Contacts of the helix formed by residues 184 - 200 (chain D) in PDB entry 5L5E
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 THR 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D THR* 3.9 3.8 - - - +
36D GLU* 3.7 24.0 - - - +
182D SER 4.4 5.6 - - - +
183D LEU* 1.3 76.6 - - - +
185D LEU* 1.3 63.6 + - - +
186D LYS* 3.7 6.7 + - - +
187D GLU* 3.1 40.7 + - - +
188D ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D THR* 4.5 2.5 - - - +
36D GLU* 3.1 25.4 + - + +
37D GLY* 4.1 28.0 - - - +
39D VAL* 3.7 25.8 - - + -
184D THR* 1.3 72.2 - - - +
186D LYS* 1.3 61.7 + - + +
188D ALA* 3.1 6.4 + - + +
189D GLU* 2.9 49.5 + - - +
213D CYS* 4.5 16.6 - - + -
215D THR* 4.2 19.7 - - + -
223D TYR* 4.6 0.2 - - - +
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLU* 5.0 0.2 + - - -
184D THR* 3.4 6.8 + - - +
185D LEU* 1.3 80.4 - - + +
187D GLU* 1.3 61.0 + - + +
189D GLU* 3.4 18.3 + - - +
190D LEU* 3.3 31.5 + - + +
231D LEU* 4.3 13.3 - - - +
234D GLU* 3.6 29.2 + - - +
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Residues in contact with GLU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D HIS* 4.2 6.9 + - - -
182D SER 4.4 1.9 - - - +
183D LEU* 3.4 26.6 - - + +
184D THR* 3.1 47.4 + - - +
186D LYS* 1.3 77.6 - - + +
188D ALA* 1.3 63.3 + - - +
190D LEU* 3.6 9.8 + - + +
191D LEU* 3.1 24.8 + - - +
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE* 4.0 15.9 - - + +
34D THR* 3.8 20.6 - - + -
39D VAL* 3.8 17.7 - - + -
183D LEU* 4.8 3.3 - - + +
184D THR 3.1 14.3 + - - +
185D LEU* 3.1 9.4 + - - +
187D GLU* 1.3 74.1 - - - +
189D GLU* 1.3 64.6 + - - +
191D LEU* 3.1 10.9 + - - +
192D VAL* 3.0 26.7 + - - +
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Residues in contact with GLU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D VAL* 4.1 20.2 - - + +
185D LEU* 2.9 30.8 + - - +
186D LYS* 3.6 21.7 + - - +
188D ALA* 1.3 77.0 - - - +
190D LEU* 1.3 64.8 + - + +
192D VAL* 3.3 3.3 + - - +
193D LEU* 3.2 24.4 + - - +
211D LEU* 4.3 7.8 - - + +
223D TYR* 2.6 43.2 + - + +
227D LYS* 5.3 3.1 + - - -
231D LEU* 3.6 29.9 - - + +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LYS* 3.3 19.8 + - + +
187D GLU* 3.8 7.9 - - + +
189D GLU* 1.3 79.5 - - - +
191D LEU* 1.3 52.6 + - - +
193D LEU* 3.4 7.5 + - + +
194D LYS* 2.8 35.4 + - - +
231D LEU* 3.9 46.0 - - + +
234D GLU* 3.8 25.8 - - + +
235D LEU* 4.0 21.3 - - + +
238D LYS* 4.4 20.9 - - + +
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE* 3.9 20.0 - - + -
175D LEU* 5.0 3.6 - - + -
178D GLU* 3.7 48.9 - - + +
179D TRP* 4.8 1.8 - - + +
183D LEU* 4.2 28.3 - - + -
187D GLU 3.1 12.7 + - - +
188D ALA* 3.1 9.8 + - - +
190D LEU* 1.3 75.1 - - - +
192D VAL* 1.3 63.7 + - - +
194D LYS* 3.6 13.7 - - + +
195D ILE* 3.1 38.5 + - + +
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 4.2 21.0 - - + +
32D ILE* 3.6 24.2 - - + -
39D VAL* 3.8 22.7 - - + +
41D GLY* 3.8 12.8 - - - +
188D ALA 3.0 16.6 + - - +
189D GLU 3.7 6.7 - - - +
191D LEU* 1.3 74.9 - - - +
193D LEU* 1.3 60.4 + - - +
195D ILE* 3.3 2.1 + - - +
196D LEU* 2.9 46.5 + - + +
211D LEU* 3.7 21.1 - - + -
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D GLU 3.2 8.6 + - - +
190D LEU* 3.6 10.5 - - - +
192D VAL* 1.3 79.0 - - - +
