Contacts of the helix formed by residues 141 - 162 (chain F) in PDB entry 4DEM
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 141 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58F ARG* 3.8 19.6 + - - +
137F GLY 4.6 6.6 - - - +
138F VAL 3.3 16.0 + - - +
139F GLY 3.1 0.8 - - - -
140F LEU* 1.3 78.5 - - - +
142F ALA* 1.3 61.2 + - - +
143F ILE 3.1 0.2 - - - -
144F ASN* 3.0 20.7 + - + +
145F ASP* 3.2 12.5 + - - +
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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
----------------------------------------------------------
115F VAL* 3.5 11.1 - - + +
119F ILE* 4.1 6.1 - - + -
132F TRP* 3.6 23.6 - - + -
133F TYR* 3.8 14.6 - - + -
138F VAL* 3.8 5.6 - - + +
139F GLY 3.1 16.5 + - - +
140F LEU 3.0 0.4 - - - -
141F ASP* 1.3 76.5 - - - +
143F ILE* 1.3 57.3 + - - +
144F ASN 3.3 0.2 - - - -
145F ASP* 3.4 12.9 + - - -
146F ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ALA* 6.2 1.1 - - - -
119F ILE* 3.9 20.4 - - + +
140F LEU* 3.0 37.3 + - + +
142F ALA* 1.3 79.0 - - - +
144F ASN* 1.3 62.4 + - - +
146F ALA* 3.4 5.3 + - - +
147F ASN* 3.3 31.1 + - - +
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Residues in contact with ASN 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F LEU 4.4 0.2 + - - -
141F ASP* 3.0 12.2 + - - +
143F ILE* 1.3 78.6 - - - +
145F ASP* 1.4 69.9 + - - +
147F ASN* 3.2 8.0 + - - +
148F LEU* 2.9 39.5 + - - +
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Residues in contact with ASP 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ARG* 2.8 42.1 + - - +
62F VAL* 3.5 28.7 - - + +
115F VAL* 5.1 0.9 - - + -
132F TRP* 2.8 29.6 + - + +
141F ASP 3.2 5.0 + - - +
142F ALA* 3.4 15.6 + - - +
144F ASN* 1.4 79.9 + - - +
146F ALA* 1.3 64.9 + - - +
148F LEU* 3.3 14.5 + - - +
149F LEU* 3.2 24.3 + - - +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.1 41.6 - - + +
115F VAL* 3.8 18.8 - - + +
116F ALA* 4.3 11.9 - - + +
142F ALA 2.8 17.6 + - - +
143F ILE* 3.6 6.7 - - - +
144F ASN 3.2 0.2 - - - -
145F ASP* 1.3 77.2 - - - +
147F ASN* 1.3 61.3 + - - +
149F LEU* 3.1 20.0 + - - +
150F GLU 3.3 4.0 + - - -
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Residues in contact with ASN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 3.8 17.8 - - - -
143F ILE* 3.3 24.5 + - - +
144F ASN* 3.2 13.0 + - - +
146F ALA* 1.3 79.0 - - - +
148F LEU* 1.3 55.3 + - - +
150F GLU* 3.1 28.7 + - - +
151F ALA* 3.0 27.1 + - - +
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Residues in contact with LEU 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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55F ALA* 5.1 5.8 - - + +
58F ARG* 5.2 5.2 - - + -
59F LEU* 4.1 41.1 - - + +
62F VAL* 5.5 1.3 - - + -
144F ASN* 2.9 31.5 + - - +
145F ASP* 3.5 20.4 - - - +
146F ALA 3.2 0.2 - - - -
147F ASN* 1.3 72.7 - - - +
149F LEU* 1.3 66.9 + - - +
151F ALA* 3.2 12.4 + - + +
152F CYS* 3.1 27.4 + - - -
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Residues in contact with LEU 149 (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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59F LEU* 4.8 3.6 - - + -
62F VAL* 3.8 27.6 - - + -
63F LEU* 3.4 37.2 - - + -
66F ASN* 4.3 4.3 - - + -
67F ALA* 5.3 0.7 - - + -
