Contacts of the helix formed by residues 183 - 192 (chain S) in PDB entry 5LN3
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 GLU 183 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177S ASN 3.5 19.6 - - - +
178S SER* 4.0 9.7 - - - -
179S LYS* 3.3 35.0 + - - +
180S ARG* 3.3 38.5 + - + +
182S LYS* 1.3 77.8 - - - +
184S ALA* 1.4 67.4 + - - +
185S GLN 3.1 2.7 + - - +
186S LYS* 3.4 24.8 - - + +
187S ILE* 4.3 7.8 - - - +
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Residues in contact with ALA 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173S ILE* 3.4 31.3 - - + +
174S PHE* 3.5 38.1 - - + -
177S ASN 4.8 0.4 - - - -
178S SER* 3.7 10.8 - - - +
180S ARG 5.2 0.7 - - - +
182S LYS 4.5 1.7 - - - +
183S GLU* 1.4 82.7 - - - +
185S GLN* 1.4 58.8 + - + +
187S ILE* 3.1 27.7 + - - +
188S SER* 3.3 6.8 + - - -
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Residues in contact with GLN 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174S PHE* 5.6 2.9 - - + -
181S TYR* 3.3 39.6 + - + -
182S LYS* 3.9 19.4 - - - +
183S GLU 3.1 2.6 - - - +
184S ALA* 1.4 74.7 - - + +
186S LYS* 1.4 69.3 + - - +
188S SER* 3.0 23.6 + - - +
189S ASP* 2.7 28.0 + - - +
213S TYR* 6.3 0.4 - - + -
214S HIS* 3.1 53.2 + - + +
217S VAL* 4.2 1.4 - - - +
224S LEU* 4.0 21.6 - - - +
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Residues in contact with LYS 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180S ARG* 6.1 1.1 - - - +
182S LYS* 4.0 21.0 - - - +
183S GLU* 3.4 23.6 - - + +
185S GLN* 1.4 81.4 + - - +
187S ILE* 1.4 61.8 + - + +
189S ASP* 3.7 23.1 + - - +
190S ASP* 3.1 16.5 + - - +
214S HIS* 6.0 1.6 + - - -
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Residues in contact with ILE 187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S LEU* 5.3 14.4 - - + -
173S ILE* 3.8 39.9 - - + -
177S ASN* 4.1 22.4 - - + +
183S GLU 4.3 7.2 - - - +
184S ALA* 3.1 14.3 + - - +
186S LYS* 1.4 77.6 - - + +
188S SER* 1.4 57.7 + - - +
190S ASP* 2.9 32.8 - - - +
191S LEU* 3.6 5.4 + - + +
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Residues in contact with SER 188 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170S LEU* 3.6 27.8 - - - +
173S ILE* 4.3 5.5 - - - +
174S PHE* 4.8 6.8 - - - -
184S ALA 3.3 11.3 + - - -
185S GLN* 3.0 16.6 + - - +
187S ILE* 1.4 75.0 - - - +
189S ASP* 1.3 56.4 + - - +
191S LEU* 3.3 7.4 + - - +
192S MET* 3.0 48.5 + - - +
210S CYS* 4.8 7.0 + - - +
213S TYR* 5.4 1.4 - - - +
214S HIS* 6.3 0.4 - - - -
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Residues in contact with ASP 189 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185S GLN* 2.7 24.6 + - - +
186S LYS* 3.8 20.5 + - - +
187S ILE 3.3 0.2 - - - -
188S SER* 1.3 73.0 - - - +
190S ASP* 1.3 67.2 + - - +
192S MET* 3.3 39.9 + - - +
193S GLN* 4.0 2.4 + - - +
214S HIS* 4.3 13.0 + - - -
230S PHE* 6.0 2.1 - - - -
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Residues in contact with ASP 190 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S LEU* 6.2 0.2 - - - +
186S LYS 3.1 14.8 + - - +
187S ILE* 2.9 29.0 - - - +
189S ASP* 1.3 81.1 - - - +
191S LEU* 1.4 73.7 + - - +
193S GLN* 3.3 21.3 - - - +
194S LYS* 3.8 5.5 + - - -
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Residues in contact with LEU 191 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166S TYR* 3.8 57.2 - - + +
169S LEU* 4.1 22.0 - - + -
170S LEU* 4.3 20.6 - - + -
187S ILE 4.0 5.8 - - - +
188S SER* 3.3 8.8 + - - +
190S ASP* 1.4 82.1 + - - +
192S MET* 1.4 63.9 + - - +
193S GLN 3.0 4.1 + - - -
194S LYS* 3.1 39.4 + - + +
195S ILE* 5.1 1.2 - - - +
210S CYS* 5.1 5.4 - - - -
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Residues in contact with MET 192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188S SER* 3.0 24.2 + - - +
189S ASP* 3.4 37.0 - - - +
190S ASP 3.3 1.0 - - - -
191S LEU* 1.4 75.6 - - - +
193S GLN* 1.4 61.7 + - - +
194S LYS 3.1 0.7 + - - -
195S ILE* 3.4 27.2 + - - +
196S SER* 3.8 6.8 + - - -
210S CYS* 3.5 43.1 - - + +
211S TYR* 3.6 51.1 + - + +
214S HIS* 4.7 12.1 - - + -
230S PHE* 6.0 1.8 - - - -
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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