Contacts of the helix formed by residues 142 - 162 (chain D) in PDB entry 4EJJ
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 LYS 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D ARG* 5.2 23.4 + - - +
139D GLY* 3.2 15.9 + - - +
140D VAL 5.0 4.9 - - - +
141D GLY* 1.3 85.0 - - - +
143D ARG* 1.3 70.5 + - + +
144D GLY 3.0 5.7 + - - +
145D ILE* 3.3 10.9 + - - +
146D GLU* 3.3 11.3 + - - +
447D MET* 4.0 5.4 - - - +
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Residues in contact with ARG 143 (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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142D LYS* 1.3 73.0 - - + +
144D GLY* 1.3 68.4 + - - +
146D GLU* 2.9 40.1 + - - +
147D GLU* 3.2 47.6 + - - +
150D GLN* 4.0 14.6 + - - +
342D LYS* 5.6 7.5 - - - +
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Residues in contact with GLY 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE 5.0 2.2 - - - -
139D GLY* 4.3 11.7 - - - -
142D LYS* 3.0 5.7 + - - +
143D ARG* 1.3 79.7 - - - +
145D ILE* 1.3 61.7 + - - +
147D GLU* 3.7 17.4 - - - +
148D ARG* 3.8 5.5 + - - +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D PHE 3.9 15.0 - - - +
139D GLY 3.3 20.8 + - - +
140D VAL* 3.9 9.4 - - + -
141D GLY 4.3 1.1 - - - +
142D LYS 3.3 4.4 + - - +
144D GLY* 1.3 72.3 - - - +
146D GLU* 1.3 61.6 + - - +
147D GLU 3.2 2.2 - - - -
148D ARG* 3.3 21.5 + - + +
149D ILE* 3.0 33.4 + - + +
181D VAL* 4.0 18.6 - - + -
184D SER* 5.3 0.2 - - - +
185D ILE* 3.6 31.2 - - + -
444D LEU* 3.8 24.2 - - + -
447D MET* 4.1 16.2 - - - -
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LYS 3.3 11.3 + - - +
143D ARG* 2.9 40.4 + - - +
145D ILE* 1.3 77.6 - - - +
147D GLU* 1.3 56.5 + - - +
149D ILE* 3.2 7.7 + - - +
150D GLN* 2.9 43.9 + - - +
342D LYS* 3.4 14.5 - - - +
343D PHE* 2.8 37.7 + - + +
344D GLU* 4.6 2.8 + - - +
447D MET* 4.0 15.3 - - + -
451D LEU* 4.4 11.0 - - + -
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ARG* 3.2 42.2 + - - +
144D GLY* 3.7 12.8 - - - +
146D GLU* 1.3 75.2 - - - +
148D ARG* 1.3 61.9 + - - +
150D GLN* 3.3 10.8 + - - +
151D GLU* 2.9 28.6 + - - +
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Residues in contact with ARG 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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144D GLY 3.8 3.1 + - - +
145D ILE* 3.3 31.5 + - + +
147D GLU* 1.3 79.0 - - - +
149D ILE* 1.3 62.8 + - - +
151D GLU* 2.3 44.3 + - - +
152D GLU* 3.0 53.6 + - - +
180D ASN 3.8 15.8 + - - -
181D VAL* 4.3 14.8 - - + -
184D SER* 3.1 28.7 + - - +
190D ARG* 4.3 12.7 - - - +
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Residues in contact with ILE 149 (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* 3.0 22.9 + - + +
146D GLU 3.2 7.4 + - - +
148D ARG* 1.3 74.6 - - - +
150D GLN* 1.3 61.4 + - - +
152D GLU 3.5 0.2 + - - -
153D ALA* 2.9 25.6 + - - +
181D VAL* 4.1 20.4 - - + -
444D LEU* 4.8 1.3 - - + +
447D MET* 3.6 36.3 - - + +
448D GLU* 3.9 31.0 - - + +
451D LEU* 3.4 33.9 - - + -
452D PHE* 3.8 12.8 - - + -
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Residues in contact with GLN 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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143D ARG* 4.0 12.2 + - - +
146D GLU* 2.9 31.4 + - - +
147D GLU* 3.5 16.2 - - - +
148D ARG 3.3 0.2 - - - -
149D ILE* 1.3 75.0 - - - +
151D GLU* 1.3 66.2 + - - +
153D ALA* 3.1 8.0 + - - +
154D GLY* 2.8 20.6 + - - -
340D GLN* 3.5 36.6 + - + +
341D PRO* 3.2 27.1 + - + +
342D LYS* 4.1 16.4 - - - +
451D LEU* 4.4 8.7 - - + -
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Residues in contact with GLU 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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147D GLU 2.9 16.7 + - - +
148D ARG* 2.3 37.7 + - - +
150D GLN* 1.3 78.5 - - - +
152D GLU* 1.3 57.9 + - - +
154D GLY* 3.2 3.7 + - - -
155D PHE* 3.1 57.3 + - + -
190D ARG* 5.7 0.4 - - - -
340D GLN* 5.0 1.8 - - - -
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Residues in contact with GLU 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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148D ARG* 3.0 41.0 + - - +
149D ILE 4.2 2.5 - - - +
151D GLU* 1.3 76.6 - - - +
153D ALA* 1.3 64.9 + - - +
155D PHE* 3.3 7.5 + - - +
156D LEU 3.0 17.0 + - - -
177D THR* 3.3 43.4 - - + +
180D ASN* 2.7 34.1 + - + -
181D VAL* 4.7 3.8 - - + -
190D ARG* 2.9 31.1 + - - -
193D TYR* 3.6 7.1 + - - +
452D PHE* 4.6 3.8 - - + -
