Contacts of the helix formed by residues 183 - 199 (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 ASN 183 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F HIS* 5.6 4.3 - - - -
182F CYS* 1.4 104.1 - - - +
184F LEU* 1.4 62.7 + - - +
185F ASN* 4.5 4.3 - - + +
186F GLU* 3.6 31.5 - - + +
187F LEU* 3.3 20.3 + - - +
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Residues in contact with LEU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F HIS* 3.5 47.3 - - + +
45F VAL* 6.0 0.2 - - - +
183F ASN* 1.4 69.1 - - - +
185F ASN* 1.3 75.1 + - - +
187F LEU* 3.3 18.6 + - - +
188F VAL* 3.5 16.1 + - - +
214F ILE* 5.0 23.7 - - + +
219F LEU* 5.4 6.7 - - + -
232F PHE* 3.8 17.7 - - + -
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Residues in contact with ASN 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ASN* 5.3 3.6 - - + +
184F LEU* 1.3 82.1 + - - +
186F GLU* 1.3 71.5 + - + +
188F VAL* 3.3 7.1 + - - +
189F LYS* 3.3 27.1 + - + +
232F PHE* 3.3 38.0 + - - +
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F GLU 6.0 1.6 - - - +
182F CYS 5.3 0.7 - - - +
183F ASN* 3.6 33.9 - - + +
184F LEU 3.3 0.2 - - - -
185F ASN* 1.3 81.4 - - + +
187F LEU* 1.3 64.0 - - + +
189F LYS* 3.2 40.2 + - - +
190F HIS* 2.8 48.4 + - + +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU* 3.9 30.5 - - + +
39F LYS* 4.6 0.7 - - - -
40F SER* 3.9 26.9 - - - +
43F HIS* 4.2 18.6 - - + +
45F VAL* 3.8 26.2 - - + +
179F PHE* 4.0 32.1 - - + +
182F CYS 4.2 1.8 - - - +
183F ASN 3.3 19.7 - - - +
184F LEU* 3.3 7.1 + - - +
186F GLU* 1.3 83.3 - - + +
188F VAL* 1.4 63.4 + - - +
190F HIS* 3.4 9.5 + - + +
191F GLY* 3.2 17.7 + - - -
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 4.0 26.0 - - + -
47F VAL* 4.4 6.5 - - + +
184F LEU 3.7 6.3 - - - +
185F ASN 3.3 8.7 + - - +
186F GLU 3.2 0.4 - - - -
187F LEU* 1.4 76.0 - - - +
189F LYS* 1.4 53.4 + - + +
191F GLY* 3.1 4.2 + - - -
192F LEU* 2.9 33.4 + - + +
212F ILE* 4.1 32.8 - - + -
214F ILE* 4.8 5.2 - - + -
232F PHE* 3.7 43.1 - - + +
233F LEU* 5.2 6.3 - - + -
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Residues in contact with LYS 189 (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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185F ASN* 3.3 17.5 + - + +
186F GLU* 3.2 35.2 + - - +
188F VAL* 1.4 75.3 - - + +
190F HIS* 1.4 71.1 + - - +
192F LEU* 3.1 9.2 + - - +
193F ARG* 3.0 38.8 + - + +
233F LEU 6.1 1.1 - - - +
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Residues in contact with HIS 190 (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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38F LEU* 5.9 2.5 - - + -
171F TYR* 3.2 25.6 + - + +
175F HIS* 3.1 31.3 + + - -
178F GLU* 3.6 17.1 + - - +
179F PHE* 4.2 29.8 - + + -
186F GLU* 2.8 49.1 + - + +
187F LEU* 3.5 10.1 - - + +
188F VAL 3.3 0.2 - - - -
189F LYS* 1.4 80.8 - - + +
191F GLY* 1.3 56.7 + - - +
193F ARG* 3.3 1.3 + - - +
194F ALA* 2.8 30.9 + - - +
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Residues in contact with GLY 191 (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* 4.6 8.8 - - - +
38F LEU* 6.1 3.1 - - - +
45F VAL* 6.3 0.7 - - - -
47F VAL* 4.0 21.1 - - - +
187F LEU 3.2 8.0 + - - -
188F VAL 3.1 8.1 + - - -
190F HIS* 1.3 74.6 - - - +
192F LEU* 1.4 57.0 + - - +
194F ALA* 3.6 6.4 - - - +
195F LEU* 2.8 33.3 + - - +
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Residues in contact with LEU 192 (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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47F VAL* 4.4 7.8 - - + +
188F VAL* 2.9 14.0 + - + +
189F LYS* 3.1 12.8 + - - +
191F GLY* 1.4 76.1 - - - +
