Contacts of the helix formed by residues 194 - 215 (chain K) in PDB entry 3D1N
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 194 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A T 3.7 6.5 + - - +
13A A 2.7 39.2 + - - +
193K ILE* 1.3 72.6 - - - +
195K PRO* 1.3 66.9 - - + +
196K LYS* 3.8 15.5 - - + +
197K SER* 2.8 9.5 + - - -
198K ALA* 2.7 32.3 + - - +
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Residues in contact with PRO 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K MSE 4.1 29.6 - - + -
147K ILE* 4.5 4.4 - - + +
193K ILE 3.4 6.0 - - - +
194K THR* 1.3 89.4 - - + +
196K LYS* 1.3 55.5 + - - +
198K ALA* 3.3 10.3 - - + +
199K GLN* 2.9 32.6 + - - +
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Residues in contact with LYS 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A A 5.4 1.6 - - - +
194K THR* 2.9 13.8 - - + -
195K PRO* 1.3 81.8 - - - +
197K SER* 1.3 57.7 + - - +
199K GLN* 4.2 5.1 + - - +
200K LYS* 3.8 15.1 + - - +
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Residues in contact with SER 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A A 3.0 29.7 + - - -
14A A 5.0 11.2 - - - -
193K ILE* 4.1 9.8 - - - +
194K THR* 2.8 20.2 + - - -
196K LYS* 1.3 76.4 - - - +
198K ALA* 1.3 65.4 + - - +
199K GLN 3.3 0.2 - - - -
200K LYS* 3.5 9.8 - - - +
201K LEU* 3.1 23.6 + - - +
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Residues in contact with ALA 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K MSE 6.2 0.2 - - + -
147K ILE* 4.0 17.7 - - + -
188K PHE* 4.1 5.0 - - + -
191K LEU* 6.0 5.4 - - + -
193K ILE* 3.4 27.7 - - + +
194K THR 2.7 17.1 + - - +
195K PRO* 3.3 16.6 - - + +
197K SER* 1.3 71.9 + - - +
199K GLN* 1.3 59.0 + - - +
201K LEU* 3.1 4.2 + - - +
202K LYS* 2.9 31.5 + - - +
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Residues in contact with GLN 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K ILE* 4.4 14.7 - - + +
195K PRO 2.9 16.4 + - - +
196K LYS* 4.3 6.3 - - - +
198K ALA* 1.3 76.2 - - - +
200K LYS* 1.3 56.4 + - - +
202K LYS* 4.2 5.7 - - - +
203K PRO* 3.0 25.9 - - - +
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Residues in contact with LYS 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K LYS 3.8 12.4 + - - +
197K SER* 3.3 14.4 + - - +
198K ALA 3.1 0.8 - - - -
199K GLN* 1.3 80.1 - - - +
201K LEU* 1.3 59.5 + - - +
203K PRO* 3.1 16.4 - - - +
204K VAL* 4.2 6.1 - - - +
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Residues in contact with LEU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180K TYR* 5.5 7.6 - - + -
188K PHE* 3.7 25.6 - - + -
193K ILE* 5.3 1.8 - - + -
197K SER 3.1 14.4 + - - +
198K ALA 3.1 1.6 + - - -
200K LYS* 1.3 76.0 - - - +
202K LYS* 1.3 68.8 + - - +
203K PRO 2.9 2.1 - - - -
204K VAL* 2.9 30.5 + - + +
205K LEU* 3.1 9.4 + - + +
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Residues in contact with LYS 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K GLU* 3.0 42.5 + - - -
147K ILE* 3.7 25.1 - - + -
150K PHE* 3.4 36.5 - - + +
188K PHE* 3.8 14.5 - - + -
198K ALA 2.9 16.0 + - - +
199K GLN* 4.2 2.2 - - - +
201K LEU* 1.3 75.5 - - - +
203K PRO* 1.3 71.4 - - + +
205K LEU* 3.3 15.7 - - - +
206K GLU* 3.4 28.6 + - - +
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Residues in contact with PRO 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K GLN 3.0 23.3 - - - +
200K LYS* 3.1 13.5 - - - +
201K LEU 2.9 0.2 - - - -
202K LYS* 1.3 92.5 - - + +
204K VAL* 1.3 62.2 - - - +
205K LEU 3.0 5.5 + - - -
206K GLU* 3.2 10.1 + - + +
207K LYS* 3.1 21.3 + - - +
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Residues in contact with VAL 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K MSE 3.1 25.1 - - + +
180K TYR* 3.7 33.4 - - + +
200K LYS 4.2 4.3 - - - +
201K LEU* 2.9 28.6 + - + +
203K PRO* 1.3 76.1 - - - +
205K LEU* 1.3 65.1 + - + +
207K LYS* 3.6 15.1 + - + +
208K TRP* 3.7 3.8 - - - +
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Residues in contact with LEU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K PHE* 3.5 13.2 - - + -
154K PHE* 4.1 25.7 - - + -
