Contacts of the helix formed by residues 197 - 214 (chain D) in PDB entry 3PJA
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 197 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LYS 4.0 1.6 + - - -
194D ARG 3.1 12.2 + - - -
195D TYR 2.8 1.8 + - - -
196D ASP* 1.3 79.0 - - - +
198D LEU* 1.3 62.7 + - - +
199D LYS 3.3 2.5 - - - -
200D TYR* 3.4 26.6 + - - +
201D ASP* 3.6 12.9 + - - +
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Residues in contact with LEU 198 (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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145D LEU* 4.0 17.7 - - + -
148D ALA* 3.5 31.4 - - + -
174D ILE* 4.4 12.3 - - + +
177D LEU* 4.4 4.0 - - + -
178D ASP* 3.7 40.6 - - + +
181D PHE* 4.2 14.4 - - + -
194D ARG 3.9 1.4 + - - -
195D TYR* 2.8 26.6 + - + +
197D GLY* 1.3 78.3 - - - +
199D LYS* 1.3 64.9 + - - +
201D ASP* 3.1 12.5 + - + +
202D VAL* 3.0 25.8 + - + +
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Residues in contact with LYS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ASP* 5.5 5.1 + - - +
195D TYR 4.3 0.8 + - - +
196D ASP* 3.1 43.6 + - - +
198D LEU* 1.3 80.2 - - - +
200D TYR* 1.3 87.2 + - + +
202D VAL* 3.5 10.3 - - - +
203D LYS* 3.0 29.8 + - - +
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Residues in contact with TYR 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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196D ASP 3.7 9.0 - - - -
197D GLY* 3.4 18.6 + - - +
198D LEU 3.2 0.4 - - - -
199D LYS* 1.3 105.8 + - + +
201D ASP* 1.3 61.0 + - - +
203D LYS* 3.9 16.6 - - + +
204D LYS* 3.0 28.5 + - - +
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Residues in contact with ASP 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU 4.5 1.0 - - - +
148D ALA* 3.8 7.6 - - - +
149D SER* 3.1 41.6 + - - -
152D SER* 3.0 26.6 + - - +
174D ILE* 4.5 5.2 - - + -
197D GLY 3.6 14.7 - - - +
198D LEU* 3.1 19.6 + - + +
200D TYR* 1.3 77.8 - - - +
202D VAL* 1.3 66.5 + - - +
204D LYS* 3.2 3.8 + - - +
205D VAL* 3.0 28.0 + - - +
203E LYS* 5.5 1.2 + - - -
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 3.7 25.1 - - + +
175D ASN* 4.0 8.0 + - - +
178D ASP* 4.0 29.2 - - + +
198D LEU* 3.0 21.8 + - + +
199D LYS* 3.5 10.1 - - - +
200D TYR 3.3 0.2 - - - -
201D ASP* 1.3 78.5 - - - +
203D LYS* 1.3 65.8 + - - +
205D VAL* 3.1 2.5 + - - +
206D GLU* 3.0 35.1 + - + +
153F ARG* 3.4 31.9 - - - +
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Residues in contact with LYS 203 (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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199D LYS 3.0 13.1 + - - +
200D TYR* 3.9 17.2 - - + +
202D VAL* 1.3 82.1 - - - +
204D LYS* 1.3 66.8 + - + +
206D GLU* 3.4 9.1 + - - +
207D GLU* 3.0 59.4 + - + +
153F ARG* 6.0 4.7 - - + +
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Residues in contact with LYS 204 (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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152D SER* 3.6 25.9 + - - +
153D ARG* 4.0 19.8 - - - +
156D VAL* 3.8 28.6 - - + +
200D TYR 3.0 19.2 + - - +
201D ASP* 3.4 7.0 - - - +
202D VAL 3.2 0.4 - - - -
203D LYS* 1.3 82.6 - - + +
205D VAL* 1.3 63.4 + - - +
207D GLU* 3.2 8.4 + - - +
208D VAL* 3.0 25.5 + - + +
203E LYS* 4.4 20.4 - - - +
207E GLU* 3.3 29.4 + - - +
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Residues in contact with VAL 205 (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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152D SER* 3.8 28.3 - - - -
155D SER* 3.9 8.5 - - - +
167D PRO 3.5 11.0 - - - +
170D ILE* 3.7 15.5 - - + -
171D SER* 3.4 36.6 - - - +
174D ILE* 4.0 11.2 - - + -
175D ASN* 6.3 0.2 - - - +
201D ASP 3.0 16.2 + - - +
202D VAL* 3.9 3.1 - - - +
204D LYS* 1.3 75.1 - - - +
