Contacts of the helix formed by residues 195 - 208 (chain J) 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 GLY 195 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151J ILE* 3.8 21.8 - - - +
154J LEU* 5.1 4.5 - - - +
193J GLY 3.3 1.0 - - - -
194J THR* 1.3 76.3 - - - +
196J LYS* 1.4 66.3 + - - +
197J THR 3.4 2.5 - - - -
198J LEU* 3.4 21.6 + - - +
199J LEU* 3.7 6.6 + - - +
254J ILE* 3.4 12.1 - - - -
317J PHE* 4.8 9.4 - - - -
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Residues in contact with LYS 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J LEU* 4.0 25.2 - - + +
189J TYR 4.6 0.7 - - - -
190J GLY 3.3 13.3 + - - +
191J PRO 2.8 29.5 + - - +
193J GLY* 3.1 16.3 - - - +
194J THR 4.2 5.2 - - - +
195J GLY* 1.4 75.9 - - - +
197J THR* 1.3 67.2 + - - +
199J LEU* 3.2 19.5 - - - +
200J ALA* 3.7 3.3 + - - +
252J ASP* 3.3 21.9 + - - +
254J ILE* 3.5 3.3 - - + +
294J ALA* 5.1 6.7 - - + -
295J THR 3.3 23.6 - - - +
317J PHE* 3.9 42.3 - - + -
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Residues in contact with THR 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195J GLY 3.4 0.6 - - - -
196J LYS* 1.3 76.5 - - - +
198J LEU* 1.3 66.5 + - - +
200J ALA* 3.0 22.1 + - + +
201J ARG* 3.5 22.5 + - + +
211J PHE* 5.4 0.2 - - + -
247J PHE* 3.8 33.5 - - + -
249J ASP* 5.6 0.2 - - - +
252J ASP* 4.5 4.7 + - - -
253J SER* 3.4 11.1 - - - -
254J ILE* 3.1 37.0 + - + +
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Residues in contact with LEU 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ASP* 5.3 2.5 - - + +
146J SER* 3.2 31.6 + - - +
150J MET* 4.1 26.0 - - + -
151J ILE* 3.9 32.1 - - + -
154J LEU* 6.4 1.1 - - + -
195J GLY* 3.5 15.9 - - - +
197J THR* 1.3 78.4 - - - +
199J LEU* 1.4 52.8 + - - +
201J ARG* 3.1 14.2 + - - +
202J ALA* 2.8 30.9 + - - +
254J ILE* 4.2 19.3 - - + -
360J LYS* 4.8 9.0 - - - +
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Residues in contact with LEU 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LEU* 4.7 23.3 - - + -
157J GLN* 3.8 28.7 - - + +
158J ILE* 5.1 13.5 - - + -
161J ILE* 3.9 39.7 - - + -
188J LEU* 4.4 16.6 - - + -
195J GLY 3.7 5.5 + - - +
196J LYS 3.2 11.6 + - - +
198J LEU* 1.4 78.6 - - - +
200J ALA* 1.4 61.9 + - - +
202J ALA* 3.3 11.0 + - + +
203J VAL* 3.0 25.9 + - + +
317J PHE* 4.5 7.9 - - + -
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Residues in contact with ALA 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J ILE* 5.7 3.6 - - - +
165J ILE* 6.4 0.2 - - - -
196J LYS 3.7 2.5 + - - +
197J THR* 3.0 17.9 + - + +
199J LEU* 1.4 81.1 - - - +
201J ARG* 1.3 60.1 + - - +
203J VAL* 3.2 11.0 + - - +
204J ALA* 3.2 19.9 + - - +
211J PHE* 4.3 14.8 - - + -
247J PHE* 5.5 2.9 - - + -
292J ILE* 4.1 34.9 - - + +
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Residues in contact with ARG 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J GLU* 3.3 27.3 + - - -
144J PRO* 3.9 13.2 - - + +
145J ASP* 3.6 25.0 + - - +
146J SER* 4.0 14.1 - - - +
197J THR* 3.5 20.0 + - - +
198J LEU* 3.1 16.6 + - - +
200J ALA* 1.3 75.4 - - - +
202J ALA* 1.4 66.1 + - - +
204J ALA* 3.2 11.8 + - - +
205J HIS 3.4 8.7 + - - -
211J PHE* 3.6 36.8 - - + -