168K VAL* 5.3 0.7 - - + -
172K MSE 3.5 30.1 - - + -
180K TYR* 5.7 3.8 - - + -
185K ILE* 5.5 4.9 - - + -
188K PHE* 3.3 49.1 - - + -
201K LEU* 3.1 13.9 + - + +
202K LYS 3.3 9.9 - - - +
203K PRO 3.0 0.4 - - - -
204K VAL* 1.3 76.3 - - + +
206K GLU* 1.3 60.8 + - - +
208K TRP* 2.8 22.5 + - - +
209K LEU* 2.8 14.8 + - - +
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Residues in contact with GLU 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K PHE* 3.0 38.2 - - + -
157K ARG* 4.9 4.7 + - - +
202K LYS* 3.4 24.3 + - - +
203K PRO* 3.2 10.4 + - + +
205K LEU* 1.3 71.9 - - - +
207K LYS* 1.3 53.9 + - - +
208K TRP 2.7 16.3 + - - -
209K LEU* 4.2 4.9 - - + -
210K ASN* 3.2 51.1 + - - +
211K GLU 3.8 0.5 + - - -
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Residues in contact with LYS 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K PRO 3.1 15.9 + - - +
204K VAL* 3.8 13.2 - - + +
205K LEU 3.1 0.8 + - - -
206K GLU* 1.3 73.6 - - - +
208K TRP* 1.3 62.6 + - - +
211K GLU* 3.7 14.4 - - - +
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Residues in contact with TRP 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K PHE* 6.1 2.0 - + - -
163K LEU* 5.2 10.1 - - + -
168K VAL* 4.3 31.4 - - + -
171K ALA* 3.6 32.9 + - + -
172K MSE 3.5 46.5 - - + +
204K VAL 3.7 0.4 - - - +
205K LEU 2.8 8.3 + - - +
206K GLU 2.7 3.2 + - - -
207K LYS* 1.3 81.9 - - - +
209K LEU* 1.3 62.0 + - + +
210K ASN 3.5 0.7 - - - -
211K GLU* 3.5 7.0 - - - +
212K ALA* 2.8 43.4 + - + +
226K PHE* 3.2 41.3 + + - -
227K VAL* 4.3 13.7 - - + -
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Residues in contact with LEU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K PHE* 4.0 16.2 - - + -
154K PHE* 3.7 36.8 - - + +
157K ARG* 3.0 49.6 - - + +
158K ARG* 5.1 1.8 - - + +
161K LEU* 5.3 1.8 - - + -
205K LEU 2.8 13.5 + - - +
206K GLU* 4.2 1.1 - - + -
208K TRP* 1.3 81.1 - - - +
210K ASN* 1.3 67.9 + - - +
212K ALA* 3.7 1.8 - - - +
213K GLU* 2.8 57.9 + - + +
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Residues in contact with ASN 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K ARG* 3.1 28.0 + - - +
206K GLU* 3.2 29.8 + - - +
209K LEU* 1.3 78.5 - - - +
211K GLU* 1.3 64.5 + - - +
212K ALA 2.9 1.6 + - - -
213K GLU* 3.1 20.5 + - - +
214K LEU* 3.4 14.4 + - - +
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Residues in contact with GLU 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K GLU 3.8 1.2 + - - -
207K LYS* 3.7 11.0 - - - +
208K TRP* 3.6 22.2 - - - +
209K LEU 3.3 0.4 - - - -
210K ASN* 1.3 78.8 - - - +
212K ALA* 1.3 55.6 + - - +
215K ARG* 3.0 23.1 - - - +
226K PHE* 3.0 23.9 - - + -
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Residues in contact with ALA 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K LEU* 4.8 3.3 - - + +
163K LEU* 6.5 1.1 - - + -
208K TRP* 2.8 29.4 + - + +
209K LEU* 4.1 2.0 - - - +
211K GLU* 1.3 71.4 - - - +
213K GLU* 1.3 63.7 + - - +
214K LEU 3.2 1.8 - - - -
216K ASN* 3.0 25.8 + - - +
217K GLN* 3.7 1.6 + - - +
223K LEU* 3.9 11.8 - - + +
226K PHE* 3.3 37.2 - - + -
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Residues in contact with GLU 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K ARG* 2.9 41.4 + - - +
161K LEU* 3.7 26.6 - - + +
209K LEU* 2.8 27.1 + - + +
210K ASN* 3.1 22.7 + - - +
212K ALA* 1.3 78.0 - - - +
214K LEU* 1.3 58.7 + - - +
217K GLN* 3.1 29.2 - - - +
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Residues in contact with LEU 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K ASN 3.4 8.7 + - - +
211K GLU* 6.0 0.2 - - - -
213K GLU* 1.3 79.4 - - + +
215K ARG* 1.3 55.8 + - + +
216K ASN 2.8 14.5 + - - -
217K GLN 3.1 13.8 - - - +
218K GLU* 3.0 30.0 - - + +
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Residues in contact with ARG 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K GLU 3.0 24.2 + - - +
212K ALA 3.9 1.6 - - - -
214K LEU* 1.3 76.3 - - + +
216K ASN* 1.3 55.0 + - - +
218K GLU* 4.4 12.4 - - - +
222K ASN 4.8 4.3 - - - +
226K PHE* 3.6 18.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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