Contacts of the helix formed by residues 169 - 181 (chain B) in PDB entry 1L0V
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 GLY 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B TYR* 3.3 14.4 - - - -
167B PHE* 2.9 26.4 + - - -
168B ILE* 1.3 79.3 - - - +
170B PRO* 1.3 80.6 - - - +
172B ALA* 3.3 2.4 + - - +
173B ILE* 3.0 22.6 + - - +
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Residues in contact with PRO 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B CYS* 3.5 38.6 - - + +
155B TYR* 3.8 14.1 - - + -
158B CYS* 4.7 5.4 - - + -
161B PHE* 5.7 0.2 - - + -
167B PHE* 4.0 14.7 - - + -
169B GLY* 1.3 83.6 - - - +
171B ALA* 1.3 67.2 + - - +
173B ILE* 3.0 2.8 + - - +
174B THR* 2.8 26.6 + - - -
210B CYS* 4.2 2.0 - - + -
220B PRO* 3.9 15.7 - - + -
224B ILE* 3.9 14.9 - - + +
245B F3S 4.1 18.2 - - - -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 3.8 20.2 - - + -
113B LEU* 6.3 0.7 - - + -
148B CYS* 4.3 10.0 - - - -
154B CYS* 3.9 12.9 - - - -
155B TYR* 3.4 19.0 - - + -
169B GLY 3.5 0.4 - - - -
170B PRO* 1.3 80.5 - - - +
172B ALA* 1.3 65.0 + - - +
174B THR* 3.0 8.6 + - - -
175B LEU* 2.9 25.3 + - - +
246B SF4 4.0 13.5 - - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 5.4 1.0 - - - -
112B SER* 4.1 24.0 - - - +
113B LEU* 4.4 11.4 - - + +
116B ILE* 3.6 12.2 - - + +
155B TYR* 3.1 6.3 + - - +
168B ILE* 3.1 36.6 - - + +
169B GLY 3.6 1.3 - - - +
170B PRO 3.2 0.2 - - - -
171B ALA* 1.3 78.0 - - - +
173B ILE* 1.3 63.7 + - - +
175B LEU* 3.3 7.1 + - - +
176B ALA 3.1 17.2 + - - -
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 5.4 0.2 - - - -
167B PHE* 4.1 11.9 - - + -
168B ILE* 3.8 19.7 - - + -
169B GLY 3.0 14.7 + - - +
170B PRO 3.5 5.8 - - - +
172B ALA* 1.3 72.4 - - - +
174B THR* 1.3 60.9 + - - +
176B ALA* 2.9 7.1 + - - +
177B HIS* 2.7 29.5 + - + +
195B LEU* 3.8 19.1 - - + -
200B GLY 3.9 7.0 - - - +
201B VAL* 3.7 41.5 - - + +
223B ALA 4.7 4.0 - - - +
224B ILE* 4.1 31.0 - - + +
227B GLY* 5.4 2.0 - - - -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE* 3.7 39.4 - - + +
148B CYS* 5.4 4.5 - - + -
170B PRO 2.8 18.2 + - - -
171B ALA* 3.0 10.7 + - - -
173B ILE* 1.3 72.0 - - - +
175B LEU* 1.3 54.0 + - - +
177B HIS* 3.1 3.2 + - - +
178B ARG* 2.7 32.9 + - - +
218B VAL* 3.8 18.2 - - + -
220B PRO* 3.2 27.2 + - - +
223B ALA* 3.5 13.8 - - + +
224B ILE* 5.0 0.5 - - - +
246B SF4 5.6 1.1 - - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLN* 3.5 23.8 - - - +
113B LEU* 3.4 44.4 - - + -
116B ILE* 4.3 5.2 - - + -
118B PRO* 3.5 20.2 - - + -
145B PHE 4.9 9.2 - - - +
146B SER* 5.9 2.9 - - - +
