Contacts of the helix formed by residues 152 - 168 (chain D) in PDB entry 1LO5
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 VAL 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D VAL 3.9 1.2 + - - -
151D THR* 1.3 70.5 - - - +
153D GLN* 1.3 62.1 + - - +
155D LEU* 3.5 5.9 + - - +
156D ASP* 3.2 19.4 + - - +
186D PHE* 3.9 16.1 - - + -
194D VAL* 3.9 14.8 - - + -
196D TYR* 3.1 40.4 - - + +
213D TYR* 5.6 0.4 - - + -
217D LYS* 2.8 42.1 + - + +
219D ILE* 3.6 31.8 - - + +
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D TYR 4.0 6.3 - - - +
89D GLY* 2.7 30.7 - - - -
90D ALA* 2.9 12.1 + - - +
107D MET* 4.7 2.6 - - - +
108D TYR 2.9 15.4 + - - -
110D GLY* 3.3 14.5 - - - +
151D THR* 2.9 9.2 + - - +
152D VAL* 1.3 78.5 - - - +
154D GLU* 1.3 55.4 + - - +
155D LEU 3.2 0.2 + - - -
156D ASP* 3.2 1.7 + - - +
157D LEU* 2.8 36.8 + - + +
210D LEU* 5.2 0.2 - - - +
213D TYR* 2.9 65.0 - - + +
217D LYS 4.6 0.6 + - - -
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D TYR* 3.4 56.5 + - + +
144D LYS 4.6 0.3 - - - +
145D THR* 3.5 29.1 + - - -
146D ASN 4.5 1.6 + - - -
147D LYS* 3.0 35.1 + - - +
150D VAL* 3.5 13.4 - - + +
151D THR* 3.0 22.4 + - - +
153D GLN* 1.3 75.3 - - - +
155D LEU* 1.3 56.2 + - - +
157D LEU 4.3 0.4 - - - -
158D GLN* 2.7 38.3 + - - +
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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
----------------------------------------------------------
125D VAL* 3.6 19.7 - - + -
143D VAL* 3.5 30.5 - - + +
144D LYS 4.6 0.9 - - - +
145D THR* 4.0 15.9 - - + -
150D VAL* 3.3 35.2 - - + -
151D THR 4.1 2.9 - - - +
152D VAL* 3.5 1.7 + - - +
153D GLN 3.2 0.4 - - - -
154D GLU* 1.3 75.3 - - - +
156D ASP* 1.3 68.5 + - - +
158D GLN* 2.9 15.9 + - - +
159D ALA* 3.1 13.0 + - - +
186D PHE* 3.7 24.0 - - + -
219D ILE* 3.6 17.3 - - + -
224D MET* 3.7 14.4 - - + -
226D ILE* 4.9 2.9 - - + -
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D VAL 3.2 11.2 + - - +
153D GLN 3.7 0.4 - - - +
155D LEU* 1.3 74.7 - - - +
157D LEU* 1.3 65.2 + - - +
158D GLN 2.7 6.7 + - - -
159D ALA* 3.1 3.4 + - - +
160D ARG* 2.2 79.6 + - - +
184D ILE* 3.5 13.0 - - - +
186D PHE* 3.2 31.8 - - + -
196D TYR* 4.5 3.6 - - + -
213D TYR* 2.5 18.3 + - + +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.7 6.1 - - + +
30D TYR* 3.4 40.4 - - + +
35D LYS* 4.1 14.8 - - + -
88D TYR* 4.6 13.7 - - + +
89D GLY* 3.5 15.7 - - - +
90D ALA* 3.5 43.5 - - + +
153D GLN* 2.8 27.8 + - + +
154D GLU 4.6 4.5 - - - +
155D LEU 3.4 0.2 - - - -
156D ASP* 1.3 72.5 - - - +
158D GLN* 1.3 60.7 + - - +
160D ARG* 4.1 3.0 + - - +
161D ARG* 3.6 15.9 + - - +
213D TYR* 4.1 7.0 - - + +
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D TYR* 2.9 30.6 + - + +
142D THR* 4.1 8.7 - - - +
143D VAL* 3.4 16.7 - - + +
144D LYS* 2.9 42.9 + - - +
154D GLU* 2.7 27.3 + - - +
155D LEU 2.9 6.2 + - - +
156D ASP 2.7 4.6 + - - -
157D LEU* 1.3 74.3 - - - +
159D ALA* 1.3 58.0 + - - +
160D ARG 3.1 1.1 - - - -
161D ARG* 2.6 33.6 + - - +
162D TYR* 3.2 5.0 + - - +
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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
----------------------------------------------------------
127D ILE* 4.5 4.7 - - + -
143D VAL* 4.1 17.3 - - + +
155D LEU 3.1 8.4 + - - +
156D ASP* 3.1 4.4 + - - +
158D GLN* 1.3 78.5 - - - +
160D ARG* 1.3 57.9 + - - +
162D TYR* 2.8 27.3 + - - +
163D LEU* 3.1 17.0 + - - +
184D ILE* 3.9 26.5 - - + -
186D PHE* 5.7 0.9 - - + -
226D ILE* 5.1 3.6 - - + -
228D ILE* 4.3 13.9 - - + -
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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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30D TYR* 2.7 66.6 + - + +
156D ASP* 2.2 60.0 + - - +
157D LEU 4.2 1.1 - - - +
159D ALA* 1.3 76.5 - - - +
161D ARG* 1.3 58.0 + - - +
163D LEU* 4.2 9.0 - - + +
164D GLN* 4.0 15.9 + - - +
169D LEU* 5.0 0.9 - - + -
170D TYR* 3.9 24.4 + - + +
184D ILE* 4.4 1.3 - - + +
196D TYR* 3.8 22.4 - - - +
