Contacts of the helix formed by residues 153 - 174 (chain D) in PDB entry 4LQL
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 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D GLY* 4.1 3.8 - - - -
150D TRP* 2.8 38.3 + - - +
152D GLY* 1.3 85.8 - - - +
154D ALA* 1.3 68.3 + - - +
155D ASP 3.4 2.2 - - - +
156D VAL* 3.4 23.9 + - + +
157D GLN* 3.7 11.4 + - - +
337F LEU* 5.3 3.9 - - - +
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Residues in contact with ALA 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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153D ASP* 1.3 76.4 - - - +
155D ASP* 1.3 60.0 + - + +
156D VAL 3.4 1.4 + - - -
157D GLN* 5.2 0.2 - - - +
158D GLU* 3.2 26.2 + - - +
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Residues in contact with ASP 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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147D VAL* 5.8 0.3 - - - +
153D ASP* 4.4 2.7 - - - +
154D ALA* 1.3 78.4 - - + +
156D VAL* 1.3 57.0 + - - +
157D GLN 3.7 0.4 - - - -
158D GLU* 4.1 9.4 - - + -
159D GLN* 3.2 28.5 - - + +
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Residues in contact with VAL 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D VAL* 4.1 11.7 - - + +
148D TYR 5.1 10.5 - - - +
149D GLY* 5.1 1.6 - - - -
150D TRP 3.5 14.8 - - - +
151D TRP* 5.0 2.2 - - - -
152D GLY 4.7 0.7 - - - +
153D ASP* 3.4 34.1 + - + +
154D ALA 3.2 1.6 - - - -
155D ASP* 1.3 78.9 - - - +
157D GLN* 1.3 65.0 + - - +
159D GLN* 5.0 1.1 - - - -
160D ILE* 3.1 27.3 - - - +
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Residues in contact with GLN 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 4.1 26.0 - - + -
42D GLY* 4.8 16.9 - - - +
44D LEU* 3.6 5.7 - - + +
151D TRP* 4.4 8.3 - - + -
152D GLY* 4.4 18.8 - - - +
153D ASP 3.7 9.9 + - - +
154D ALA 5.2 0.2 - - - +
156D VAL* 1.3 83.6 - - - +
158D GLU* 1.3 53.2 + - - +
159D GLN 3.5 0.4 - - - -
160D ILE* 3.5 12.9 + - + +
161D ALA* 2.7 31.7 + - - +
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Residues in contact with GLU 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 ALA 3.2 21.8 + - - +
155D ASP* 4.1 6.7 - - + -
157D GLN* 1.3 75.2 - - - +
159D GLN* 1.3 60.1 + - + +
161D ALA* 2.6 32.8 + - + +
162D ASP* 2.8 25.4 + - - +
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Residues in contact with GLN 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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147D VAL* 4.8 17.3 - - + -
155D ASP* 3.2 34.7 - - + +
156D VAL 5.0 2.5 - - - -
158D GLU* 1.3 81.2 + - + +
160D ILE* 1.3 61.2 + - - +
162D ASP* 3.3 28.8 + - - +
163D TRP* 3.4 6.3 + - - +
461D GLN* 5.5 1.0 - - - +
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Residues in contact with ILE 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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38D LEU* 5.0 16.2 - - + -
44D LEU* 4.0 22.4 - - + -
77D ILE* 6.0 3.4 - - + -
101D LEU* 5.3 13.5 - - + -
103D LEU* 5.4 10.1 - - + -
147D VAL* 4.3 22.7 - - + -
151D TRP* 5.8 4.0 - - + -
156D VAL 3.1 26.0 - - - +
157D GLN* 3.5 16.4 + - + +
158D GLU 3.1 0.4 - - - -
159D GLN* 1.3 73.2 - - - +
161D ALA* 1.3 65.4 + - - +
163D TRP* 3.3 22.1 + - + +
164D GLN* 3.3 18.2 + - + +
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Residues in contact with ALA 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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42D GLY 5.3 0.7 - - - +
43D LYS 3.6 22.4 - - - +
