Contacts of the helix formed by residues 172 - 186 (chain N) in PDB entry 5L4K
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 172 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147N TYR* 3.0 38.5 - - + -
148N LYS* 3.8 16.8 + - - +
167N ILE 3.5 4.9 - - - +
169N GLU 3.8 7.0 - - - +
170N SER* 3.1 15.3 - - - -
171N ASN* 1.3 80.4 + - - +
173N VAL* 1.3 60.1 + - - +
174N PRO* 3.8 1.8 - - - -
175N GLY* 4.3 4.9 - - - +
176N MET* 2.9 33.2 + - + +
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Residues in contact with VAL 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N ILE* 3.5 20.1 - - + +
168N LEU* 4.0 9.6 - - + +
170N SER 3.9 15.3 - - - +
171N ASN* 4.6 3.8 - - - +
172N ASP* 1.3 75.1 - - - +
174N PRO* 1.3 76.2 - - + +
175N GLY 3.2 1.5 + - - -
176N MET* 3.4 3.6 + - - +
177N LEU* 3.0 37.4 + - + +
208N LEU* 3.6 35.4 - - + -
209N GLU* 3.9 20.4 - - - +
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Residues in contact with PRO 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N ASN 4.1 10.8 - - - +
172N ASP* 4.0 0.9 - - - -
173N VAL* 1.3 95.0 - - + +
175N GLY* 1.3 59.5 + - - +
177N LEU* 3.7 15.8 - - + +
178N ALA* 3.6 15.2 + - - +
209N GLU* 4.4 14.4 - - - +
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Residues in contact with GLY 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172N ASP* 4.3 5.6 + - - +
173N VAL 3.2 0.6 - - - -
174N PRO* 1.3 78.3 - - - +
176N MET* 1.3 62.1 + - - +
177N LEU 3.0 1.1 - - - -
178N ALA* 2.5 30.4 + - - +
179N TYR* 3.1 17.1 + - - -
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Residues in contact with MET 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147N TYR* 3.5 43.7 - - + +
148N LYS* 4.2 13.0 - - + +
151N ILE* 4.3 11.8 - - + +
166N THR* 4.2 10.8 - - - +
167N ILE* 3.8 34.8 - - + -
172N ASP* 2.9 28.8 + - + +
173N VAL 3.4 3.7 + - - +
175N GLY* 1.3 75.0 - - - +
177N LEU* 1.3 62.5 + - - +
179N TYR* 3.1 32.3 + - + +
180N SER* 3.0 27.9 + - - -
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Residues in contact with LEU 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N ILE* 5.7 2.7 - - + -
173N VAL* 3.0 33.6 + - + +
174N PRO* 3.7 15.7 - - + +
175N GLY 3.0 0.8 - - - -
176N MET* 1.3 75.8 - - - +
178N ALA* 1.3 58.2 + - - +
180N SER* 3.8 7.0 + - - +
181N LEU* 3.4 27.5 - - - +
201N LEU* 3.7 16.4 - - + -
204N ILE* 3.5 39.5 - - + +
205N TYR* 3.7 38.5 + - + +
208N LEU* 5.8 0.9 - - + -
212N ASP* 6.0 0.2 - - - +
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Residues in contact with ALA 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174N PRO 3.6 7.2 + - - +
175N GLY* 2.5 23.8 + - - +
177N LEU* 1.3 72.3 - - - +
179N TYR* 1.3 67.2 + - + +
181N LEU* 3.8 5.2 + - - +
182N LYS* 3.2 39.1 + - - +
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Residues in contact with TYR 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LYS* 3.6 33.1 - - + +
151N ILE* 3.8 28.9 - - + -
175N GLY* 3.1 14.7 + - - -
176N MET* 3.1 35.9 + - + +
178N ALA* 1.3 82.4 - - + +
180N SER* 1.3 56.5 + - - +
181N LEU 3.1 0.9 - - - -
182N LYS* 3.0 36.3 + - + +
183N LEU* 3.0 24.7 + - + +
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Residues in contact with SER 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N ILE* 4.4 2.5 - - - -
163N PHE* 3.6 35.9 - - - -
167N ILE* 5.6 0.2 - - - +
176N MET 3.0 17.0 + - - -
177N LEU* 3.8 7.6 + - - +
179N TYR* 1.3 75.7 - - - +
181N LEU* 1.3 58.2 + - - +
183N LEU* 4.6 9.6 - - - +
184N CYS* 3.2 29.9 + - - +
197N VAL* 5.3 2.0 - - - +
201N LEU* 3.7 24.5 - - - +
204N ILE* 5.3 0.2 - - - +
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N LEU 3.4 21.4 + - - +
178N ALA* 4.3 5.6 - - - +
179N TYR 3.1 1.0 - - - -
180N SER* 1.3 79.7 + - - +
182N LYS* 1.3 62.6 + - + +
183N LEU 3.4 0.2 - - - -
184N CYS* 3.9 3.8 - - + +
185N MET* 3.2 35.2 + - + +
198N LEU* 5.6 0.9 - - + -
201N LEU* 3.6 25.8 - - + -
205N TYR* 3.8 17.3 - - + +
215N ASN* 3.8 18.2 - - + +
218N GLN* 6.1 4.3 - - + +
219N CYS* 4.0 13.9 - - - -
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Residues in contact with LYS 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N ALA* 3.2 31.6 - - - +
179N TYR* 3.0 22.9 + - + +
181N LEU* 1.3 80.3 - - + +
183N LEU* 1.3 55.9 + - + +
185N MET* 3.6 2.9 + - - +
186N SER* 2.6 38.6 + - - +
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Residues in contact with LEU 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N ILE* 4.2 25.4 - - + +
152N GLY* 5.4 2.5 - - - -
155N LEU* 4.2 24.9 - - + -
179N TYR* 3.0 26.0 + - + +
180N SER* 4.7 4.5 - - - -
182N LYS* 1.3 78.2 - - + +
184N CYS* 1.3 60.6 + - - +
185N MET 3.1 2.0 - - - -
186N SER* 5.3 2.0 - - - +
187N LEU* 3.1 34.3 + - + +
188N MET* 3.0 30.9 + - - +
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Residues in contact with CYS 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N SER 3.2 21.1 + - - +
181N LEU* 3.8 6.9 + - + +
182N LYS 3.4 0.6 - - - -
183N LEU* 1.3 78.2 - - - +
185N MET* 1.3 62.3 + - + +
188N MET* 3.8 12.0 - - - +
194N ARG* 2.8 36.9 + - - -
197N VAL* 3.6 36.6 - - - -
198N LEU* 3.8 32.5 - - + -
201N LEU* 4.5 4.0 - - + -
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Residues in contact with MET 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N LEU* 3.2 24.3 + - + +
182N LYS* 3.6 3.8 + - - +
183N LEU 3.1 0.4 - - - -
184N CYS* 1.3 83.1 - - + +
186N SER* 1.3 60.1 + - - +
188N MET 5.0 4.5 - - - +
194N ARG* 3.6 23.7 + - - +
198N LEU* 6.2 1.3 - - - -
222N PHE* 3.5 40.4 - - + -
753N GLY* 4.4 11.9 - - - +
754N HIS* 5.2 0.7 - - - +
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Residues in contact with SER 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N LYS* 2.6 23.3 + - - +
183N LEU* 4.2 2.8 - - - +
185N MET* 1.3 79.3 - - - +
187N LEU* 1.3 71.0 + - - +
188N MET 3.5 1.6 - - - +
189N GLN* 3.2 15.1 + - - -
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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