Contacts of the helix formed by residues 185 - 201 (chain D) in PDB entry 3TDD
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 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D SER 4.3 5.2 - - - -
42D THR* 4.2 3.4 - - - -
44D GLU* 3.7 23.1 - - - +
184D LEU* 1.3 79.2 - - - +
186D LEU* 1.3 65.2 + - - +
187D LYS* 3.5 9.4 + - - +
188D GLU* 2.9 42.5 + - + +
189D ALA* 2.9 22.5 + - - +
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Residues in contact with LEU 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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42D THR* 4.2 4.5 - - - +
44D GLU* 3.1 28.2 + - + +
45D GLY* 4.1 24.0 - - - +
47D VAL* 3.5 28.0 - - + -
185D THR* 1.3 73.7 - - - +
187D LYS* 1.3 58.5 + - + +
189D ALA* 3.2 4.6 + - + +
190D GLU* 2.8 49.3 + - - +
214D CYS* 4.4 10.8 - - + -
216D THR* 4.0 22.0 - - + -
224D TYR* 4.3 6.1 - - - +
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Residues in contact with LYS 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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44D GLU* 4.9 0.4 + - - -
185D THR* 3.2 8.8 + - - +
186D LEU* 1.3 80.0 - - + +
188D GLU* 1.3 62.1 + - + +
190D GLU* 3.4 21.2 + - - +
191D LEU* 3.1 32.0 + - + +
232D LEU* 4.5 10.0 - - + +
236D GLU* 3.8 28.8 + - - +
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Residues in contact with GLU 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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18D HIS* 4.0 10.6 + - - -
184D LEU* 3.3 28.3 - - + +
185D THR* 2.9 50.9 + - - +
187D LYS* 1.3 73.4 - - + +
189D ALA* 1.3 62.3 + - - +
190D GLU 3.2 0.2 + - - -
191D LEU* 3.3 8.3 + - - +
192D LEU* 2.8 32.4 + - - +
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Residues in contact with ALA 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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40D ILE* 3.5 18.6 - - + +
42D THR* 3.7 23.1 - - + -
47D VAL* 4.0 15.7 - - + -
184D LEU* 4.5 2.1 - - - +
185D THR 2.9 13.2 + - - +
186D LEU* 3.5 8.5 - - - +
188D GLU* 1.3 76.9 - - - +
190D GLU* 1.3 56.0 + - - +
192D LEU* 3.3 9.4 + - - +
193D VAL* 2.8 35.4 + - - +
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Residues in contact with GLU 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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47D VAL* 3.9 23.6 - - + -
186D LEU* 2.8 37.7 + - - +
187D LYS* 3.5 19.6 + - - +
188D GLU 3.2 0.2 - - - -
189D ALA* 1.3 76.3 - - - +
191D LEU* 1.3 65.0 + - - +
193D VAL* 3.0 4.7 + - - +
194D LEU* 2.9 23.4 + - - +
212D LEU* 4.4 8.4 - - + +
224D TYR* 2.7 34.6 + - + +
228D LYS* 5.5 1.6 - - - -
232D LEU* 3.1 35.6 - - + +
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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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187D LYS* 3.1 23.0 + - + +
188D GLU* 3.8 5.4 - - - +
190D GLU* 1.3 78.9 - - - +
192D LEU* 1.3 57.6 + - - +
194D LEU* 3.3 6.5 + - + +
195D LYS* 2.8 30.9 + - - +
232D LEU* 3.2 51.1 - - + +
236D GLU* 3.1 29.8 - - + +
237D LEU* 4.0 24.7 - - + +
240D LYS* 4.2 17.0 - - + +
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Residues in contact with LEU 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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40D ILE* 3.8 18.4 - - + -
176D LEU* 5.0 1.8 - - + -
179D GLU* 3.5 57.4 - - + +
180D TRP* 4.8 1.3 - - + +
184D LEU* 4.3 23.3 - - + -
188D GLU 2.8 16.7 + - - +
189D ALA* 3.4 6.1 - - - +
191D LEU* 1.3 77.3 - - - +
193D VAL* 1.3 61.5 + - - +
195D LYS* 3.4 12.5 + - + +
196D ILE* 3.2 41.9 + - + +
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Residues in contact with VAL 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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38D ILE* 4.2 24.2 - - + +
40D ILE* 3.2 33.9 - - + +
47D VAL* 3.8 16.4 - - + -
49D GLY* 3.9 18.6 - - - +
189D ALA 2.8 12.1 + - - +
190D GLU 3.5 6.5 - - - +
192D LEU* 1.3 76.5 - - - +
194D LEU* 1.3 64.4 + - - +
195D LYS 3.2 0.2 + - - -
196D ILE* 3.4 3.0 + - - +
197D LEU* 3.0 31.0 + - + +
212D LEU* 3.6 23.1 - - + -