197D ASP 3.8 20.6 + - - -
198D LEU* 3.6 27.9 - - + +
212D ILE* 4.8 7.1 - - - +
213D TYR* 3.3 6.5 + - - -
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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
----------------------------------------------------------
30D TYR 3.9 16.8 - - - +
31D TYR* 3.8 40.9 + - + -
157D LEU 3.6 10.9 + - - +
158D GLN* 2.6 21.7 + - - +
160D ARG* 1.3 74.4 - - - +
162D TYR* 1.3 57.8 - - - +
164D GLN* 3.7 4.9 + - - +
165D GLU* 3.0 45.0 + - + +
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Residues in contact with TYR 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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127D ILE* 6.3 0.7 - - + -
129D LEU* 3.9 2.5 - - + -
137D THR 4.7 2.3 + - - -
138D VAL* 3.1 45.3 - - + +
139D PRO* 4.3 12.7 - - + +
142D THR* 3.7 31.4 - - + -
158D GLN 3.2 4.5 + - - +
159D ALA* 2.8 11.3 + - - +
161D ARG* 1.3 74.0 - - - +
163D LEU* 1.3 70.8 + - + +
164D GLN 2.8 4.6 + - - -
165D GLU* 3.0 7.2 + - + +
166D LYS* 2.7 60.8 + - + +
167D TYR* 3.5 25.6 + + - -
228D ILE* 5.7 1.3 - - + -
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.9 13.7 - - + -
159D ALA 3.1 16.4 + - - +
160D ARG* 4.6 4.5 - - - +
161D ARG 3.5 0.2 - - - -
162D TYR* 1.3 95.5 - - + +
164D GLN* 1.3 56.3 + - - +
167D TYR* 3.0 30.5 + - + +
168D ASN 3.2 0.2 + - - -
169D LEU* 3.1 37.1 + - + -
184D ILE* 5.5 2.9 - - + -
198D LEU* 4.0 25.8 - - + -
228D ILE* 3.8 41.3 - - + -
230D LEU* 4.2 6.3 - - + -
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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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27D LYS* 3.6 34.7 - - + +
30D TYR* 5.8 0.2 - - + -
31D TYR* 3.3 40.1 - - + +
160D ARG 4.0 10.1 + - - +
161D ARG 3.7 4.8 + - - +
162D TYR 2.9 1.0 - - - -
163D LEU* 1.3 77.3 - - - +
165D GLU* 1.3 64.0 + - - +
166D LYS 3.2 0.2 - - - -
168D ASN* 2.8 43.5 + - - +
169D LEU* 2.6 29.8 + - - +
170D TYR* 3.0 24.9 + - + -
171D ASN* 3.8 9.0 + - - +
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Residues in contact with GLU 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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31D TYR* 3.3 29.7 + - + +
161D ARG* 3.0 43.8 + - + +
162D TYR* 3.0 7.8 + - + +
164D GLN* 1.3 81.3 - - - +
166D LYS* 1.3 58.9 + - - +
168D ASN* 5.0 2.9 - - - +
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Residues in contact with LYS 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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136D ASN* 5.8 1.0 + - - -
162D TYR* 2.7 51.5 + - + +
165D GLU* 1.3 75.9 - - + +
167D TYR* 1.3 92.8 + - + +
168D ASN* 3.8 4.7 + - - -
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Residues in contact with TYR 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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129D LEU* 3.3 43.4 - - + +
131D LEU* 3.4 41.1 - - + -
136D ASN* 3.3 16.3 + - - +
138D VAL* 4.6 0.3 - - - +
162D TYR* 3.5 19.4 + + - -
163D LEU* 3.0 23.6 + - + +
166D LYS* 1.3 104.0 + - + +
168D ASN* 1.3 76.6 + - - +
169D LEU* 3.1 2.9 + - - +
177D GLY* 4.7 3.6 - - - -
178D LYS* 5.3 10.3 + - - +
179D VAL* 4.0 23.2 - - + +
230D LEU* 4.3 11.0 - - + -
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Residues in contact with ASN 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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163D LEU 3.2 0.2 + - - -
164D GLN* 2.8 43.5 + - - +
165D GLU 5.0 2.8 - - - +
166D LYS 5.1 3.0 + - - -
167D TYR* 1.3 74.2 - - - +
169D LEU* 1.3 64.7 + - - +
170D TYR 3.4 0.6 + - - -
171D ASN* 3.6 24.6 + - + -
175D PHE 5.0 0.6 + - - -
176D ASP* 3.4 26.6 + - - +
177D GLY* 3.5 16.6 - - - -
178D LYS* 5.9 4.6 - - - +
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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
------------------------------------------------------------
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