108F LEU* 4.0 19.4 - - + +
111F ALA* 3.8 33.7 - - + +
112F PHE* 3.9 11.4 - - - +
115F VAL* 4.3 12.6 - - + -
145F ASP 3.2 10.5 + - - +
146F ALA* 3.1 8.7 + - - +
148F LEU* 1.3 76.7 - - - +
150F GLU* 1.3 62.4 + - - +
152F CYS* 3.2 19.4 + - - +
153F ILE* 3.6 8.5 + - - +
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Residues in contact with GLU 150 (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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109F LEU* 5.1 1.6 - - + -
112F PHE* 3.6 42.9 - - + +
146F ALA 3.3 2.4 + - - -
147F ASN* 3.1 32.0 + - - +
149F LEU* 1.3 78.3 - - - +
151F ALA* 1.3 62.6 + - - +
153F ILE* 3.1 32.6 + - + +
154F TYR* 3.5 21.3 + - + +
175F LEU* 5.7 2.6 - - - +
178F SER* 4.6 10.9 + - - -
182F GLU* 4.6 4.2 - - - +
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Residues in contact with ALA 151 (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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147F ASN 3.0 12.3 + - - +
148F LEU* 3.2 18.6 + - + +
150F GLU* 1.3 77.1 - - - +
152F CYS* 1.3 62.2 + - - +
154F TYR* 3.1 20.3 + - - +
155F ARG* 3.2 20.0 + - + +
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Residues in contact with CYS 152 (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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42F LEU* 3.9 22.0 - - + -
59F LEU* 3.7 35.7 - - - -
63F LEU* 4.9 3.4 - - - -
108F LEU* 3.8 17.9 - - + -
148F LEU* 3.1 19.5 + - - -
149F LEU* 3.4 12.3 - - - +
150F GLU 3.1 0.4 - - - -
151F ALA* 1.3 75.8 - - - +
153F ILE* 1.3 63.5 + - - +
155F ARG* 3.7 10.7 - - - +
156F LEU* 3.0 27.4 + - - +
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Residues in contact with ILE 153 (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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105F CYS* 3.6 33.2 - - + +
108F LEU* 3.9 13.0 - - + +
109F LEU* 3.7 45.5 - - + +
149F LEU 4.0 0.7 - - - +
150F GLU* 3.1 25.1 + - + +
152F CYS* 1.3 79.8 - - - +
154F TYR* 1.3 70.7 + - + +
156F LEU 3.2 0.5 + - - -
157F LEU* 2.9 35.6 + - + +
174F PHE* 3.8 28.7 - - + -
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Residues in contact with TYR 154 (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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150F GLU* 3.5 35.4 + - + -
151F ALA* 3.1 9.4 + - - +
153F ILE* 1.3 83.1 - - + +
155F ARG* 1.3 59.8 + - - +
157F LEU* 3.8 15.7 - - + +
158F LYS* 3.0 29.3 + - - +
167F TYR* 4.9 1.2 + - - -
171F ILE* 4.1 18.8 - - + -
174F PHE* 3.5 25.1 + - + +
175F LEU* 3.3 53.2 + - + +
178F SER* 4.2 6.1 + - - -
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Residues in contact with ARG 155 (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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41F VAL 4.8 3.2 + - - -
42F LEU* 4.0 37.2 + - + +
44F GLU* 6.0 0.2 - - - +
45F ASP* 3.3 30.5 + - - +
56F ILE* 5.8 3.2 - - - +
59F LEU* 6.2 1.8 - - - +
151F ALA* 3.2 22.8 + - + +
152F CYS* 3.7 11.0 - - - +
154F TYR* 1.3 77.8 - - + +
156F LEU* 1.3 58.0 + - - +
158F LYS* 3.4 6.9 + - - +
159F LEU* 2.9 46.5 + - + +
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Residues in contact with LEU 156 (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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38F ILE* 4.1 32.3 - - + +
