Contacts of the helix formed by residues 130 - 145 (chain E) in PDB entry 3VZD
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 130 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLN 5.2 0.7 - - - -
129E VAL* 1.3 76.4 - - - +
131E ASN* 1.3 90.7 + - + +
132E GLU 3.3 0.3 + - - -
133E ASP* 3.2 13.6 + - - +
134E LEU* 3.1 14.8 + - - -
189E GLU* 3.2 23.1 + - - +
270E SER* 3.3 19.0 + - - -
271E GLU* 4.2 15.9 + - - +
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Residues in contact with ASN 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LYS* 4.8 15.3 - - - +
109E PRO* 4.9 3.0 - - - +
114E ASN* 6.0 2.2 - - - +
130E THR* 1.3 92.9 + - + +
132E GLU* 1.3 77.8 + - - +
134E LEU* 3.1 8.9 + - - +
135E LEU* 2.9 26.8 + - - +
188E GLY* 5.8 0.8 - - - -
189E GLU* 3.6 25.5 + - - +
270E SER* 5.9 0.2 - - - -
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.8 24.8 - - + +
37E HIS* 3.5 32.4 + - + +
130E THR 3.3 0.2 + - - -
131E ASN* 1.3 97.1 - - - +
133E ASP* 1.3 55.0 + - - +
135E LEU* 3.6 8.6 - - - +
136E THR* 2.8 39.0 + - - -
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Residues in contact with ASP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 3.6 26.3 - - + +
130E THR* 3.2 12.0 + - - +
132E GLU* 1.3 78.8 - - - +
134E LEU* 1.3 61.4 + - - +
136E THR* 3.4 6.4 + - - -
137E ASN* 3.1 30.2 + - - +
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Residues in contact with LEU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E PRO* 3.6 24.7 - - + -
114E ASN* 4.3 6.5 - - + +
117E ALA 4.0 7.0 - - - +
118E ALA* 4.2 15.7 - - - +
121E ASN* 3.6 36.3 - - + +
129E VAL* 3.7 18.5 - - + +
130E THR* 3.1 12.8 + - - -
131E ASN 3.1 11.7 + - - +
133E ASP* 1.3 75.7 - - - +
135E LEU* 1.3 67.3 + - - +
137E ASN* 3.2 1.7 + - - -
138E CYS* 3.0 27.6 + - - -
270E SER* 3.9 28.5 - - - -
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.8 35.9 - - + -
37E HIS* 4.0 20.6 - - + -
38E VAL* 3.9 12.8 - - + -
78E MET* 3.8 16.2 - - + -
108E LEU* 3.8 18.4 - - + -
109E PRO* 3.6 38.6 - - + +
131E ASN 2.9 14.5 + - - +
132E GLU* 3.6 10.3 - - - +
134E LEU* 1.3 76.2 - - - +
136E THR* 1.3 59.7 + - - +
138E CYS* 3.4 0.7 + - - -
139E THR* 2.7 33.6 + - - +
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Residues in contact with THR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E HIS* 3.8 23.0 + - - +
41E LEU* 4.4 10.9 - - + +
132E GLU 2.8 20.2 + - - -
133E ASP* 3.6 7.6 - - - -
134E LEU 3.2 0.2 - - - -
135E LEU* 1.3 76.5 - - - +
137E ASN* 1.3 61.3 + - - +
139E THR* 3.1 9.0 + - - -
140E LEU* 2.8 46.1 + - + +
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Residues in contact with ASN 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ASN* 3.1 29.4 + - - +
126E TYR* 3.6 37.8 - - + +
129E VAL* 3.4 23.4 - - - +
133E ASP* 3.1 12.6 + - - +
134E LEU 3.2 3.3 + - - +
136E THR* 1.3 82.4 - - - +
138E CYS* 1.3 56.9 + - - +
140E LEU* 3.1 14.6 + - - +
141E LEU* 2.9 33.3 + - - +
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Residues in contact with CYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E CYS* 4.8 2.3 - - - -
107E SER 3.8 5.6 - - - +
