Contacts of the helix formed by residues 164 - 175 (chain F) 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 ARG 164 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162F GLY 3.8 0.2 - - - -
163F ALA* 1.4 76.4 - - + +
165F SER* 1.4 66.5 + - - +
166F GLN* 3.3 3.8 + - - +
167F SER* 3.5 29.3 + - - +
168F ALA 4.1 1.4 + - - -
197F GLU 3.4 14.0 + - - +
198F THR* 3.4 30.1 + - - +
199F LEU 3.7 14.3 + - - -
200F PRO* 3.4 30.6 + - - +
201F ALA* 5.5 3.2 - - - +
202F GLU* 5.6 0.2 + - - -
383M GLU* 4.9 4.7 - - - +
418M GLU* 4.3 20.4 + - - +
421M MET* 4.5 23.0 - - - +
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Residues in contact with SER 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F SER* 3.2 40.8 + - - -
161F ILE* 4.7 2.2 - - - -
162F GLY 3.1 16.3 + - - -
164F ARG* 1.4 77.7 - - - +
166F GLN* 1.4 79.7 + - - +
167F SER 3.2 0.5 + - - -
168F ALA* 3.3 5.2 + - - +
169F ARG* 3.2 19.3 + - - +
198F THR* 4.9 4.0 - - - -
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Residues in contact with GLN 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ARG* 3.3 1.1 - - - -
165F SER* 1.4 93.7 + - - +
167F SER* 1.4 61.5 + - - +
169F ARG* 3.1 44.7 + - - +
170F THR* 3.1 26.7 + - - -
383M GLU* 3.5 28.9 - - + +
386M ARG* 4.1 37.1 + - + +
387M CYS* 4.7 11.9 - - - -
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Residues in contact with SER 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F ARG* 3.5 30.3 + - - +
166F GLN* 1.4 73.5 - - - +
168F ALA* 1.4 63.8 + - - +
170F THR* 3.4 15.6 + - - -
171F TYR* 3.5 11.1 + - - +
197F GLU* 3.8 25.9 + - - +
383M GLU* 3.1 27.6 + - - -
421M MET* 5.6 1.2 - - - +
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F VAL* 5.3 3.4 - - + -
160F SER* 4.8 9.9 - - - -
164F ARG 4.7 0.2 - - - +
165F SER 3.3 8.1 + - - +
167F SER* 1.4 76.2 - - - +
169F ARG* 1.4 57.2 + - - +
171F TYR* 3.2 8.2 + - - +
172F LEU* 2.9 36.8 + - + +
194F ALA* 3.6 31.2 - - + +
197F GLU* 4.1 7.4 - - + -
198F THR* 3.8 15.5 - - - +
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Residues in contact with ARG 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F MET* 4.3 15.3 - - - +
160F SER* 3.3 23.7 + - - +
165F SER* 3.2 12.3 + - - +
166F GLN* 3.1 49.4 + - - +
168F ALA* 1.4 72.5 - - - +
170F THR* 1.4 57.8 + - - +
172F LEU* 3.2 12.1 + - + +
173F GLU* 2.8 38.9 + - - +
55G LEU* 5.1 5.1 - - - +
56G SER* 3.5 26.1 + - - -
58G LEU* 3.7 22.1 - - + +
59G TYR* 3.6 26.3 + - - -
386M ARG* 5.6 3.6 - - - +
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Residues in contact with THR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F GLN* 3.1 13.5 + - - -
167F SER* 3.6 10.4 - - - -
168F ALA 3.3 0.2 - - - -
169F ARG* 1.4 76.2 - - - +
171F TYR* 1.4 56.8 + - - +
173F GLU* 3.4 15.4 + - + +
174F ARG* 3.0 31.5 + - + +
382M GLU* 6.0 2.0 - - - +
383M GLU* 5.6 3.8 + - - +
386M ARG* 4.5 15.6 + - - +
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Residues in contact with TYR 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F SER 3.5 8.7 + - - +
168F ALA* 3.2 9.5 + - - +
170F THR* 1.4 78.8 - - - +
172F LEU* 1.4 58.1 + - + +
174F ARG* 3.1 8.8 + - + +
175F HIS* 2.8 77.1 + + + +
179F PHE* 6.1 0.9 - + - -
190F HIS* 3.2 47.2 + - + -
193F ARG* 3.7 17.5 - - + +
194F ALA* 3.7 24.2 - - + -
197F GLU* 4.9 11.7 - - + -
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Residues in contact with LEU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 4.1 14.8 - - + -
37F GLY 4.2 0.2 - - - +
38F LEU* 4.4 13.5 - - + -
158F ALA* 3.8 25.4 - - + -
159F MET* 3.7 28.5 - - - +
160F SER* 5.1 1.3 - - - +
168F ALA 2.9 25.4 + - - +
169F ARG* 3.3 17.3 - - + +
171F TYR* 1.4 75.3 - - + +
173F GLU* 1.4 55.0 + - - +
175F HIS 3.6 0.5 - - - -
176F MET* 2.8 41.1 + - - +
179F PHE* 3.7 11.1 - - + -
194F ALA* 4.0 23.3 - - + -
58G LEU* 4.5 9.6 - - + -
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Residues in contact with GLU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F ARG* 2.8 23.3 + - - +
170F THR* 3.6 17.1 + - + +
171F TYR 3.3 0.2 - - - -
172F LEU* 1.4 76.4 - - - +
174F ARG* 1.4 60.9 + - - +
176F MET* 3.2 12.1 - - - +
177F SER* 4.7 0.3 + - - -
56G SER* 3.4 28.2 - - - -
57G LYS* 3.1 43.3 + - + +
58G LEU* 3.7 25.5 - - + +
386M ARG* 5.2 7.7 + - - -
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F THR* 3.0 20.1 + - + +
171F TYR* 3.1 12.5 + - + +
173F GLU* 1.4 75.0 - - - +
175F HIS* 1.3 66.2 - - + +
176F MET 3.1 8.2 + - - -
177F SER* 4.3 7.1 + - - -
178F GLU* 5.0 4.0 - - - +
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Residues in contact with HIS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F TYR* 2.8 61.1 + + + +
172F LEU 3.6 0.4 - - - -
174F ARG* 1.3 79.6 - - + +
176F MET* 1.3 62.6 + - - +
177F SER 3.3 2.7 - - - -
178F GLU* 3.0 51.9 + - - +
179F PHE* 3.3 28.8 - - + -
190F HIS* 3.1 21.2 + + - -
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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