148B CYS* 5.0 16.2 - - + +
150B ASN* 5.3 5.2 - - - +
171B ALA 2.9 10.9 + - - +
172B ALA* 3.4 9.4 - - - +
174B THR* 1.3 78.4 - - - +
176B ALA* 1.3 65.5 + - - +
178B ARG* 2.9 26.5 + - - +
179B TYR* 3.2 12.4 + - + -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.8 35.5 - - + +
172B ALA 3.1 5.0 + - - +
173B ILE* 2.9 11.3 + - - +
175B LEU* 1.3 78.6 - - - +
177B HIS* 1.3 66.9 - - - +
179B TYR* 3.0 5.8 + - - +
180B ASN* 2.9 23.0 + - - -
191B ARG* 4.3 14.0 - - + +
195B LEU* 4.3 19.3 - - + -
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 3.8 24.6 - + - -
173B ILE* 2.7 18.7 + - + +
174B THR* 3.3 11.9 - - - +
176B ALA* 1.3 72.8 - - - +
178B ARG* 1.3 63.3 + - - +
180B ASN* 2.8 26.8 + - + +
181B GLU* 2.8 46.5 + - + +
195B LEU* 5.5 1.7 - - - +
223B ALA* 3.9 21.7 + - + +
226B GLN* 2.6 48.7 + - + +
227B GLY* 4.6 6.0 + - - -
230B GLU* 5.5 6.7 - - + +
95C ASN* 4.7 0.2 + - - -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 2.9 30.1 + - - -
102A PRO* 4.2 7.5 - - - +
138A THR* 5.6 0.6 + - - -
141A GLN* 4.6 4.3 - - - +
142B TYR* 3.4 41.0 - - + +
145B PHE* 3.8 26.9 - - + +
146B SER* 4.1 13.6 - - - +
174B THR 2.7 16.2 + - - +
175B LEU* 2.9 15.7 + - + +
177B HIS* 1.3 72.9 - - - +
179B TYR* 1.3 107.4 + - - +
181B GLU* 4.8 0.4 - - - -
182B ASP* 3.0 39.4 + - - +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TRP 4.3 7.8 + - - -
100A GLY* 5.2 0.7 - - - -
138A THR* 4.8 7.1 + - - -
141A GLN* 2.7 37.7 + - - +
142A THR* 5.6 0.5 + - - -
118B PRO* 3.2 32.2 + - + -
119B TYR* 3.7 16.3 - - - -
120B ILE* 3.5 38.8 - - + -
175B LEU* 3.2 9.3 + - + -
176B ALA* 3.0 6.2 + - - +
178B ARG* 1.3 116.1 + - - +
180B ASN* 1.3 68.2 + - - +
181B GLU 3.0 1.3 - - - -
182B ASP 2.9 11.1 + - - -
185B ASP* 3.5 17.9 - - - +
191B ARG* 3.6 23.1 - - - +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ALA 2.9 17.6 + - - -
177B HIS* 2.8 15.8 + - - +
179B TYR* 1.3 77.7 - - - +
181B GLU* 1.3 65.0 + - + +
182B ASP 3.6 3.1 + - - +
185B ASP* 4.6 4.1 - - - +
188B LYS* 3.3 44.1 - - + +
191B ARG* 3.1 28.1 + - - +
192B MET* 4.4 4.4 - - - -
195B LEU* 3.7 27.3 - - - +
230B GLU* 5.9 2.3 - - + +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B GLN 4.8 0.9 - - - +
141B LYS* 3.4 47.1 - - + +
142B TYR* 3.7 26.2 - - + -
177B HIS* 2.8 54.7 + - + +
178B ARG 3.9 0.7 - - - -
180B ASN* 1.3 80.8 - - + +
182B ASP* 1.3 61.4 + - - +
183B SER* 3.3 3.6 + - - -
226B GLN* 4.7 1.6 - - - +
230B GLU* 5.0 6.6 - - - +
95C ASN* 5.0 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
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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