194D LYS* 1.3 62.4 + - - +
196D LEU* 4.5 10.8 - - + -
197D LYS* 3.0 26.7 + - - +
204D LEU* 3.8 16.2 - - + +
209D ALA* 5.5 4.0 - - + -
210D GLN 5.9 0.7 - - - -
211D LEU* 3.5 38.8 - - + -
228D THR* 4.4 9.2 - - + +
231D LEU* 3.7 43.3 - - + +
232D ILE* 3.9 18.2 - - + -
235D LEU* 4.0 10.9 - - + +
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Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLU* 3.8 18.8 + - - +
178D GLU* 3.8 17.3 + - - +
190D LEU 2.8 20.7 + - - +
191D LEU* 3.6 17.5 - - + +
193D LEU* 1.3 75.1 - - - +
195D ILE* 1.3 59.6 + - + +
197D LYS* 3.5 7.0 + - - +
198D GLN* 2.8 54.2 + - - +
235D LEU* 3.7 19.0 - - + +
239D GLU* 3.5 28.3 - - + +
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Residues in contact with ILE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.7 13.0 - - + -
171D ALA* 3.4 38.1 - - + +
174D GLU* 3.8 28.5 - - + +
175D LEU* 3.4 37.0 - - + +
178D GLU* 5.2 1.3 - - + -
191D LEU* 3.1 30.7 + - + +
192D VAL* 5.1 0.9 - - - -
194D LYS* 1.3 79.7 - - + +
196D LEU* 1.3 65.9 + - - +
198D GLN* 3.2 17.9 + - + +
199D VAL* 3.2 16.2 + - + +
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Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 4.2 19.7 - - + +
30D ILE* 4.0 19.7 - - + +
41D GLY* 4.1 1.6 - - - +
42D VAL* 4.0 24.2 - - - +
43D GLU* 4.0 24.9 - - + +
192D VAL* 2.9 36.6 + - + +
193D LEU* 4.7 7.4 - - + -
195D ILE* 1.3 77.0 - - - +
197D LYS* 1.3 57.4 + - - +
198D GLN 3.3 0.2 + - - -
199D VAL* 3.3 4.1 + - - +
200D MET* 3.0 38.5 + - + +
204D LEU* 3.6 20.9 - - + -
209D ALA* 4.7 4.9 - - + -
210D GLN 4.9 2.0 - - - +
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Residues in contact with LYS 197 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D LEU 3.0 17.9 + - - +
194D LYS* 3.6 6.7 - - - +
196D LEU* 1.3 76.0 - - - +
198D GLN* 1.3 63.7 + - - +
200D MET* 4.0 12.1 + - - +
202D GLU 5.3 1.4 - - - +
203D LYS* 6.1 2.7 - - + -
204D LEU* 3.6 37.9 + - + +
232D ILE* 6.2 2.7 - - + -
235D LEU* 4.1 18.8 - - + +
236D LYS* 5.3 9.1 - - - +
239D GLU* 2.8 32.4 + - - -
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170D GLY 5.6 1.4 + - - -
174D GLU* 3.5 32.4 + - - +
194D LYS* 2.8 48.1 + - + +
195D ILE* 3.4 13.6 - - + +
196D LEU 3.2 0.6 - - - -
197D LYS* 1.3 81.5 - - - +
199D VAL* 1.3 63.8 + - + +
200D MET 4.5 2.4 - - - +
239D GLU* 5.4 0.2 - - - +
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 3.9 35.0 + - + +
43D GLU* 5.5 0.5 - - - +
166D SER* 5.7 0.9 + - - -
167D GLY* 3.6 30.4 - - - +
170D GLY* 4.7 4.9 - - - -
171D ALA* 4.3 16.4 - - + +
195D ILE* 3.2 17.4 + - + +
196D LEU* 3.7 8.3 - - - +
198D GLN* 1.3 81.8 - - + +
200D MET* 1.3 67.9 + - + +
201D GLU* 3.7 4.9 + - - +
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Residues in contact with MET 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLU* 3.7 42.0 - - + +
196D LEU* 3.0 28.0 + - - +
197D LYS* 4.0 10.9 + - - +
198D GLN 3.6 3.2 - - - +
199D VAL* 1.3 82.8 - - + +
201D GLU* 1.3 64.8 + - - +
202D GLU* 3.6 28.6 - - + +
204D LEU* 3.9 25.4 - - + -
208D ASN* 3.6 41.5 - - + +
209D ALA* 4.5 5.4 - - - -
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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