41F VAL* 4.3 11.4 - - + -
42F LEU* 4.0 24.5 - - + -
101F THR* 3.9 10.1 - - + +
104F TRP* 5.0 0.2 - - + -
105F CYS* 3.7 18.8 - - - +
108F LEU* 3.6 30.7 - - + -
152F CYS 3.0 14.8 + - - +
153F ILE 3.6 3.8 - - - +
155F ARG* 1.3 73.9 - - - +
157F LEU* 1.3 65.4 + - - +
159F LEU* 3.2 2.5 + - + +
160F TYR* 3.0 52.7 + - + +
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Residues in contact with LEU 157 (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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101F THR* 5.8 0.7 - - + -
102F VAL* 4.0 27.8 - - + -
105F CYS* 4.1 11.2 - - - -
153F ILE* 2.9 28.1 + - + +
154F TYR* 3.8 18.8 - - + +
155F ARG 3.4 0.2 - - - -
156F LEU* 1.3 75.6 - - - +
158F LYS* 1.3 58.8 + - - +
161F CYS* 2.8 39.8 + - + +
167F TYR* 3.4 16.4 - - + -
170F LEU* 4.0 17.3 - - + -
171F ILE* 4.3 20.4 - - + +
174F PHE* 4.1 26.7 - - + -
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Residues in contact with LYS 158 (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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154F TYR 3.0 18.2 + - - +
155F ARG* 3.6 7.2 - - - +
157F LEU* 1.3 77.2 - - - +
159F LEU* 1.3 67.5 + - + +
160F TYR 3.3 0.2 + - - -
162F ARG* 3.1 59.4 + - - +
167F TYR* 3.6 23.0 - - - +
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Residues in contact with LEU 159 (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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41F VAL* 3.6 31.4 - - + +
42F LEU* 5.3 1.3 - - + -
44F GLU* 4.3 12.8 - - - +
155F ARG* 2.9 39.7 + - + +
156F LEU* 3.2 7.2 + - + +
158F LYS* 1.3 83.6 - - + +
160F TYR* 1.3 71.8 + - + +
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Residues in contact with TYR 160 (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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37F GLN* 3.9 18.8 + - - +
38F ILE* 5.3 3.9 - - + +
41F VAL* 3.4 34.0 - - + +
97F GLN* 3.7 39.0 - - + -
98F ARG* 3.4 30.5 + - + +
101F THR* 3.7 28.9 - - + -
156F LEU* 3.0 38.4 + - + +
159F LEU* 1.3 86.9 - - + +
161F CYS* 1.3 67.7 + - - +
162F ARG 3.8 1.1 - - - -
164F GLN* 4.7 1.9 + - - +
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Residues in contact with CYS 161 (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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98F ARG* 4.2 12.3 - - - -
101F THR* 5.8 0.7 - - - -
102F VAL* 4.0 26.5 - - - -
157F LEU* 2.8 26.4 + - - +
160F TYR* 1.3 86.4 - - - +
162F ARG* 1.3 65.9 + - - +
163F GLU 3.2 3.4 - - - -
164F GLN* 3.0 23.6 + - - +
166F TYR* 4.1 24.7 - - + -
167F TYR* 3.4 17.2 - - + +
170F LEU* 4.4 4.7 - - + -
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Residues in contact with ARG 162 (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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157F LEU 3.5 1.2 + - - -
158F LYS* 3.1 59.5 + - - +
160F TYR 3.8 0.8 - - - -
161F CYS* 1.3 77.2 - - - +
163F GLU* 1.3 75.2 + - + +
164F GLN 3.3 2.3 + - - +
167F TYR* 3.7 39.1 + - + +
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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
------------------------------------------------------------
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