Contacts of the helix formed by residues 130 - 146 (chain G) in PDB entry 3ZNI
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 ASP 130 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C GLU* 4.4 9.0 - - - +
125C ARG* 5.7 3.1 - - - +
126G ILE* 2.8 20.0 + - + +
129G THR* 1.3 80.5 + - - +
131G ARG* 1.3 62.6 + - - +
132G GLU* 3.0 15.0 + - - +
133G LYS* 3.3 39.0 + - + +
134G TYR 3.0 16.8 + - - -
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Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G ILE 3.8 0.2 + - - -
127G TYR* 3.1 76.1 + - - +
128G LYS* 5.4 1.4 - - - +
129G THR 4.1 0.4 - - - -
130G ASP* 1.3 72.9 - - - +
132G GLU* 1.3 76.3 + - - +
133G LYS 3.5 0.2 - - - -
134G TYR* 3.5 8.2 - - - +
135G ASN* 3.0 40.1 + - - +
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Residues in contact with GLU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ASP* 3.5 13.1 - - - +
131G ARG* 1.3 100.5 + - + +
133G LYS* 1.3 62.7 + - - +
135G ASN* 3.9 10.5 - - - +
136G ARG* 3.2 37.2 + - - +
139G ARG* 4.6 3.5 + - - +
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Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLU* 3.3 36.7 + - - +
126C ILE* 5.5 4.6 - - - +
133C LYS* 5.8 2.4 - - - +
126G ILE* 4.0 30.6 - - + +
130G ASP* 3.2 34.9 + - + +
132G GLU* 1.3 75.8 - - - +
134G TYR* 1.3 64.9 + - - +
136G ARG* 3.3 18.9 + - - +
137G ILE* 2.9 52.5 + - + +
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Residues in contact with TYR 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PRO* 5.1 3.1 - - + -
45G TYR* 3.1 26.4 + + - -
74G TYR* 3.7 25.0 + + - -
75G HIS* 3.8 3.1 - - - -
76G PRO* 3.2 20.2 - - + +
110G LEU 4.8 2.0 + - - -
113G PRO* 4.8 0.9 - - - +
123G ILE* 3.5 28.7 - - + -
126G ILE* 3.6 12.0 - - + +
127G TYR* 3.4 51.3 - + + -
130G ASP 3.0 14.4 + - - +
131G ARG* 3.5 9.6 - - - +
133G LYS* 1.3 76.5 - - - +
135G ASN* 1.3 78.7 + - - +
137G ILE* 3.9 2.0 - - - +
138G ALA* 2.9 27.8 + - + +
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Residues in contact with ASN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PRO* 3.3 26.9 - - + +
127G TYR* 5.7 0.2 - - - -
131G ARG* 3.0 35.8 + - - +
132G GLU* 4.1 8.8 - - - +
133G LYS 3.3 0.2 - - - -
134G TYR* 1.3 88.6 - - - +
136G ARG* 1.3 58.2 + - - +
138G ALA* 3.3 2.9 + - - +
139G ARG* 2.8 49.9 + - - +
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Residues in contact with ARG 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G GLU* 3.2 25.1 + - - +
133G LYS* 3.3 20.7 + - - +
135G ASN* 1.3 78.6 - - - +
137G ILE* 1.3 56.0 + - + +
139G ARG* 3.2 27.5 + - - +
140G GLU* 2.7 58.5 + - + +
47I GLU* 6.5 1.3 - - - -
50I TRP* 3.2 41.3 - - - -
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Residues in contact with ILE 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G TYR* 3.7 38.6 - - + +
126G ILE* 5.1 2.2 - - + -
133G LYS* 2.9 49.3 + - + +
134G TYR 3.9 2.7 - - - +
136G ARG* 1.3 75.8 - - + +
138G ALA* 1.3 60.8 + - - +
140G GLU* 3.2 17.8 + - - +
141G TRP* 2.9 46.2 + - + +
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PRO* 3.7 17.7 - - + -
