Contacts of the helix formed by residues 179 - 192 (chain A) in PDB entry 1L4E
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 ASN 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A HIS* 3.3 24.9 - - + +
174A GLU* 2.8 28.3 + - - +
176A GLY 3.0 23.8 + - - +
177A MET 3.3 1.2 + - - -
178A ALA* 1.3 77.5 - - - +
180A THR* 1.3 59.8 + - - +
181A THR 3.1 2.1 + - - -
182A PRO* 3.4 10.0 - - + +
183A ALA* 3.3 21.0 + - - +
242A ASP* 3.1 16.4 + - - +
266A LEU* 3.5 27.5 - - + +
990A RBZ 3.1 22.6 + - - +
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN* 1.3 75.7 - - - +
181A THR* 1.3 58.8 + - - +
183A ALA* 3.8 2.5 - - - +
184A ALA* 3.1 26.5 + - - +
200A GLY 5.8 0.7 + - - -
202A GLY* 3.7 14.0 - - - -
213A LYS* 2.8 31.3 + - - -
265A PHE* 4.4 3.1 - - + -
266A LEU* 3.8 22.0 - - + -
293A GLU* 3.8 21.8 - - - +
990A RBZ 2.8 36.6 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 4.1 22.7 - - + -
77A VAL* 3.3 30.8 + - + +
137A ILE* 4.4 6.5 - - + -
178A ALA* 3.2 6.9 + - - -
179A ASN 3.1 0.8 - - - -
180A THR* 1.3 76.5 + - - +
182A PRO* 1.4 74.8 - - + +
184A ALA* 3.0 7.0 + - - +
185A ALA* 3.0 19.8 + - - +
213A LYS* 3.4 16.2 - - + +
216A VAL* 4.3 10.8 - - + -
217A VAL* 3.9 20.3 - - + +
990A RBZ 5.2 0.2 + - - -
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A HIS* 3.9 24.9 - - + +
72A VAL* 4.2 10.3 - - + -
137A ILE* 4.0 12.6 - - + -
178A ALA 3.2 14.4 - - - +
179A ASN* 3.4 12.1 - - - +
181A THR* 1.4 91.2 - - + +
183A ALA* 1.3 60.5 + - - +
185A ALA* 3.2 3.0 + - + +
186A MET* 2.9 25.3 + - - +
238A VAL 3.1 25.0 - - - +
239A GLY* 3.6 15.9 - - - +
243A LEU* 4.2 7.0 - - + -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN 3.3 17.8 + - - +
180A THR 3.8 4.5 - - - +
181A THR 3.1 0.4 - - - -
182A PRO* 1.3 79.7 - - - +
184A ALA* 1.3 62.0 + - - +
186A MET* 4.7 0.4 - - - -
187A VAL* 3.0 14.7 + - - +
243A LEU* 4.5 4.6 - - - +
265A PHE* 3.9 12.6 - - + -
266A LEU* 3.6 29.2 - - + -
269A SER* 2.9 32.8 + - - +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A THR 3.1 18.2 + - - +
181A THR* 3.0 6.5 + - - +
183A ALA* 1.3 74.3 - - - +
185A ALA* 1.3 66.1 + - - +
187A VAL* 3.3 1.2 + - - +
188A SER* 2.8 26.0 + - - -
195A ALA* 6.0 0.2 - - - -
198A VAL* 3.8 32.4 - - + +
199A VAL* 4.0 24.2 - - + -
200A GLY 5.4 0.2 - - - +
217A VAL* 4.4 5.6 - - + -
265A PHE* 3.8 3.8 - - + -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 4.7 6.7 - - + -
181A THR 3.0 11.4 + - - +
182A PRO* 3.5 11.4 - - + +
184A ALA* 1.3 76.7 - - - +
186A MET* 1.3 62.5 + - - +
188A SER* 3.3 2.3 + - - -
189A VAL* 3.1 29.5 + - - +
217A VAL* 3.7 25.0 - - + +
220A ALA* 5.0 1.1 - - + -
221A ILE* 4.4 8.7 - - + -
238A VAL* 3.9 24.0 - - + +
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Residues in contact with MET 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO 2.9 13.4 + - - +
185A ALA* 1.3 76.1 - - - +
187A VAL* 1.3 63.6 + - - +
189A VAL* 3.2 3.0 + - - +
190A PHE* 2.9 34.6 + - + -
234A VAL* 3.6 26.9 - - + +
235A LEU* 3.7 34.8 - - + -
238A VAL* 4.1 9.8 - - + +
239A GLY* 3.9 17.7 - - - -
243A LEU* 4.1 12.8 - - + -
269A SER* 3.2 45.1 - - - +
270A ALA* 4.2 2.0 - - - +
273A ALA* 4.0 9.9 - - + -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA 3.0 18.7 + - - +
186A MET* 1.3 74.4 - - - +
188A SER* 1.3 61.9 + - - +
191A THR* 2.7 44.0 + - + +
198A VAL* 3.5 33.9 - - + -
265A PHE* 3.8 21.1 - - + -
269A SER* 3.5 17.5 - - - +
272A LEU* 4.1 18.6 - - + -
295A GLY 4.7 0.9 - - - +
298A ILE* 4.7 3.6 - - + -
299A ALA* 4.4 12.3 - - + -
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA 2.8 17.8 + - - -
185A ALA* 3.5 5.2 - - - -
187A VAL* 1.3 78.0 - - - +
189A VAL* 1.3 53.8 + - - +
191A THR* 4.2 2.2 - - - -
192A GLY* 2.7 32.6 + - - -
193A SER* 2.6 32.7 + - - -
194A ASP 4.8 0.4 - - - -
195A ALA* 4.1 18.2 + - - +
198A VAL* 4.6 3.8 - - - +
217A VAL* 5.1 0.7 - - - -
221A ILE* 3.8 18.5 - - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA 3.1 15.9 + - - +
186A MET 3.6 6.5 - - - +
188A SER* 1.3 78.0 - - - +
190A PHE* 1.3 63.0 + - - +
192A GLY* 3.7 6.3 + - - -
221A ILE* 3.9 24.9 - - + -
226A PRO* 3.8 29.4 - - + +
228A PRO* 3.6 38.6 - - + +
234A VAL* 4.1 17.5 - - + -
238A VAL* 4.8 3.1 - - + -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A MET* 2.9 38.2 + - + +
187A VAL 4.2 1.6 - - - +
189A VAL* 1.3 75.9 - - - +
191A THR* 1.3 61.3 + - + +
228A PRO* 3.6 28.2 - - - +
231A GLY* 4.0 6.1 - - - -
234A VAL* 3.7 37.0 - - + -
269A SER 4.7 0.7 - - - -
272A LEU* 3.8 33.0 - - + -
273A ALA* 3.6 36.6 - - + -
276A GLN* 3.9 23.3 - - + -
302A HIS* 4.8 3.3 + - - -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 2.7 23.8 + - + +
190A PHE* 1.3 79.5 - - - +
192A GLY* 1.3 62.4 + - - +
193A SER* 2.8 28.7 + - - -
272A LEU* 4.2 16.6 - - + -
298A ILE* 3.8 11.2 - - + +
299A ALA* 4.9 0.2 - - - -
302A HIS* 3.4 57.3 + - + -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER 2.7 15.5 + - - -
189A VAL* 3.7 5.4 + - - -
190A PHE 3.5 2.2 - - - -
191A THR* 1.3 75.0 - - - +
193A SER* 1.3 61.2 + - - +
194A ASP 4.1 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