Contacts of the helix formed by residues 146 - 164 (chain D) in PDB entry 4KEU
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 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D TYR 3.8 17.5 - - - +
100D ILE* 2.6 36.4 + - + +
101D ASP* 5.0 2.9 - - - -
143D PRO* 4.0 20.9 - - + +
144D GLY 3.2 2.7 + - - +
145D ILE* 1.3 75.3 - - - +
147D LYS* 1.3 59.0 + - - +
148D ASP 3.5 1.2 + - - -
149D VAL* 3.0 19.8 + - - +
150D GLU* 2.8 28.5 + - - +
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D THR* 1.3 73.5 - - - +
148D ASP* 1.3 64.0 + - - +
150D GLU* 3.3 15.1 + - - +
151D LYS* 3.1 35.0 + - - +
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Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 3.9 5.2 - - + -
100D ILE 3.5 15.3 - - - +
101D ASP* 3.4 16.6 + - - +
102D LEU* 2.8 43.3 + - + +
146D THR* 3.2 2.2 + - - -
147D LYS* 1.3 75.8 - - - +
149D VAL* 1.3 65.9 + - - +
151D LYS* 3.2 33.0 + - - +
152D VAL* 3.2 27.2 + - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE* 4.0 19.1 - - + +
99D TYR* 3.4 26.9 - - - +
100D ILE 4.1 2.0 - - - +
139D ALA 3.5 20.0 - - - +
140D ALA* 3.8 15.5 - - + -
144D GLY 4.1 3.4 - - - +
145D ILE* 4.1 9.4 - - + -
146D THR* 3.0 36.1 + - - +
148D ASP* 1.3 76.0 - - - +
150D GLU* 1.3 62.6 + - - +
152D VAL* 3.3 7.2 + - - +
153D ILE* 3.0 38.3 + - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ILE* 4.0 12.8 - - + +
146D THR 2.8 13.6 + - - +
147D LYS* 3.5 16.7 - - - +
149D VAL* 1.3 74.5 - - - +
151D LYS* 1.4 65.1 + - - +
153D ILE* 3.2 7.3 + - - +
154D ARG* 2.8 69.5 + - - +
184D ILE* 4.2 18.6 - - + +
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Residues in contact with LYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.3 12.2 - - + +
106D PHE 5.0 6.1 + - - -
107D LEU* 6.2 0.2 - - - +
108D ASN 5.6 4.2 - - - +
109D ARG 4.8 14.5 + - - +
111D ILE* 3.6 32.9 - - + +
114D ILE* 4.2 15.9 - - + +
147D LYS* 3.1 18.6 + - - +
148D ASP* 3.2 32.6 + - - +
149D VAL 3.4 0.2 - - - -
150D GLU* 1.4 75.2 - - - +
152D VAL* 1.3 58.1 + - - +
154D ARG 3.3 1.0 + - - -
155D ALA* 2.9 30.2 + - - +
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ILE* 3.8 31.2 - - + +
98D ILE* 4.0 13.0 - - + -
102D LEU* 3.8 27.6 - - + -
114D ILE* 5.0 3.6 - - + -
118D PHE* 4.2 8.9 - - + -
138D ILE* 3.7 23.8 - - + -
139D ALA 5.3 2.2 - - - +
148D ASP 3.2 16.1 + - - +
149D VAL* 3.5 7.2 - - - +
150D GLU 3.2 0.4 - - - -
151D LYS* 1.3 76.6 - - - +
153D ILE* 1.3 64.3 + - + +
155D ALA* 3.2 7.5 + - - +
156D ALA* 2.9 22.3 + - - +
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Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 4.1 21.1 - - + -
139D ALA 5.2 0.2 - - - +
145D ILE* 4.1 13.9 - - + -
149D VAL* 3.0 32.6 + - + +
150D GLU* 3.2 11.4 + - - +
152D VAL* 1.3 77.2 - - + +
154D ARG* 1.3 60.5 + - - +
156D ALA* 3.3 5.9 + - - +
157D ALA* 3.2 16.8 + - - +
181D GLN* 4.0 26.5 - - + +
184D ILE* 3.6 29.4 - - + -
185D LEU* 3.4 31.8 - - + +
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 3.9 29.6 - - + -
150D GLU* 2.8 54.1 + - - +
151D LYS 3.8 4.0 - - - +
153D ILE* 1.3 73.0 - - - +
155D ALA* 1.3 64.0 + - - +
157D ALA* 3.2 10.3 + - - +
158D ILE* 3.2 25.2 + - + +
183D ARG* 5.6 2.0 - - - +
184D ILE* 4.0 25.8 + - + +
187D GLU* 5.2 9.5 + - - +
188D GLU* 2.4 53.3 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 3.5 27.1 - - + +
114D ILE* 3.7 17.7 - - + -
115D ALA* 3.4 24.9 - - - +
118D PHE* 3.8 5.7 - - + -