206D GLU* 1.3 63.7 + - - +
208D VAL* 3.2 8.4 + - - +
209D VAL* 3.0 22.0 + - - +
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D SER* 4.0 17.3 - - - +
175D ASN* 3.2 14.8 + - - +
202D VAL* 3.0 24.1 + - + +
203D LYS* 3.7 8.0 - - - +
205D VAL* 1.3 76.0 - - - +
207D GLU* 1.3 59.7 + - + +
209D VAL* 3.3 6.3 + - - +
210D TYR* 3.0 26.5 + - - +
46F HIS* 5.3 1.0 - - - +
153F ARG* 2.8 51.3 + - - +
156F VAL* 4.2 4.5 - - + +
157F ASN* 3.1 34.6 + - - +
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Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D LYS* 3.0 57.6 + - + +
204D LYS* 3.6 6.6 - - - +
206D GLU* 1.3 75.0 - - + +
208D VAL* 1.3 64.4 + - - +
210D TYR* 3.4 10.4 + - + +
211D ASP* 2.9 30.5 + - - +
156F VAL* 4.4 22.1 - - + +
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D SER 5.5 0.2 - - - +
155D SER* 3.6 21.8 - - - +
156D VAL* 3.9 26.9 - - + -
159D VAL* 3.6 31.2 - - + -
167D PRO* 3.9 7.9 - - + -
204D LYS* 3.0 19.2 + - + +
205D VAL* 3.2 7.8 + - - +
207D GLU* 1.3 76.6 - - - +
209D VAL* 1.3 63.4 + - - +
211D ASP* 3.1 6.1 + - - +
212D LEU* 3.0 20.7 + - + +
210E TYR* 3.6 19.7 - - + +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO* 3.5 28.9 - - + +
168D LEU* 3.9 26.7 - - + +
171D SER* 3.8 15.0 - - - +
205D VAL 3.0 14.5 + - - +
206D GLU* 3.6 9.6 - - - +
207D GLU 3.3 0.2 - - - -
208D VAL* 1.3 76.4 - - - +
210D TYR* 1.3 65.7 + - - +
212D LEU* 3.2 8.8 + - + +
213D SER* 3.0 29.8 + - - +
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Residues in contact with TYR 210 (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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206D GLU 3.0 7.5 + - - +
207D GLU* 3.6 10.1 - - + +
208D VAL 3.3 0.2 - - - -
209D VAL* 1.3 75.6 - - - +
211D ASP* 1.3 78.1 + - - +
213D SER* 3.2 6.4 + - - -
214D ILE* 3.1 63.9 + - + +
155F SER 4.9 2.9 - - - -
156F VAL* 3.3 59.7 - - + +
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Residues in contact with ASP 211 (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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207D GLU* 2.9 16.5 + - - +
208D VAL 3.2 11.9 - - - +
210D TYR* 1.3 93.1 - - - +
212D LEU* 1.3 58.8 + - - +
214D ILE* 3.8 1.3 - - - +
215D ARG* 2.8 47.1 + - - +
210E TYR* 2.9 32.6 + - - +
211E ASP* 4.7 0.5 - - - +
214E ILE* 3.7 10.1 - - + +
215E ARG* 4.3 15.6 + - - -
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Residues in contact with LEU 212 (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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159D VAL* 4.1 13.7 - - + -
164D TYR* 3.9 47.6 - - + +
167D PRO* 3.8 32.8 - - + -
168D LEU* 4.4 7.4 - - + -
208D VAL 3.0 15.0 + - - +
209D VAL* 3.6 8.7 - - - +
210D TYR 3.1 0.4 - - - -
211D ASP* 1.3 76.6 - - - +
213D SER* 1.3 64.3 + - - +
215D ARG* 3.0 7.7 + - - -
216D GLY 3.1 2.1 + - - -
217D PHE* 3.0 41.0 + - + +
214E ILE* 4.0 20.4 - - + -
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Residues in contact with SER 213 (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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168D LEU* 6.0 0.9 - - - +
209D VAL* 3.0 25.8 + - - +
210D TYR* 3.2 7.4 + - - -
212D LEU* 1.3 71.4 - - - +
214D ILE* 1.3 61.1 + - - +
215D ARG 2.8 4.7 - - - -
216D GLY* 2.7 21.5 + - - -
217D PHE 4.1 15.0 + - - +
218D ASN* 5.0 5.3 - - - +
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Residues in contact with ILE 214 (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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210D TYR* 3.1 58.6 + - + +
211D ASP* 3.8 0.7 - - - +
213D SER* 1.3 74.6 - - - +
215D ARG* 1.3 94.7 + - + +
216D GLY 3.4 0.4 - - - -
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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