Contacts of the helix formed by residues 150 - 169 (chain D) in PDB entry 4K71
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 TYR 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR 3.1 3.2 + - - -
149D PHE* 1.3 73.6 - - - +
151D ALA* 1.3 66.1 + - - +
152D PRO* 3.7 16.6 - - + -
153D GLU* 3.1 44.9 + - + +
154D LEU 3.1 9.9 + - - -
192D SER* 5.3 1.0 + - - +
196D GLN* 3.5 41.6 - - + +
238D LEU* 5.1 2.4 - - - +
241D VAL* 3.4 12.7 - - + +
242D HIS* 3.5 27.2 + + - -
245D CYS* 3.8 18.4 - - + -
253D CYS* 4.1 3.4 - - - -
257D ARG* 3.1 50.7 + - - +
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 3.7 22.0 - - + -
25D ILE* 4.0 9.8 - - + +
149D PHE 3.0 8.2 + - - +
150D TYR* 1.3 71.5 - - - +
152D PRO* 1.4 70.4 - - + +
154D LEU* 3.1 17.8 + - - +
155D LEU* 3.2 15.8 + - - +
245D CYS* 4.3 4.4 - - - -
250D LEU* 3.8 35.6 - - + +
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Residues in contact with PRO 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.5 0.4 - - + -
150D TYR* 3.4 23.8 - - + -
151D ALA* 1.4 93.0 - - + +
153D GLU* 1.3 60.5 + - - +
155D LEU* 3.3 25.4 + - + +
156D PHE* 3.4 9.4 + - - +
245D CYS* 3.9 2.9 - - - -
253D CYS* 4.2 12.8 - - - -
254D ALA* 4.2 19.3 - - + -
257D ARG* 3.6 41.5 + - + +
284D LEU* 4.9 3.5 - - - +
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Residues in contact with GLU 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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172A ALA* 5.9 0.3 - - - +
149D PHE* 4.5 2.2 - - + -
150D TYR* 3.1 34.2 + - + +
152D PRO* 1.3 77.3 - - - +
154D LEU* 1.3 58.8 + - - +
156D PHE* 2.8 24.6 + - + +
157D PHE* 3.0 31.3 + - + -
192D SER* 2.7 32.0 + - - +
257D ARG* 4.3 9.3 - - - +
288D HIS* 4.9 14.5 + - + +
292D GLU* 4.4 12.3 - - - +
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Residues in contact with LEU 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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25D ILE* 3.9 16.4 - - + -
139D LEU* 3.3 28.1 - - + +
142D ILE* 3.9 28.7 - - + -
143D ALA* 3.9 30.5 - - + +
149D PHE* 3.8 36.0 - - + -
150D TYR 3.1 7.3 + - - +
151D ALA* 3.1 10.3 + - - +
153D GLU* 1.3 74.5 - - - +
155D LEU* 1.3 55.9 + - - +
157D PHE* 3.2 11.2 + - + +
158D ALA* 3.0 28.5 + - - +
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Residues in contact with LEU 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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18D ASN* 4.2 22.4 - - + +
21D ALA* 3.3 34.3 - - + -
22D LEU* 3.7 31.6 - - + -
25D ILE* 4.0 13.9 - - + -
139D LEU* 4.8 3.8 - - + -
151D ALA 3.2 10.8 + - - +
152D PRO* 3.4 15.7 - - + +
153D GLU 3.2 0.4 - - - -
154D LEU* 1.3 77.9 - - - +
156D PHE* 1.3 58.2 + - - +
158D ALA* 3.3 20.0 - - + +
159D LYS 3.5 4.2 + - - -
254D ALA* 5.3 2.2 - - + -
284D LEU* 3.9 25.4 - - + +
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Residues in contact with PHE 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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172A ALA* 3.4 19.1 - - + -
152D PRO 3.4 5.5 + - - +
153D GLU* 2.8 16.7 + - + +
155D LEU* 1.3 76.0 - - - +
157D PHE* 1.3 65.5 + + + +
159D LYS* 3.0 27.4 + - + +
160D ARG* 3.5 38.0 + - + +
257D ARG* 6.3 0.7 - - - +
284D LEU* 4.2 25.0 - - + +
285D GLU* 4.1 23.8 - - + -
288D HIS* 3.3 64.4 - + + +
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Residues in contact with PHE 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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172A ALA* 3.8 22.4 - - + -
142D ILE* 5.6 1.6 - - + -
149D PHE* 4.0 20.2 - + - -
153D GLU* 3.0 39.2 + - + -
154D LEU* 3.2 14.6 + - + +
156D PHE* 1.3 76.8 - - + +
158D ALA* 1.3 63.0 - - - +
160D ARG* 2.9 20.3 + - - +
161D TYR* 3.0 34.2 + + + -
185D LEU* 3.5 30.3 - - + -
188D GLU* 3.9 13.7 - - + -
189D GLY* 3.5 37.5 - - - -
192D SER* 4.4 3.6 - - - -
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Residues in contact with ALA 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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135D LEU* 5.1 4.1 - - + +
139D LEU* 4.5 21.7 - - + +
154D LEU* 3.0 12.0 + - - +
155D LEU* 3.3 16.8 - - + +
157D PHE* 1.3 75.2 - - - +
159D LYS* 1.3 63.4 + - - +
161D TYR* 3.4 10.4 + - - +
162D LYS* 3.1 23.6 + - - +
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Residues in contact with LYS 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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155D LEU 3.5 6.2 + - - +
156D PHE* 3.0 26.7 + - + +
158D ALA* 1.3 79.3 - - - +
160D ARG* 1.3 83.3 + - - +
162D LYS* 3.5 10.0 + - + +
163D ALA* 3.0 30.3 + - - +
284D LEU* 4.5 11.9 - - + -
285D GLU* 2.8 40.0 + - - +
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Residues in contact with ARG 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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170A GLN* 3.3 40.2 + - - +