108E LEU* 3.5 17.2 - - + +
109E PRO* 3.7 15.9 - - + -
117E ALA* 3.7 42.8 - - - -
120E LEU* 5.5 2.2 - - - -
121E ASN* 4.7 4.9 - - - -
134E LEU* 3.0 26.2 + - - +
135E LEU 3.9 0.4 - - - +
137E ASN* 1.3 75.0 - - - +
139E THR* 1.3 60.6 + - - +
141E LEU* 3.4 18.1 + - + +
142E LEU* 3.2 16.1 + - - +
362E VAL* 4.8 0.7 - - - +
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Residues in contact with THR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E HIS 4.4 1.2 + - - -
38E VAL* 3.8 42.5 - - + +
41E LEU* 3.9 30.1 - - + -
42E LEU* 4.5 4.9 - - + -
108E LEU* 4.0 12.2 - - + +
135E LEU* 2.7 20.0 + - - +
136E THR* 3.4 9.4 - - - -
138E CYS* 1.3 74.3 - - - +
140E LEU* 1.4 58.5 + - - +
142E LEU* 2.8 22.6 + - + +
143E CYS* 2.9 23.7 + - - -
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 3.8 30.3 - - + -
126E TYR* 4.1 8.1 - - + +
136E THR* 2.8 35.1 + - + +
137E ASN* 3.1 17.9 + - - +
139E THR* 1.4 70.4 - - - +
141E LEU* 1.3 61.7 + - - +
143E CYS* 3.5 8.4 + - + +
144E ARG* 3.2 56.3 + - - +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E LEU* 4.1 31.4 - - + +
121E ASN* 4.5 5.4 - - - +
124E ALA* 3.6 23.8 - - + -
126E TYR* 4.1 12.6 - - + -
137E ASN 2.9 19.3 + - - +
138E CYS* 3.5 17.5 - - - +
139E THR 3.1 0.2 - - - -
140E LEU* 1.3 76.6 - - - +
142E LEU* 1.3 64.8 + - - +
144E ARG* 3.3 19.0 + - - +
145E ARG* 3.3 13.9 + - - -
146E LEU 4.4 2.6 + - - -
362E VAL* 3.8 17.2 - - + +
363E SER* 4.4 19.0 - - - +
364E GLY* 4.3 11.0 - - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.1 21.1 - - + -
17E VAL* 4.8 9.9 - - + -
42E LEU* 3.9 22.4 - - + -
47E ILE* 4.1 15.5 - - + +
74E ALA* 5.4 1.1 - - + -
76E VAL* 3.7 34.5 - - + -
106E CYS* 3.9 20.4 - - + -
108E LEU* 4.4 8.5 - - + -
138E CYS 3.2 8.9 + - - +
139E THR* 2.8 15.1 + - - +
141E LEU* 1.3 71.0 - - - +
143E CYS* 1.3 57.4 + - - +
145E ARG* 2.9 27.9 + - - +
362E VAL* 3.6 18.8 - - + +
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Residues in contact with CYS 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ARG* 4.6 4.3 + - - -
41E LEU* 3.7 43.5 - - - -
42E LEU* 4.1 14.1 - - - -
45E ALA* 3.8 15.2 - - + +
47E ILE* 4.0 7.9 - - - -
139E THR* 2.9 18.1 + - - +
140E LEU* 3.7 11.0 - - + +
142E LEU* 1.3 74.7 - - - +
144E ARG* 1.3 60.4 + - + +
145E ARG* 3.4 18.8 + - - +
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E TYR* 2.9 30.5 + - - -
140E LEU* 3.2 39.0 + - - +
141E LEU* 3.8 22.6 - - + +
142E LEU 3.1 1.0 - - - -
143E CYS* 1.3 77.0 - - + +
145E ARG* 1.4 66.4 + - - +
146E LEU* 3.1 28.1 + - + +
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Residues in contact with ARG 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 3.4 6.0 - - + -
11E LEU* 2.9 56.3 + - + +
12E PRO 2.8 22.9 + - - -
13E ARG* 3.4 48.8 - - - +
15E CYS* 3.6 13.1 - - - +
45E ALA* 2.8 33.1 + - - +
46E GLU 3.3 16.4 + - - -
47E ILE* 3.7 8.9 - - + +
141E LEU 3.3 4.4 + - - -
142E LEU* 2.9 20.0 + - - +
143E CYS 3.9 10.4 + - - +
144E ARG* 1.4 78.1 - - - +
146E LEU* 1.3 65.3 + - + +
147E LEU* 3.8 1.0 + - - +
362E VAL* 5.4 1.3 - - - -
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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