45G TYR* 4.1 17.5 - - + +
74G TYR* 3.9 29.2 - - + +
134G TYR* 2.9 21.6 + - + +
135G ASN 3.7 4.3 - - - +
137G ILE* 1.3 76.9 - - - +
139G ARG* 1.3 53.3 + - - +
141G TRP* 3.6 1.7 + - - +
142G THR* 2.7 37.1 + - - -
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Residues in contact with ARG 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G SER 5.2 1.1 - - - +
44G PRO* 3.4 29.0 - - + +
46G GLN* 6.6 0.4 - - - -
132G GLU* 4.6 4.0 + - - +
135G ASN* 2.8 28.6 + - - +
136G ARG* 3.3 48.9 - - - +
138G ALA* 1.3 74.8 - - - +
140G GLU* 1.3 64.6 + - + +
142G THR* 3.4 1.9 + - - -
143G GLN* 3.1 24.6 + - - +
147G MET* 5.6 0.3 - - - +
43I ARG* 5.1 14.8 - - - +
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Residues in contact with GLU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G ARG* 2.7 43.7 + - + +
137G ILE* 3.2 23.6 + - - +
139G ARG* 1.3 72.9 - - - +
141G TRP* 1.3 68.4 + - + +
143G GLN* 3.3 9.4 + - - +
144G LYS* 3.0 24.8 + - - +
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Residues in contact with TRP 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 4.5 19.0 - - + +
73G ILE* 3.8 23.8 - - - -
74G TYR* 3.8 50.7 - + + +
80G SER* 4.7 15.7 - - - -
123G ILE* 5.7 3.1 - - + -
137G ILE* 2.9 35.8 + - + +
138G ALA 3.9 3.8 - - - +
140G GLU* 1.3 83.3 + - + +
142G THR* 1.3 58.2 + - - +
144G LYS* 4.6 0.7 - - + -
145G TYR* 2.8 56.7 + + + +
146G ALA* 4.7 0.3 - - - +
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Residues in contact with THR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PRO 3.1 12.7 + - - +
45G TYR* 3.5 40.7 - - - +
46G GLN 3.9 6.1 - - - +
48G GLY* 3.7 20.2 - - - +
50G PHE* 4.2 4.9 - - + -
138G ALA 2.7 23.3 + - - -
139G ARG* 3.6 5.6 - - - -
141G TRP* 1.3 76.8 - - - +
143G GLN* 1.3 59.5 + - - +
146G ALA* 2.9 39.9 + - + +
147G MET* 3.5 9.8 + - + +
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Residues in contact with GLN 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ARG 3.1 14.3 + - - +
140G GLU* 3.8 6.6 - - - +
142G THR* 1.3 80.7 - - - +
144G LYS* 1.3 61.7 + - - +
147G MET* 3.7 38.9 - - + +
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G GLU 3.0 16.9 + - - +
141G TRP* 4.0 2.0 - - + +
143G GLN* 1.3 81.0 - - - +
145G TYR* 1.3 101.8 + - + +
146G ALA 3.6 0.2 - - - -
147G MET 5.0 1.6 + - - -
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Residues in contact with TYR 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G THR* 3.4 14.0 - - - +
72G ARG* 3.3 72.4 + - + +
141G TRP* 2.8 57.3 + + + +
144G LYS* 1.3 117.2 + - + +
146G ALA* 1.3 58.9 + - - +
147G MET 3.7 2.5 - - - +
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G GLY 4.1 0.5 - - - +
48G GLY* 3.3 5.6 - - - -
49G VAL* 2.7 44.5 + - - +
50G PHE* 3.5 41.7 - - + -
71G THR* 4.0 2.2 - - + -
72G ARG 4.9 0.4 - - - +
141G TRP 4.7 0.4 - - - +
142G THR* 2.9 16.7 + - - +
145G TYR* 1.3 80.5 - - - +
147G MET* 1.3 61.8 + - - +
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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