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Residues in contact with ALA 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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149D ILE* 2.9 16.2 + - + +
150D GLN* 3.3 13.5 - - - +
152D GLU* 1.3 74.4 - - - +
154D GLY* 1.3 65.3 + - - +
156D LEU* 2.8 16.8 + - - +
157D ILE* 3.2 17.1 + - - +
340D GLN* 5.8 1.6 - - + +
451D LEU* 5.0 4.0 - - + +
452D PHE* 3.6 22.0 - - + -
455D THR* 4.0 27.6 - - + +
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Residues in contact with GLY 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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150D GLN 2.8 16.0 + - - -
151D GLU* 3.3 7.2 - - - -
153D ALA* 1.3 74.9 - - - +
155D PHE* 1.3 60.4 + - - -
156D LEU 3.0 0.2 + - - -
157D ILE* 3.2 14.2 + - - +
158D ASP* 3.2 21.9 + - - +
340D GLN* 5.2 3.3 + - - -
455D THR* 5.1 1.9 - - - +
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Residues in contact with PHE 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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151D GLU* 3.1 59.5 + - + -
152D GLU* 3.3 16.5 + - - +
154D GLY* 1.3 74.0 - - - +
156D LEU* 1.3 58.3 + - - +
158D ASP* 3.8 19.6 + - + +
159D ALA* 3.4 21.5 + - - +
190D ARG* 4.4 26.0 - - - +
193D TYR* 3.6 26.0 - - + +
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Residues in contact with LEU 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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152D GLU 3.0 8.7 + - - +
153D ALA* 2.8 18.7 + - - +
155D PHE* 1.3 70.2 - - - +
157D ILE* 1.3 58.4 + - + +
159D ALA* 3.5 8.0 + - + +
160D LEU* 3.1 52.2 + - + +
173D PHE* 3.7 22.7 - - + +
174D LEU* 4.3 16.6 - - + +
177D THR* 3.3 33.4 - - + +
193D TYR* 4.0 3.8 + - + +
452D PHE* 5.0 11.4 - - + +
456D VAL* 3.6 28.0 - - + -
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Residues in contact with ILE 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 ALA 3.2 12.0 + - - +
154D GLY* 3.2 7.3 + - - +
156D LEU* 1.3 72.2 - - + +
158D ASP* 1.3 70.9 + - - +
159D ALA 3.1 2.1 + - - -
160D LEU* 4.5 0.2 - - + -
161D ARG* 2.9 42.4 + - - +
455D THR* 3.4 44.0 - - + +
456D VAL* 4.0 14.1 - - + -
459D ASN* 3.5 26.9 - - + +
460D PHE* 3.7 26.7 - - + -
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Residues in contact with ASP 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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154D GLY* 3.2 18.3 + - - +
155D PHE* 3.8 26.0 + - + +
157D ILE* 1.3 77.7 - - - +
159D ALA* 1.3 57.1 + - - +
161D ARG* 4.1 4.8 - - - +
162D GLY* 2.9 24.9 + - - -
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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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155D PHE 3.4 17.4 + - - +
156D LEU* 3.6 9.4 - - + +
157D ILE 3.1 0.4 - - - -
158D ASP* 1.3 80.1 - - - +
160D LEU* 1.3 56.6 + - - +
162D GLY* 3.3 17.9 + - - -
163D THR* 3.6 11.8 + - - +
173D PHE* 4.7 23.1 - - + -
193D TYR* 4.3 17.9 - - + -
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Residues in contact with LEU 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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156D LEU* 3.1 50.3 + - + +
157D ILE 3.1 2.2 + - - +
159D ALA* 1.3 75.1 - - - +
161D ARG* 1.3 64.8 + - - +
163D THR* 3.2 16.4 + - - +
164D GLY 4.0 2.9 + - - -
165D GLY 4.7 3.6 + - - -
168D ILE* 4.8 6.7 - - + -
173D PHE* 4.7 16.8 - - + -
174D LEU* 6.0 3.4 - - + -
456D VAL* 3.8 25.4 - - + -
460D PHE* 3.6 33.8 - - + -
491D PHE* 3.8 41.7 - - + +
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Residues in contact with ARG 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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469B LYS* 3.8 32.2 - - - +
157D ILE* 2.9 29.0 + - - +
158D ASP* 4.1 5.5 - - - +
160D LEU* 1.3 73.0 - - - +
162D GLY* 1.3 52.2 + - - +
163D THR 2.6 15.3 + - - -
164D GLY* 2.7 19.5 + - - -
337D LYS* 5.8 6.1 - - - +
459D ASN* 3.2 32.9 + - - +
460D PHE* 3.5 11.2 - - + -
493D PRO* 3.8 35.8 - - + +
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Residues in contact with GLY 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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467B SER* 3.1 32.0 - - - -
468B PRO* 4.6 0.5 - - - +
469B LYS* 5.1 4.4 - - - +
158D ASP 2.9 18.9 + - - -
159D ALA* 3.3 12.9 + - - -
161D ARG* 1.3 72.1 - - - +
163D THR* 1.3 60.2 + - - +
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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