44D LEU* 3.7 11.4 - - + +
45D ASP* 3.7 24.2 - - - +
157D GLN 2.7 14.5 + - - +
158D GLU* 2.6 29.8 + - - +
160D ILE* 1.3 73.9 - - - +
162D ASP* 1.3 53.9 + - + +
163D TRP 3.2 4.2 + - - -
164D GLN* 3.9 2.8 + - - +
165D HIS* 4.3 2.3 + - - +
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Residues in contact with ASP 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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158D GLU* 2.8 30.8 + - - +
159D GLN* 3.4 15.3 - - - +
161D ALA* 1.3 75.2 - - - +
163D TRP* 1.3 59.4 + - - +
165D HIS* 4.6 10.5 - - - -
166D VAL* 4.7 5.4 - - - +
455D SER* 5.9 0.7 - - - -
458D GLN* 3.6 36.5 - - + +
461D GLN* 4.4 3.1 - - - +
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Residues in contact with TRP 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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9D PHE* 5.2 8.5 - + - -
75D GLY* 5.0 0.4 - - - -
76D VAL 4.3 10.1 - - - -
77D ILE* 4.2 16.4 - - + -
99D PRO* 4.0 19.5 - - + -
100D LEU 4.3 12.6 - - - -
101D LEU* 3.9 34.1 - - + -
145D ALA* 3.7 8.7 - - + +
147D VAL* 6.3 1.3 - - + -
159D GLN 3.6 11.9 - - - +
160D ILE* 3.3 13.2 + - + +
161D ALA 3.1 1.4 + - - -
162D ASP* 1.3 80.4 - - - +
164D GLN* 1.3 80.0 - - + +
165D HIS 2.9 2.5 + - - +
166D VAL* 3.3 13.7 + - + +
167D ALA* 3.3 43.0 + - + +
461D GLN* 3.1 38.9 - - + +
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Residues in contact with GLN 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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9D PHE* 4.6 13.2 - - + -
44D LEU* 4.3 13.2 - - + -
45D ASP* 3.7 29.8 - - + +
46D TYR* 4.1 31.4 - - + +
48D VAL* 6.1 0.4 - - + -
74D ALA* 5.0 0.2 - - - +
160D ILE* 3.3 18.3 + - + +
163D TRP* 1.3 85.9 - - + +
165D HIS* 1.3 62.9 + - - +
167D ALA* 3.7 2.3 + - - +
168D VAL* 3.2 29.7 + - - +
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Residues in contact with HIS 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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4D MET* 5.4 3.4 - - + -
45D ASP* 4.4 12.5 - - - -
161D ALA 4.3 6.6 + - - +
162D ASP* 4.6 5.6 - - - -
163D TRP 2.9 8.6 - - - +
164D GLN* 1.3 75.2 - - - +
166D VAL* 1.3 71.8 + - + +
168D VAL* 3.2 10.5 - - - +
169D ALA* 3.0 17.0 + - - +
321D ALA* 3.1 44.2 - - + +
323D ASP* 4.9 10.5 - - - -
324D ASN* 5.5 7.0 - - + -
454D LEU* 5.5 0.7 - - + -
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Residues in contact with VAL 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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162D ASP 4.7 10.5 - - - +
163D TRP* 3.3 15.7 + - + +
165D HIS* 1.3 80.5 - - + +
167D ALA* 1.3 55.3 + - - +
169D ALA* 2.2 40.5 + - - +
170D TYR* 3.0 7.8 + - - -
321D ALA* 4.7 6.3 - - + -
454D LEU* 6.0 4.7 - - + -
458D GLN* 3.3 28.5 - - + +
459D LEU* 5.4 0.4 - - - -
461D GLN* 5.3 2.7 - - + +
462D LEU* 3.9 28.3 - - + +
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Residues in contact with ALA 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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74D ALA* 3.6 21.9 - - + +
75D GLY 4.7 0.2 - - - +
99D PRO* 3.9 18.5 - - + +
163D TRP* 3.3 46.3 + - + +
164D GLN 3.9 3.1 - - - +
166D VAL* 1.3 74.3 - - - +
168D VAL* 1.3 65.2 - - - +
170D TYR* 3.0 16.8 + - - +
171D ASN* 3.2 9.9 + - - -
465D LEU* 6.5 0.4 - - - -
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Residues in contact with VAL 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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3D LYS* 5.4 2.7 - - + -
