Contacts of the helix formed by residues 130 - 140 (chain P) 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 PRO 130 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129P PHE* 1.3 85.1 - - + +
131P LYS* 1.3 65.1 + - - +
132P ALA* 3.2 7.9 + - + +
133P ALA* 3.4 9.8 + - + +
134P ILE* 3.3 23.2 + - - +
31S LEU 4.5 7.9 - - - +
32S PHE* 3.7 19.1 - - + -
35S GLU* 3.6 39.0 - - + +
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Residues in contact with LYS 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 4.9 3.8 + - - -
60A ASP* 3.5 35.4 + - - +
61A GLU* 5.2 9.4 + - - +
64A LYS* 3.4 31.2 - - - +
65A HIS* 5.6 2.2 - - - -
129P PHE 4.5 6.7 + - - +
130P PRO* 1.3 73.2 - - - +
132P ALA* 1.3 57.2 + - - +
134P ILE* 4.0 1.1 - - - +
135P LYS* 2.9 34.5 + - - +
148P GLN* 4.2 11.7 - - + +
151P VAL* 4.0 23.3 - - + +
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Residues in contact with ALA 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P PRO* 3.2 6.0 - - + -
131P LYS* 1.3 78.3 - - - +
133P ALA* 1.3 56.7 + - - +
135P LYS* 3.8 6.2 - - - +
136P ARG* 2.9 30.8 + - - +
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Residues in contact with ALA 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P PRO* 3.4 9.9 + - + +
131P LYS 3.4 0.2 - - - -
132P ALA* 1.3 77.3 - - - +
134P ILE* 1.3 60.0 + - - +
136P ARG* 3.4 8.3 + - - +
137P LEU* 3.0 30.3 + - - +
31S LEU* 4.4 28.1 - - + +
32S PHE* 3.7 30.3 - - + -
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Residues in contact with ILE 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 3.8 17.5 - - + -
130P PRO 3.3 16.9 + - - +
133P ALA* 1.3 75.7 - - - +
135P LYS* 1.3 58.3 + - - +
137P LEU* 3.4 4.5 + - - +
138P ILE* 3.0 56.1 + - + +
151P VAL* 3.8 23.6 - - + +
154P MET* 4.2 11.2 - - + -
155P SER* 3.4 21.5 - - - +
158P SER* 5.5 0.2 - - - +
32S PHE* 3.6 26.5 - - + -
65S ILE* 3.7 20.2 - - + -
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Residues in contact with LYS 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P LYS* 2.9 20.2 + - + +
132P ALA* 3.8 4.9 - - - +
134P ILE* 1.3 77.0 - - - +
136P ARG* 1.3 56.7 + - - +
138P ILE* 4.0 2.9 - - - -
139P GLN* 2.9 70.3 + - + +
145P SER* 4.5 3.6 + - - -
146P VAL* 3.5 20.5 + - + -
147P SER 5.7 0.6 - - - -
148P GLN* 5.9 1.4 - - - +
151P VAL* 4.3 20.2 - - + +
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Residues in contact with ARG 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ALA 2.9 19.2 + - - +
133P ALA* 3.7 9.2 - - - +
135P LYS* 1.3 77.6 - - - +
137P LEU* 1.3 57.8 + - - +
139P GLN* 3.7 4.9 - - - +
140P SER* 2.9 35.2 + - - +
31S LEU* 5.9 6.7 - - + -
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P ALA 3.0 17.2 + - - +
134P ILE* 4.0 4.5 - - - +
136P ARG* 1.3 75.9 - - - +
138P ILE* 1.3 64.0 + - - +
140P SER* 3.0 12.6 + - - +
141P ILE* 3.0 46.4 + - + +
31S LEU* 6.0 6.5 - - + -
32S PHE* 5.8 3.4 - - + -
62S ILE* 3.6 51.4 - - + +
65S ILE* 3.7 26.9 - - + -
66S THR* 4.5 1.8 - - - +
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Residues in contact with ILE 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134P ILE* 3.0 37.1 + - + +
135P LYS 4.2 1.8 - - - +
137P LEU* 1.3 75.7 - - - +
139P GLN* 1.3 53.2 + - - +
141P ILE* 4.5 4.7 - - - +
142P THR* 2.6 47.4 + - + -
146P VAL* 3.7 31.0 - - + -
150P VAL* 4.3 18.6 - - + +
151P VAL* 4.9 5.6 - - + -
154P MET* 3.8 24.2 - - + -
65S ILE* 3.8 17.9 - - + -
69S THR* 4.2 10.8 - - + +
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Residues in contact with GLN 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P LYS* 2.9 60.1 + - - +
136P ARG* 4.1 3.9 - - - +
138P ILE* 1.3 77.1 - - - +
140P SER* 1.3 55.5 + - - +
141P ILE 3.3 1.3 - - - -
142P THR* 3.7 5.2 - - - -
143P GLY* 3.3 23.2 + - - -
144P THR 3.4 17.3 - - - +
145P SER* 3.6 22.9 + - - +
146P VAL* 3.7 11.8 - - + +
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Residues in contact with SER 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P ARG* 2.9 26.2 + - - +
137P LEU* 3.0 21.3 + - - +
139P GLN* 1.3 74.4 - - - +
141P ILE* 1.3 60.1 + - - +
143P GLY* 4.7 1.1 - - - -
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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