Contacts of the helix formed by residues 132 - 148 (chain F) in PDB entry 4DHZ
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 ASN 132 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128F GLN* 3.1 39.0 + - - +
129F TRP 4.0 2.0 - - - -
130F LYS 3.2 2.0 - - - -
131F THR* 1.3 99.5 + - - +
133F GLU* 1.3 66.6 + - - +
134F ALA* 4.3 9.0 - - + +
135F GLN* 3.9 12.7 - - + +
136F ALA* 3.7 8.5 + - - +
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Residues in contact with GLU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F PRO* 5.9 4.3 - - - +
129F TRP* 3.8 34.4 + - + +
130F LYS 4.7 1.2 + - - -
132F ASN* 1.3 70.1 - - - +
134F ALA* 1.3 65.4 + - - +
136F ALA* 3.2 2.3 + - - +
137F ILE* 3.0 51.5 + - + +
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ASN* 3.2 7.4 - - + -
133F GLU* 1.3 80.8 - - - +
135F GLN* 1.3 64.3 + - - +
137F ILE* 3.7 3.5 + - - +
138F GLU* 3.6 21.8 + - - +
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Residues in contact with GLN 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLN* 3.8 18.4 - - - +
132F ASN* 3.8 15.1 + - - +
133F GLU 3.5 0.4 - - - -
134F ALA* 1.3 79.0 - - - +
136F ALA* 1.3 63.7 + - - +
138F GLU* 3.4 7.3 + - - +
139F THR* 3.1 25.2 + - - +
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TYR* 4.0 9.1 - - + -
128F GLN* 4.0 22.8 - - + +
129F TRP* 3.6 37.4 - - + -
132F ASN 3.7 11.3 + - - +
133F GLU 3.2 6.4 + - - +
135F GLN* 1.3 76.5 - - - +
137F ILE* 1.3 65.8 + - - +
139F THR* 3.2 18.7 + - - -
140F ALA 3.2 9.9 + - - -
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PRO* 3.6 27.2 - - + +
115F PRO* 6.3 2.5 - - + -
129F TRP* 3.8 30.1 - - + +
133F GLU* 3.0 45.3 + - - +
134F ALA* 4.1 3.8 - - - +
136F ALA* 1.3 75.9 - - - +
138F GLU* 1.3 72.6 + - - +
140F ALA 3.5 1.0 + - - -
141F ARG* 3.3 29.8 + - - +
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Residues in contact with GLU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F ALA 3.6 11.5 + - - +
135F GLN* 3.4 9.3 + - - +
136F ALA 3.2 0.6 - - - -
137F ILE* 1.3 80.9 - - - +
139F THR* 1.3 65.8 + - - +
141F ARG* 2.9 50.2 + - - +
142F ALA* 3.0 13.0 + - - +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F TYR* 3.7 37.5 + - + -
128F GLN* 5.1 3.8 + - - -
135F GLN* 3.1 17.1 + - - +
136F ALA* 3.2 10.4 + - - -
138F GLU* 1.3 75.7 - - - +
140F ALA* 1.3 57.4 + - - +
142F ALA* 3.0 10.7 + - + +
143F TRP* 2.9 41.1 + - + +
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PRO* 3.6 22.5 - - + +
47F PHE* 3.7 10.9 - - + -
76F TYR* 3.6 35.8 - - + +
129F TRP* 4.2 5.6 - - + -
136F ALA 3.2 8.4 + - - +
137F ILE 3.8 3.6 - - - +
138F GLU 3.2 0.2 - - - -
139F THR* 1.3 79.0 - - - +
141F ARG* 1.3 53.5 + - - +
143F TRP* 3.9 1.9 - - - +
144F THR* 2.6 34.1 + - - -
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Residues in contact with ARG 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASP* 5.6 2.4 - - - +
45F SER* 3.9 11.7 + - - +
46F PRO* 3.4 35.1 + - + +
48F GLU* 4.2 16.8 + - - +
137F ILE* 3.3 24.5 + - - +
138F GLU* 2.9 39.8 + - - +
140F ALA* 1.3 75.8 - - - +
142F ALA* 1.3 62.7 + - - +
144F THR* 3.5 4.9 + - - -
145F ARG* 3.3 19.4 + - - +
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F GLU 3.0 10.7 + - - +
139F THR* 3.2 13.2 - - + +
141F ARG* 1.3 78.2 - - - +
143F TRP* 1.3 62.6 + - + +
145F ARG* 3.0 29.2 + - - +
146F LEU* 3.0 31.7 + - + +
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Residues in contact with TRP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F LYS* 3.5 35.2 - - + +
75F ILE* 3.7 12.8 - - - -
76F TYR* 3.3 64.4 - + + +
82F LYS* 6.3 2.5 - - - -
139F THR* 2.9 31.7 + - + +
140F ALA* 4.2 4.3 - - - +
141F ARG 3.4 0.2 - - - -
142F ALA* 1.3 75.8 - - + +
144F THR* 1.3 66.4 + - - +
145F ARG 3.1 0.4 - - - -
146F LEU* 4.1 17.0 - - + +
147F TYR* 2.9 51.7 + + + +
148F ALA 3.8 0.2 + - - -
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PRO 3.3 11.0 + - - -
47F PHE* 3.4 20.4 - - - -
48F GLU 3.9 20.9 - - - +
50F GLY* 3.9 13.9 - - - +
52F PHE* 4.5 3.0 - - + -
140F ALA 2.6 23.3 + - - -
141F ARG 3.5 10.1 - - - -
143F TRP* 1.3 76.2 - - - +
145F ARG* 1.3 58.9 + - - +
148F ALA* 3.0 46.9 + - + +
149F MET* 3.5 13.4 - - + +
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ARG 3.3 9.2 + - - +
142F ALA* 3.0 28.9 + - - +
144F THR* 1.3 81.3 - - - +
146F LEU* 1.3 89.2 + - - +
149F MET* 3.7 34.8 - - + +
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Residues in contact with LEU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 3.0 20.0 + - + +
143F TRP* 4.0 23.6 - - + +
145F ARG* 1.3 104.6 - - - +
147F TYR* 1.3 88.5 + - + +
149F MET 4.2 5.2 - - - +
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Residues in contact with TYR 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F THR* 4.5 6.0 - - + +
74F LYS* 3.9 63.5 - - + +
143F TRP* 2.9 47.9 + + + +
145F ARG 3.4 0.2 - - - -
146F LEU* 1.3 103.4 - - + +
148F ALA* 1.3 59.7 + - - +
149F MET 3.1 12.8 + - - +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F GLY* 3.9 7.0 - - - -
51F THR* 3.2 28.7 + - - +
52F PHE* 3.7 29.8 - - + -
73F THR* 4.0 11.4 - - + -
74F LYS 5.4 0.2 - - - +
143F TRP 3.8 0.6 + - - +
144F THR* 3.0 31.2 + - + +
147F TYR* 1.3 77.4 - - + +
149F MET* 1.3 58.4 + - - +
150F ASN* 4.1 3.3 - - - +
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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