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Residues in contact with LEU 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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190D GLU 2.9 9.1 + - - +
191D LEU* 3.5 12.1 - - + +
193D VAL* 1.3 79.0 - - - +
195D LYS* 1.3 59.6 + - - +
197D LEU* 4.6 7.9 - - + -
198D LYS* 3.3 5.9 + - - +
207D LEU* 3.0 46.0 - - + +
210D ALA* 4.9 5.4 - - + -
211D GLN 5.9 0.4 - - - -
212D LEU* 3.5 39.9 - - + -
229D THR* 4.2 11.0 - - + -
232D LEU* 3.7 35.4 - - + +
233D ILE* 4.0 16.8 - - + -
237D LEU* 4.9 8.3 - - + +
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Residues in contact with LYS 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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175D GLU* 4.7 6.6 - - - +
179D GLU* 3.1 26.5 + - - -
191D LEU 2.8 17.0 + - - +
192D LEU* 3.6 16.8 - - + +
193D VAL 3.1 0.4 - - - -
194D LEU* 1.3 75.0 - - - +
196D ILE* 1.3 62.9 + - + +
198D LYS* 2.9 21.9 + - - +
199D GLN* 3.1 36.3 + - + +
237D LEU* 4.1 20.2 - - + +
241D GLU* 4.2 28.0 - - - +
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Residues in contact with ILE 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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38D ILE* 3.9 12.1 - - + -
172D ALA* 3.2 36.8 - - + -
175D GLU* 3.4 35.9 - - + -
176D LEU* 3.4 35.7 - - + +
192D LEU* 3.2 28.7 + - + +
193D VAL* 5.0 0.2 - - - -
195D LYS* 1.3 75.2 - - + +
197D LEU* 1.3 66.2 + - - +
199D GLN* 3.2 18.3 + - - +
200D VAL* 3.2 15.6 + - + +
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Residues in contact with LEU 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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36D THR* 3.9 30.5 - - + +
38D ILE* 3.7 21.7 - - + +
49D GLY* 4.1 4.9 - - - -
50D VAL* 3.9 28.7 - - - +
51D GLU* 4.2 12.3 - - + +
193D VAL* 3.0 29.3 + - + +
194D LEU* 4.7 8.5 - - + -
195D LYS 3.2 0.2 - - - -
196D ILE* 1.3 76.1 - - - +
198D LYS* 1.3 57.8 + - - +
200D VAL* 3.3 3.3 + - - +
201D MET* 2.9 39.6 + - + +
207D LEU* 3.8 10.8 - - + -
210D ALA* 4.6 12.1 - - + -
211D GLN 4.9 1.3 - - - +
212D LEU* 5.4 0.2 - - + -
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Residues in contact with LYS 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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194D LEU 3.3 11.2 + - - +
195D LYS* 2.9 13.0 + - + +
197D LEU* 1.3 80.6 - - - +
199D GLN* 1.3 59.8 + - + +
201D MET* 3.8 14.1 + - - +
205D GLU 4.8 2.1 - - - +
206D LYS* 3.9 31.1 - - - +
207D LEU* 3.6 33.8 + - + +
233D ILE* 6.4 1.3 - - + -
237D LEU* 4.5 11.0 - - + -
241D GLU* 4.5 16.8 - - - +
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Residues in contact with GLN 199 (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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171D GLY 5.9 1.0 + - - -
172D ALA* 6.1 0.8 - - - +
175D GLU* 2.7 38.2 + - - +
195D LYS* 3.1 43.8 + - + +
196D ILE* 3.2 11.3 + - - +
198D LYS* 1.3 79.5 - - + +
200D VAL* 1.3 65.6 + - + +
201D MET 4.5 2.1 - - - +
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Residues in contact with VAL 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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36D THR* 3.8 34.0 + - + +
51D GLU* 5.5 0.9 - - - +
167D SER* 5.6 1.7 + - - -
168D GLY* 3.6 31.7 + - - +
171D GLY* 4.9 3.6 - - - -
172D ALA* 4.0 16.6 - - + +
196D ILE* 3.4 17.3 - - + +
197D LEU* 3.4 7.2 - - - +
199D GLN* 1.3 84.0 - - + +
201D MET* 1.3 67.5 + - + +
202D GLU* 3.5 6.8 + - - +
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Residues in contact with MET 201 (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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20D ASN* 3.2 45.8 - - + +
51D GLU* 3.8 41.7 - - + +
53D ARG* 6.3 0.4 - - - -
197D LEU* 2.9 34.7 + - + +
198D LYS* 4.0 9.9 - - - +
199D GLN 3.5 3.2 - - - +
200D VAL* 1.3 80.2 - - + +
202D GLU* 1.3 66.0 + - - +
205D GLU* 3.2 28.7 - - + +
207D LEU* 4.2 17.5 - - - -
210D ALA* 4.6 3.6 - - - -
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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