 1.3 88.0 - - + +
115Q ASP* 1.3 63.0 + - - +
117Q GLN* 3.4 16.3 + - - +
118Q LEU* 2.9 30.7 + - - +
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Residues in contact with ASP 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L HIS* 5.9 2.8 - - - +
99Q ALA* 4.8 5.0 - - - +
102Q LEU* 2.9 58.5 - - + +
103Q ALA* 3.5 14.7 - - - +
105Q HIS* 5.2 2.4 + - - -
106Q ARG* 3.0 35.5 + - - +
111Q LEU* 3.9 20.2 - - + +
112Q GLU 3.9 1.6 + - - +
113Q VAL 3.4 0.4 - - - -
114Q LYS* 1.3 76.3 - - - +
116Q VAL* 1.3 65.5 + - - +
118Q LEU 3.3 1.2 + - - -
119Q HIS* 3.1 21.3 + - - +
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Residues in contact with VAL 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898D VAL* 4.1 6.7 - - + +
901D TYR* 3.8 22.2 - - + +
902D VAL* 3.7 24.9 - - + -
905D ALA* 5.9 0.9 - - + -
95Q VAL* 6.3 2.5 - - + -
99Q ALA* 5.2 6.1 - - + -
111Q LEU* 3.7 31.6 - - + -
112Q GLU 3.7 5.1 + - - +
113Q VAL* 3.5 7.6 + - + +
114Q LYS 3.4 0.2 - - - -
115Q ASP* 1.3 74.4 - - - +
117Q GLN* 1.3 57.1 + - - +
119Q HIS* 3.3 7.9 + - - +
120Q LEU* 2.9 49.9 + - + +
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Residues in contact with GLN 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D TYR* 5.8 0.6 - - - -
60L HIS* 5.8 5.7 - - + -
113Q VAL* 2.9 26.8 + - + +
114Q LYS* 3.6 17.5 - - - +
116Q VAL* 1.3 77.6 - - - +
118Q LEU* 1.3 56.6 + - - +
120Q LEU* 3.3 13.8 + - + +
121Q GLU* 2.9 45.1 + - + +
126Q MET* 6.3 2.2 - - + -
128Q ILE* 5.8 4.0 - - + -
63S GLU* 2.7 40.7 + - - +
66S THR* 6.4 0.4 - - - +
67S GLU* 4.5 9.9 + - - +
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Residues in contact with LEU 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ILE* 3.7 20.6 - - + -
57L TYR* 3.6 35.4 - - + +
60L HIS* 3.5 40.6 - - + +
102Q LEU* 3.7 15.0 - - + -
105Q HIS* 5.7 0.2 - - - +
114Q LYS 2.9 18.3 + - - +
115Q ASP 3.3 0.2 + - - -
117Q GLN* 1.3 73.2 - - - +
119Q HIS* 1.3 61.7 + - - +
121Q GLU* 3.2 26.8 + - + +
122Q ARG* 3.0 31.1 + - + +
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Residues in contact with HIS 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Q PHE* 4.7 5.1 - + - -
94Q SER* 4.9 4.0 - - - -
95Q VAL* 3.7 38.0 - - + +
98Q ALA* 3.4 33.9 - - + +
99Q ALA* 5.9 0.9 - - - +
102Q LEU* 4.2 4.8 - - + +
115Q ASP 3.1 13.5 + - - +
116Q VAL* 3.7 9.4 - - - +
118Q LEU* 1.3 75.9 - - - +
120Q LEU* 1.3 65.0 + - + +
122Q ARG* 3.2 27.0 + - - +
123Q GLN* 3.0 52.9 + - + +
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Residues in contact with LEU 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901D TYR* 3.5 32.5 - - + +
905D ALA* 3.7 22.4 - - + -
116Q VAL* 2.9 31.9 + - + +
117Q GLN* 3.5 12.1 - - + +
119Q HIS* 1.3 81.5 - - + +
121Q GLU* 1.3 55.0 + - - +
123Q GLN* 2.9 2.4 + - + +
124Q TRP* 2.4 59.2 + - + +
125Q ASN* 2.6 11.2 + - - -
126Q MET* 3.6 28.0 - - + +
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Residues in contact with GLU 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ILE* 5.9 1.2 - - - +
60L HIS* 4.8 5.1 + - - -
117Q GLN* 2.9 35.3 + - + +
118Q LEU* 3.2 29.6 + - + +
120Q LEU* 1.3 76.4 - - + +
122Q ARG* 1.3 61.8 + - - +
123Q GLN 4.8 0.3 - - - -
125Q ASN* 3.9 33.1 + - - +
126Q MET 5.6 0.9 - - - +
67S GLU* 3.4 28.6 - - - +
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Residues in contact with ARG 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L TYR* 2.3 31.1 + - - -
77L CYS* 2.7 39.1 - - - +
81L GLN* 5.4 12.5 - - - +
98Q ALA* 4.0 14.1 - - - +
101Q GLN* 5.2 0.8 + - - -
102Q LEU* 3.4 18.1 - - - +
118Q LEU* 3.0 20.1 + - + +
119Q HIS* 3.2 35.5 + - - +
120Q LEU 3.2 0.2 - - - -
121Q GLU* 1.3 78.6 - - - +
123Q GLN* 1.3 69.2 + - + +
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Residues in contact with GLN 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909D ARG* 5.5 2.1 - - - -
91Q PHE* 4.3 22.0 - - + -
119Q HIS* 3.0 43.7 + - + +
120Q LEU* 2.9 4.0 + - - -
121Q GLU 4.8 0.4 - - - -
122Q ARG* 1.3 89.1 + - + +
124Q TRP* 1.3 83.3 + - + +
125Q ASN 3.9 0.2 - - - -
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Residues in contact with TRP 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905D ALA* 4.6 9.5 + - + +
908D GLN* 3.6 8.5 - - + -
909D ARG* 3.6 35.9 - - + -
912D ASN* 3.3 44.9 - - + -
195P LYS* 4.5 15.3 - - + +
196P SER* 3.8 32.5 - - - -
200P ILE 4.9 2.4 - - - +
201P PRO* 5.4 0.2 - - - +
91Q PHE* 5.0 8.1 - - - -
120Q LEU* 2.4 48.8 + - + +
123Q GLN* 1.3 89.9 - - + +
125Q ASN* 1.3 68.4 + - - +
126Q MET* 3.5 25.1 - - + +
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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