193F ARG* 1.3 71.1 + - + +
195F LEU* 3.4 11.7 + - + +
196F ARG* 3.5 11.8 + - - +
205F LEU* 4.2 37.6 - - + +
206F THR 6.0 0.4 - - - +
210F VAL* 4.8 19.1 - - + -
212F ILE* 6.6 0.2 - - + -
233F LEU* 4.0 28.7 - - + -
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Residues in contact with ARG 193 (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* 3.7 20.0 - - + +
189F LYS* 3.0 25.9 + - + +
190F HIS 3.5 7.2 - - - +
192F LEU* 1.3 84.3 - - + +
194F ALA* 1.3 63.5 + - - +
195F LEU 3.2 0.4 - - - -
196F ARG* 3.1 13.7 - - - +
197F GLU* 3.1 24.8 - - - +
205F LEU* 5.4 11.7 - - - +
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Residues in contact with ALA 194 (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* 4.8 8.3 - - + -
168F ALA* 3.6 12.8 - - + +
171F TYR* 3.7 20.2 - - + -
172F LEU* 4.0 16.8 - - + -
190F HIS 2.8 18.5 + - - +
191F GLY* 3.6 8.5 - - - +
193F ARG* 1.3 77.0 - - - +
195F LEU* 1.4 64.1 + - - +
197F GLU* 3.0 27.4 + - - +
198F THR* 3.5 4.2 + - - -
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Residues in contact with LEU 195 (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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34F ALA* 4.0 33.7 - - + +
35F THR* 4.4 10.1 - - - +
36F VAL* 4.7 7.9 - - + +
47F VAL* 4.0 27.8 - - + +
49F LEU* 4.3 26.0 - - + +
191F GLY 2.8 19.6 + - - +
192F LEU* 3.7 8.1 - - + +
193F ARG 3.2 0.4 - - - -
194F ALA* 1.4 77.0 - - - +
196F ARG* 1.4 61.2 + - - +
198F THR* 3.3 19.8 + - - +
199F LEU* 3.4 19.1 + - + +
205F LEU* 5.5 3.8 - - + -
210F VAL* 4.5 16.4 - - + -
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Residues in contact with ARG 196 (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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192F LEU 3.5 7.5 + - - +
193F ARG* 3.1 19.5 + - - +
195F LEU* 1.4 78.3 - - - +
197F GLU* 1.4 64.5 + - - +
199F LEU* 3.5 22.8 + - - +
201F ALA* 3.2 45.8 + - + +
203F GLN 3.8 11.1 + - - -
204F ASP* 3.4 34.2 + - - +
205F LEU* 3.8 38.8 - - + +
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Residues in contact with GLU 197 (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* 3.4 17.9 + - - +
167F SER* 3.8 27.8 - - - +
168F ALA* 4.1 10.1 - - - +
171F TYR* 4.9 13.2 - - + -
193F ARG* 3.1 23.0 - - - +
194F ALA* 3.0 16.1 + - - +
196F ARG* 1.4 84.0 - - - +
198F THR* 1.4 60.5 + - - +
199F LEU 3.4 7.1 - - - +
201F ALA* 5.8 0.9 - - - -
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Residues in contact with THR 198 (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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34F ALA* 3.6 29.2 - - + -
35F THR 5.1 1.7 + - - +
36F VAL* 5.9 1.4 - - - +
160F SER* 5.5 3.5 - - - -
161F ILE 4.4 4.9 - - - +
162F GLY 4.2 12.8 - - - +
163F ALA 2.8 35.7 - - - +
164F ARG* 3.4 20.7 - - - +
165F SER* 4.7 2.4 - - - +
168F ALA* 3.8 12.8 - - - +
194F ALA 3.6 10.0 + - - -
195F LEU* 3.3 16.8 + - - +
197F GLU* 1.4 71.5 - - - +
199F LEU* 1.3 64.8 + - - +
200F PRO* 4.3 1.2 - - - +
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Residues in contact with LEU 199 (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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34F ALA* 4.7 7.2 - - + -
49F LEU* 4.0 39.3 - - + -
51F ARG* 6.1 0.7 - - - -
164F ARG* 3.6 5.7 + - - -
195F LEU* 3.4 18.7 + - + +
196F ARG* 3.5 14.2 - - - +
197F GLU 3.4 11.3 - - - +
198F THR* 1.3 79.4 - - - +
200F PRO* 1.3 73.3 - - + +
201F ALA* 3.0 11.4 + - - +
203F GLN* 4.0 37.7 - - + +
204F ASP 5.8 1.3 - - - +
205F LEU* 5.1 10.8 - - + -
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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