151D LYS 2.9 16.8 + - - +
152D VAL 3.6 4.7 - - - +
154D ARG* 1.3 76.5 - - - +
156D ALA* 1.3 61.6 + - - +
158D ILE* 3.3 1.3 + - - -
159D ALA* 3.1 21.1 + - - +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D PHE* 3.9 4.2 - - + -
136D VAL* 3.6 21.5 - - + +
138D ILE* 3.5 31.6 - - + -
152D VAL 2.9 5.6 + - - +
153D ILE* 3.5 9.2 - - - +
155D ALA* 1.3 77.6 - - - +
157D ALA* 1.3 56.2 + - - +
159D ALA* 3.3 3.5 + - - +
160D ASN* 3.0 23.4 + - - +
167D ILE* 3.5 23.7 - - + +
185D LEU* 4.5 2.2 - - + -
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Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE 3.2 12.3 + - - +
154D ARG 3.3 9.9 - - - +
156D ALA* 1.3 74.8 - - - +
158D ILE* 1.3 64.9 + - - +
160D ASN* 3.2 3.5 + - - +
161D LYS* 3.0 32.4 + - - +
167D ILE* 4.4 0.7 - - - -
185D LEU* 4.2 4.4 - - + +
188D GLU* 3.4 33.2 - - + -
190D VAL* 3.7 22.6 - - + +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE* 3.9 19.1 - - + -
112D ASP* 3.5 26.5 - - - +
115D ALA* 3.8 19.3 - - + -
119D ILE* 4.6 4.7 - - + -
154D ARG* 3.2 14.3 + - + +
155D ALA 3.3 6.3 + - - +
157D ALA* 1.3 75.6 - - - +
159D ALA* 1.3 62.9 + - - +
161D LYS* 3.4 16.5 + - + +
162D GLU* 3.1 36.1 + - + +
188D GLU* 5.6 4.0 - - - +
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ALA* 4.5 1.3 - - - +
118D PHE* 3.7 28.0 - - + -
119D ILE* 4.2 15.0 - - + -
122D ILE* 4.1 6.3 - - + -
136D VAL* 4.0 12.8 - - + -
155D ALA 3.1 13.8 + - - +
156D ALA 3.6 8.3 - - - +
157D ALA 3.2 0.2 - - - -
158D ILE* 1.3 76.9 - - - +
160D ASN* 1.3 53.6 + - - +
162D GLU 3.6 0.3 + - - -
163D THR* 2.6 40.6 + - - +
165D VAL* 4.9 0.7 - - - -
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Residues in contact with ASN 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D VAL* 5.2 0.2 - - - +
156D ALA 3.0 13.0 + - - +
157D ALA 3.2 7.2 + - - +
159D ALA* 1.3 75.6 - - - +
161D LYS* 1.3 65.0 + - - +
163D THR* 4.4 0.2 - - - -
164D LYS* 2.5 42.0 + - - +
165D VAL* 2.4 42.3 + - - +
166D PRO* 4.2 1.2 - - - +
167D ILE* 4.0 12.5 - - + +
189D GLY 5.0 0.5 - - - +
190D VAL* 3.7 30.4 - - + +
191D ASP* 4.5 2.6 + - - +
194D LYS* 4.2 17.3 - - - +
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ALA* 3.0 32.6 + - - +
158D ILE* 3.8 14.3 - - - +
160D ASN* 1.3 80.6 - - - +
162D GLU* 1.3 62.1 + - + +
164D LYS* 2.9 27.7 + - - +
188D GLU* 2.4 40.6 + - - +
189D GLY* 4.0 16.8 - - - +
190D VAL 5.4 0.2 - - - +
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 3.9 24.2 - - + -
123D LYS* 4.3 20.2 + - - +
158D ILE* 3.1 24.2 + - + +
159D ALA 4.0 3.6 - - - +
161D LYS* 1.3 85.8 - - + +
163D THR* 1.3 64.4 + - + +
164D LYS* 3.8 9.6 + - - +
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Residues in contact with THR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 5.2 1.7 + - - -
119D ILE* 4.7 6.5 - - + -
122D ILE* 3.4 34.1 - - + +
123D LYS* 3.8 26.9 - - + +
159D ALA 2.6 22.4 + - - +
162D GLU* 1.3 84.0 - - + +
164D LYS* 1.3 71.0 + - - +
165D VAL* 3.1 28.5 + - - +
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Residues in contact with LYS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 4.0 19.9 + - - +
160D ASN* 2.5 27.2 + - - +
161D LYS* 2.9 24.4 + - - +
162D GLU* 3.8 8.8 + - - +
163D THR* 1.3 77.2 + - - +
165D VAL* 1.3 61.1 + - - +
194D LYS* 3.0 29.9 + - - +
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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