213J ARG* 3.5 27.5 - - - +
256J SER* 5.0 12.8 + - - -
323K ARG* 3.2 27.3 - - - +
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Residues in contact with ALA 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J SER* 3.9 13.1 - - - -
147J THR* 3.9 29.2 - - - +
148J TYR* 5.4 1.8 - - + -
198J LEU 2.8 13.4 + - - +
199J LEU* 3.5 16.8 - - + +
201J ARG* 1.4 74.8 - - - +
203J VAL* 1.3 65.0 - - + +
205J HIS* 3.3 9.5 + - - +
206J HIS* 3.2 29.7 + - + +
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Residues in contact with VAL 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J ILE* 4.5 29.4 - - + -
162J LYS* 5.4 1.3 - - + -
165J ILE* 3.9 35.4 - - + -
166J GLU* 3.9 19.0 - - + +
199J LEU* 3.0 16.8 + - + +
200J ALA* 3.2 12.1 + - - +
202J ALA* 1.3 80.2 - - + +
204J ALA* 1.4 58.1 + - - +
206J HIS* 3.5 7.3 + - - +
207J THR* 2.9 35.2 + - - +
245J ILE* 4.2 11.7 - - + -
292J ILE* 5.2 1.3 - - + -
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Residues in contact with ALA 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J ALA 3.2 7.6 + - - +
201J ARG 3.2 9.6 + - - +
203J VAL* 1.4 75.6 - - - +
205J HIS* 1.4 57.4 + - - +
207J THR* 3.4 1.5 + - - -
208J ASP 3.0 22.3 + - - -
209J CYS* 3.4 20.8 + - - +
211J PHE* 4.0 40.6 - - + +
245J ILE* 4.0 18.6 - - + -
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Residues in contact with HIS 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LYS 5.7 4.9 - - - -
143J VAL* 5.8 1.3 - - - -
144J PRO* 3.6 45.2 - - + +
146J SER 4.5 3.4 + - - -
147J THR* 4.9 3.6 + - - -
201J ARG 3.4 2.0 + - - -
202J ALA* 3.3 9.6 + - - +
203J VAL 3.3 0.4 - - - -
204J ALA* 1.4 76.7 - - - +
206J HIS* 1.3 70.2 + + - +
208J ASP* 3.1 25.2 + - - +
209J CYS 5.3 1.1 - - - -
132R VAL* 2.9 40.0 + - - +
133R ALA* 4.3 6.3 - - - -
134R LEU* 6.5 1.1 - - + -
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Residues in contact with HIS 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J THR* 4.2 7.7 + - - -
148J TYR* 3.3 54.4 + + - +
166J GLU* 3.5 30.3 + - - +
170J LYS* 5.4 2.4 - - - +
202J ALA* 3.2 31.5 + - + -
203J VAL* 3.8 3.6 - - - +
204J ALA 3.4 0.2 - - - -
205J HIS* 1.3 93.7 + + - +
207J THR* 1.3 58.1 + - - +
208J ASP* 2.9 16.7 - - - +
97R GLU* 4.3 17.3 - - - +
132R VAL* 3.7 26.4 + - + +
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Residues in contact with THR 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J ILE* 4.8 3.2 - - + +
166J GLU* 3.8 22.8 - - - +
169J VAL* 3.8 36.6 - - + +
170J LYS* 5.5 10.5 - - + +
203J VAL* 2.9 24.2 + - - +
204J ALA* 3.8 5.4 - - - -
205J HIS 3.2 0.2 - - - -
206J HIS* 1.3 76.1 - - - +
208J ASP* 1.4 67.9 + - - +
209J CYS* 4.1 21.5 - - + +
243J PRO* 5.7 1.9 - - + +
245J ILE* 5.3 2.9 - - + -
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Residues in contact with ASP 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J LYS* 4.1 8.6 + - - -
204J ALA 3.0 5.2 + - - -
205J HIS* 3.1 18.5 + - - +
206J HIS 2.9 18.7 - - - +
207J THR* 1.4 81.3 - - - +
209J CYS* 1.3 57.5 + - - +
243J PRO* 4.3 10.4 - - - +
132R VAL* 5.2 7.8 - - - +
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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