4D MET* 3.6 26.2 - - + -
7D TYR* 3.5 38.2 - - + -
46D TYR* 4.2 11.2 - - + -
74D ALA* 3.6 26.0 + - + -
164D GLN 3.2 13.4 + - - +
165D HIS 3.2 10.8 - - - +
166D VAL 2.7 2.6 + - - -
167D ALA* 1.3 76.3 - - - +
169D ALA* 1.3 62.2 + - - +
170D TYR 2.9 0.9 + - - -
171D ASN* 3.1 6.7 + - - +
172D GLU* 2.7 29.2 + - + +
320D ILE 4.7 4.7 - - - +
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Residues in contact with ALA 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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165D HIS 3.0 11.4 + - - +
166D VAL* 2.2 24.6 + - - +
168D VAL* 1.3 70.6 - - - +
170D TYR* 1.3 55.0 + - - -
172D GLU* 3.7 10.3 - - - +
173D SER* 2.9 34.3 + - - +
317D LEU* 4.3 13.4 - - + +
320D ILE* 4.3 11.0 - - + +
321D ALA* 3.8 21.5 - - + -
462D LEU* 4.9 8.9 - - + +
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Residues in contact with TYR 170 (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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99D PRO* 5.1 9.6 - - + -
166D VAL 3.0 6.1 + - - +
167D ALA* 3.5 13.2 - - - +
168D VAL 2.9 0.4 + - - -
169D ALA* 1.3 74.7 - - - +
171D ASN* 1.3 68.8 + - - +
172D GLU 3.2 0.6 + - - -
173D SER* 3.6 9.6 + - - -
174D PHE* 3.8 15.2 + + - -
462D LEU* 4.7 12.9 - - + +
465D LEU* 4.6 22.0 - - + -
466D PHE* 4.7 22.2 - + + -
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Residues in contact with ASN 171 (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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7D TYR* 3.1 25.1 - - + +
71D ASP 5.7 0.4 - - - -
73D VAL 4.0 11.2 - - - -
74D ALA 3.2 26.9 - - - -
98D LYS* 4.8 17.5 - - - -
99D PRO* 4.9 4.5 - - - -
167D ALA 3.2 2.4 + - - -
168D VAL 3.1 5.5 + - - +
170D TYR* 1.3 79.1 - - - +
172D GLU* 1.3 62.7 + - - +
174D PHE* 3.4 18.0 + - - +
175D HIS* 3.9 9.9 + - - +
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Residues in contact with GLU 172 (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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3D LYS* 4.6 17.0 - - + -
7D TYR* 4.4 12.8 - - + -
168D VAL* 2.7 23.6 + - + +
169D ALA* 4.0 9.0 - - - -
171D ASN* 1.3 71.5 - - - +
173D SER* 1.3 55.3 + - - +
175D HIS* 2.7 49.4 + - + +
176D ILE* 5.4 0.3 - - - +
316D ARG* 5.1 8.5 - - - +
320D ILE* 4.6 22.0 - - + -
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Residues in contact with SER 173 (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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169D ALA* 2.9 27.4 + - - +
170D TYR* 4.2 4.9 - - - -
171D ASN 3.5 0.6 - - - -
172D GLU* 1.3 67.0 - - - +
174D PHE* 1.3 53.8 + - - +
175D HIS 2.6 16.6 + - - -
176D ILE* 2.7 30.3 + - - +
202D LEU* 4.0 16.4 - - - -
204D TRP* 4.0 7.9 - - - -
313D GLY 6.0 0.2 - - - -
317D LEU* 3.1 32.8 - - - +
466D PHE* 5.6 7.4 - - - -
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Residues in contact with PHE 174 (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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91C ARG* 4.5 19.8 - - + +
170D TYR* 3.8 12.1 + + - -
171D ASN* 3.4 10.7 + - - +
172D GLU 3.2 1.0 + - - -
173D SER* 1.3 73.2 - - - +
175D HIS* 1.3 74.1 + - + +
176D ILE 3.6 1.1 - - - -
202D LEU 4.6 1.1 - - - -
203D GLY* 3.5 37.8 - - - +
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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
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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