Contacts of the helix formed by residues 150 - 164 (chain D) in PDB entry 1L9W
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 SER 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D PRO* 1.3 81.5 - - - +
151D ALA* 1.3 63.0 + - - +
152D GLU* 3.3 8.4 + - - +
153D GLU* 2.9 26.3 + - - +
154D MET* 3.1 18.5 + - - +
183D THR* 4.2 4.5 - - - -
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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
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150D SER* 1.3 73.6 - - - +
152D GLU* 1.3 59.6 + - - +
154D MET* 3.2 2.9 + - - +
155D VAL* 2.9 34.5 + - - +
183D THR* 3.7 22.3 - - + +
186D THR* 5.1 8.3 - - + -
187D ALA* 3.8 22.3 - - + +
190D GLU* 4.6 10.1 - - - +
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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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150D SER* 3.9 5.8 - - - +
151D ALA* 1.3 81.3 - - - +
153D GLU* 1.3 56.6 + - - +
155D VAL* 3.4 7.3 + - - +
156D SER* 2.9 30.0 + - - +
190D GLU* 5.3 3.6 - - - -
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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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149D PRO* 3.7 20.6 - - + -
150D SER* 2.9 23.4 + - - +
152D GLU* 1.3 78.9 + - - +
154D MET* 1.3 58.2 + - - +
156D SER* 3.3 8.1 + - - +
157D ARG* 3.2 58.1 + - - +
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Residues in contact with MET 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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148D THR* 4.1 3.1 - - + -
149D PRO* 3.7 27.8 - - + +
150D SER 3.1 21.5 + - - +
151D ALA 3.2 3.1 + - - +
153D GLU* 1.3 71.8 - - - +
155D VAL* 1.3 65.4 + - - +
157D ARG* 3.5 2.9 + - - +
158D LEU* 3.2 32.0 + - + +
171D ILE* 3.7 23.9 - - + +
173D VAL* 4.1 20.2 - - - -
183D THR* 3.8 30.7 - - + +
184D LEU* 3.8 31.0 - - - -
187D ALA* 3.8 13.7 - - + -
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Residues in contact with VAL 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 ALA 2.9 17.7 + - - +
152D GLU* 3.8 6.3 - - - +
154D MET* 1.3 74.4 - - - +
156D SER* 1.3 64.0 + - - +
158D LEU* 3.4 5.8 + - + +
159D ARG* 2.9 48.1 + - + +
187D ALA* 3.7 31.4 - - + +
190D GLU* 4.1 23.3 - - + +
191D MET* 4.2 8.7 - - + +
195D TYR* 3.9 21.1 - - + -
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLU* 2.9 21.2 + - - +
153D GLU* 3.3 10.6 + - - -
155D VAL* 1.3 74.9 - - - +
157D ARG* 1.3 54.1 + - - +
159D ARG* 3.2 17.6 + - - +
160D LYS* 2.8 35.4 + - - +
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Residues in contact with ARG 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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117D LEU* 4.3 10.8 - - + +
118D PHE* 4.2 22.9 - - + -
142D ASN* 2.8 43.0 + - - +
143D HIS 5.3 0.6 + - - -
144D ASP* 4.7 14.3 + - - +
147D GLN* 5.6 0.6 + - - -
149D PRO* 4.0 25.7 - - - +
153D GLU* 3.2 47.9 + - - +
154D MET* 3.9 4.5 - - - +
155D VAL 3.4 0.2 - - - -
156D SER* 1.3 75.6 - - - +
158D LEU* 1.3 58.6 - - - +
160D LYS* 3.4 9.1 + - - +
161D MET* 3.2 35.0 + - + +
171D ILE* 4.4 13.9 - - + +
173D VAL* 5.7 0.6 - - - +
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Residues in contact with LEU 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 MET* 3.2 23.5 + - + +
155D VAL* 3.9 5.2 - - + +
156D SER 3.2 0.8 - - - -
157D ARG* 1.3 77.8 - - - +
159D ARG* 1.4 63.2 + - - +
161D MET* 3.3 10.0 + - + +
162D GLN* 3.1 19.6 + - - +
169D PRO* 3.6 26.1 - - + +
170D LYS 4.2 3.4 - - - +
171D ILE* 4.4 24.0 - - + +
187D ALA* 5.0 7.2 - - + +
191D MET* 3.9 37.1 - - + +
200D VAL* 3.4 30.5 - - + -
202D THR* 4.3 12.1 - - + -
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Residues in contact with ARG 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 VAL* 2.9 34.1 + - - +
156D SER* 3.7 13.6 + - - +
158D LEU* 1.4 71.4 - - - +
160D LYS* 1.3 66.8 + - - +
162D GLN* 3.1 12.9 + - - +
163D ALA* 2.9 24.0 + - - +
191D MET* 3.9 18.4 - - + -
195D TYR* 3.3 48.7 + - + +
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Residues in contact with LYS 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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117D LEU* 4.0 26.2 - - + -
121D ASP* 2.3 44.3 + - - -
156D SER 2.8 18.1 + - - +
157D ARG* 3.6 8.1 - - - +
158D LEU 3.3 0.2 - - - -
159D ARG* 1.3 75.4 - - - +
161D MET* 1.3 58.3 + - - +
163D ALA* 2.9 24.8 + - + +
164D LEU* 3.0 28.5 + - + +
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Residues in contact with MET 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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117D LEU* 3.7 22.7 - - + -
140D MET* 3.3 36.6 - - - +
141D SER 3.4 34.3 - - - +
142D ASN* 3.5 18.4 - - + +
157D ARG* 3.2 18.8 + - + +
158D LEU* 3.5 11.7 - - - +
159D ARG 3.2 0.2 - - - -
160D LYS* 1.3 73.7 - - - +
162D GLN* 1.3 63.1 + - - +
164D LEU* 3.4 9.7 + - - +
166D ALA* 3.1 28.6 + - + +
169D PRO* 3.8 12.6 - - + -
170D LYS 3.5 15.9 - - - +
171D ILE* 5.5 2.0 - - + -
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Residues in contact with GLN 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 LEU 3.1 12.1 + - - +
159D ARG* 3.1 13.6 + - - +
161D MET* 1.3 76.7 - - - +
163D ALA* 1.3 62.8 + - - +
165D GLY* 3.1 11.1 + - - -
166D ALA 4.6 2.0 - - - -
169D PRO* 4.4 5.7 - - + +
191D MET* 4.2 9.7 - - - +
195D TYR* 3.2 21.1 - - - +
196D ALA* 3.7 6.8 - - - +
197D ASP* 2.7 38.4 + - - +
198D ARG* 3.3 48.7 + - - +
200D VAL* 5.7 0.2 - - - +
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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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125D LYS* 4.6 6.1 - - - +
159D ARG 2.9 10.5 + - - +
160D LYS* 2.9 12.6 + - + +
162D GLN* 1.3 77.1 - - - +
164D LEU* 1.3 57.1 + - + +
165D GLY 3.2 4.2 + - - -
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Residues in contact with LEU 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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117D LEU* 3.6 31.9 - - + -
121D ASP* 4.3 16.2 - - + +
124D VAL* 3.9 18.8 - - + -
125D LYS* 2.9 44.3 + - + +
128D VAL* 3.6 9.9 - - - +
140D MET* 3.8 10.5 - - + -
160D LYS* 3.0 37.8 + - + +
161D MET 3.7 8.3 - - - +
162D GLN 3.3 0.6 - - - -
163D ALA* 1.3 75.0 - - + +
165D GLY* 1.3 59.3 + - - +
166D ALA 3.7 0.3 + - - -
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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