171A ALA 2.8 23.3 + - - +
172A ALA* 3.6 18.1 + - - -
174A LYS* 3.8 28.5 - - - +
156D PHE* 3.5 41.1 + - + +
157D PHE* 2.9 8.6 + - - +
159D LYS* 1.3 98.2 - - + +
161D TYR* 1.3 56.4 + - - +
163D ALA* 3.3 4.4 + - - +
164D ALA* 2.7 36.0 + - - +
185D LEU* 3.9 14.5 - - + +
288D HIS* 4.9 1.2 + - - -
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Residues in contact with TYR 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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135D LEU* 4.3 10.3 - - + -
138D TYR* 3.3 38.8 - + + -
142D ILE* 3.3 35.8 - - + +
157D PHE* 3.0 42.6 + + + -
158D ALA* 3.8 10.3 - - - +
160D ARG* 1.3 74.6 - - - +
162D LYS* 1.3 64.7 + - - +
164D ALA* 3.1 3.9 + - - -
165D PHE* 2.9 34.7 + + + -
182D LEU* 3.7 29.2 + - + -
185D LEU* 3.5 41.0 + - + +
186D ARG* 3.9 5.9 + - - +
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Residues in contact with LYS 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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17D GLU* 5.6 3.8 + - - -
127D PHE* 4.2 1.9 - - + -
131D GLU* 3.7 19.1 + - - +
135D LEU* 3.8 34.6 - - + +
158D ALA 3.1 14.7 + - - +
159D LYS* 3.6 12.1 - - + +
161D TYR* 1.3 76.9 - - - +
163D ALA* 1.3 52.6 + - - +
165D PHE* 3.3 1.4 + - - +
166D THR* 2.7 49.1 + - - +
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Residues in contact with ALA 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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170A GLN* 3.4 32.2 + - - +
159D LYS* 3.0 22.0 + - + +
160D ARG* 3.6 4.0 - - - +
162D LYS* 1.3 76.4 - - - +
164D ALA* 1.3 58.0 + - - +
166D THR* 3.3 6.1 + - - -
167D GLU* 2.8 32.1 + - - +
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Residues in contact with ALA 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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170A GLN* 4.5 9.6 - - + -
160D ARG 2.7 21.3 + - - +
161D TYR* 3.1 6.7 + - - +
163D ALA* 1.3 74.2 - - - +
165D PHE* 1.3 56.4 + - - +
167D GLU* 4.0 1.5 - - - +
168D CYS* 3.0 36.0 + - - +
178D LEU* 4.3 9.2 - - + -
181D LYS* 4.0 33.9 - - + -
182D LEU* 4.9 5.8 - - + -
185D LEU* 4.9 3.4 - - + -
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Residues in contact with PHE 165 (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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123D MET* 4.1 13.2 - - + -
127D PHE* 3.5 28.9 - - + -
134D PHE* 3.5 42.6 - + - -
135D LEU* 4.8 3.1 - - + -
138D TYR* 3.9 15.0 - + - -
161D TYR* 2.9 34.9 + + + +
164D ALA* 1.3 74.4 - - - +
166D THR* 1.3 65.0 + - - +
169D CYS* 3.0 48.6 + - - +
178D LEU* 3.8 20.4 - - + -
182D LEU* 3.7 39.3 - - + -
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Residues in contact with THR 166 (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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127D PHE* 3.5 20.0 - - + -
131D GLU* 4.4 3.5 + - - +
162D LYS* 2.7 38.8 + - - +
163D ALA* 3.6 6.9 - - - -
165D PHE* 1.3 73.5 - - - +
167D GLU* 1.3 62.9 + - - +
169D CYS* 5.0 0.5 - - - +
170D GLN* 3.5 28.6 + - - +
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Residues in contact with GLU 167 (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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127A PHE* 5.6 5.9 - - - -
128A HIS* 3.4 40.4 - - + +
131A GLU* 5.6 1.4 - - - +
169A CYS* 6.0 0.9 - - - +
170A GLN* 3.8 18.7 + - - +
163D ALA 2.8 20.7 + - - +
164D ALA* 4.0 2.7 - - - +
166D THR* 1.3 75.7 - - - +
168D CYS* 1.3 64.5 + - - +
170D GLN* 3.4 23.3 + - - +
171D ALA* 3.9 4.5 + - - +
177D CYS* 4.4 15.5 - - - -
181D LYS* 3.8 18.8 + - - -
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Residues in contact with CYS 168 (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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124D CYS* 5.0 0.2 - - - -
164D ALA 3.0 21.1 + - - +
165D PHE 4.7 0.2 - - - +
167D GLU* 1.3 77.0 - - - +
169D CYS* 1.3 60.4 + - - +
171D ALA* 3.1 23.8 + - - +
174D LYS* 3.7 13.7 - - - +
177D CYS* 2.1 64.4 - - + -
178D LEU* 3.5 21.1 - - + -
181D LYS* 3.6 14.8 - - - -
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Residues in contact with CYS 169 (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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124D CYS* 2.0 58.3 - - + +
127D PHE* 4.1 11.7 - - + -
165D PHE* 3.0 41.2 + - - +
166D THR 5.2 0.7 - - - +
168D CYS* 1.3 76.7 - - - +
170D GLN* 1.3 57.9 + - - +
171D ALA 3.4 0.6 - - - +
174D LYS* 4.3 14.4 - - - +
178D LEU* 5.0 1.8 - - - -
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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
------------------------------------------------------------
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