Contacts of the helix formed by residues 196 - 210 (chain B) in PDB entry 1PJQ
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 ASP 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A PHE 4.6 2.4 - - - +
455A SER* 3.9 8.0 + - - +
456A ASN* 2.6 51.0 + - - +
457A HIS* 4.7 8.0 - - - +
191B SER* 3.2 13.8 + - - +
194B ASN* 4.2 13.7 - - + +
195B ALA* 1.3 74.0 - - - +
197B GLU* 1.3 61.4 + - - +
198B LYS* 3.7 5.9 + - - +
199B ALA* 3.6 19.6 + - + +
200B VAL* 2.9 26.9 + - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ALA 3.6 5.6 + - - +
196B ASP* 1.3 74.2 + - - +
198B LYS* 1.3 58.3 + - + +
200B VAL* 3.3 11.3 + - + +
201B ASN* 2.8 47.5 + - - +
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ASN* 5.2 9.6 - - + +
196B ASP* 3.4 7.2 + - - +
197B GLU* 1.3 77.7 - - + +
199B ALA* 1.3 58.5 + - - +
201B ASN* 3.2 9.0 + - - +
202B ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A PHE 6.1 0.2 - - - +
456A ASN* 4.1 7.1 - - - +
191B SER* 3.6 20.2 - - - +
196B ASP* 3.3 27.9 + - - +
198B LYS* 1.3 78.7 - - - +
200B VAL* 1.3 58.6 + - - +
202B ALA* 4.1 6.7 - - - -
203B THR* 2.8 38.3 + - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 4.0 19.3 - - + +
188B LEU* 4.2 8.8 - - + +
191B SER* 3.7 30.1 - - - +
192B LEU* 3.6 31.4 - - + +
196B ASP 2.9 27.1 + - - +
197B GLU* 3.4 13.5 - - + +
198B LYS 3.2 0.2 - - - -
199B ALA* 1.3 77.8 - - - +
201B ASN* 1.3 54.0 + - - +
203B THR 4.0 0.3 - - - -
204B THR* 2.5 39.0 + - - +
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B TYR* 5.7 1.3 + - - -
197B GLU* 2.8 42.4 + - - +
198B LYS* 3.2 7.8 + - - +
200B VAL* 1.3 77.6 - - - +
202B ALA* 1.3 65.5 + - - +
204B THR* 3.6 4.4 - - - -
205B GLU* 3.0 35.8 + - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LYS 2.8 20.8 + - - +
199B ALA* 3.6 8.5 - - - +
201B ASN* 1.3 75.8 - - - +
203B THR* 1.3 64.0 + - - +
205B GLU* 3.5 3.6 + - - +
206B ARG* 3.2 21.9 + - - +
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Residues in contact with THR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ASN* 3.8 20.6 - - - +
187B ARG* 3.7 24.6 + - - +
188B LEU* 3.6 37.4 + - + -
191B SER* 4.9 3.5 + - - -
199B ALA* 2.8 23.5 + - - +
200B VAL 4.3 2.5 - - - -
202B ALA* 1.3 73.6 - - - +
204B THR* 1.3 60.1 + - - +
206B ARG* 3.8 7.0 + - - +
207B LEU* 3.2 21.8 + - - +
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Residues in contact with THR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B TYR* 3.0 32.3 + - - +
161B LEU* 4.1 16.4 - - + -
164B ARG* 4.7 6.1 - - - +
188B LEU* 4.1 3.4 - - - +
200B VAL 2.5 24.7 + - - -
201B ASN* 3.6 6.7 - - - -
203B THR* 1.3 75.8 - - - +
205B GLU* 1.3 69.2 + - - +
207B LEU* 3.0 21.6 + - + +
208B PHE* 3.2 37.3 - - + -
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ARG* 2.5 44.4 + - - +
201B ASN* 3.0 26.3 + - - +
202B ALA* 4.0 4.3 - - - +
204B THR* 1.3 78.9 - - - +
206B ARG* 1.3 52.9 + - - +
208B PHE* 2.9 6.2 + - - +
209B SER* 2.7 40.4 + - - -
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ARG* 5.6 5.5 - - - +
202B ALA 3.2 15.5 + - - +
203B THR* 3.9 8.7 - - - +
205B GLU* 1.3 79.0 - - - +
207B LEU* 1.3 63.7 + - + +
209B SER* 4.0 10.3 - - - +
210B GLU* 3.0 56.3 + - + +
216B GLY* 3.6 24.2 + - - -
290B ALA 5.2 2.2 + - - -
321B GLY 2.6 27.5 + - - -
322B ILE* 4.6 5.7 - - - +
323B PRO* 3.5 24.9 - - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 5.5 2.7 - - + -
169B PHE* 5.1 2.8 - - - -
178B PHE* 3.6 28.0 - - + -
181B LYS* 3.7 39.3 + - + +
182B PHE* 3.9 22.9 - - + -
185B ASN* 3.4 25.4 - - + +
187B ARG* 5.9 0.4 - - - +
188B LEU* 3.9 26.7 - - + -
203B THR 3.2 17.0 + - - +
204B THR* 3.0 14.6 + - - +
206B ARG* 1.3 79.5 - - + +
208B PHE* 1.3 59.0 + - + +
210B GLU* 4.1 11.8 - - - +
212B LEU* 5.9 0.5 - - - +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.0 21.1 - - + -
164B ARG* 3.3 62.1 - - + +
165B VAL* 3.9 15.3 - - + -
168B GLN* 3.6 26.7 - - - +
169B PHE* 4.5 10.7 - + - -
178B PHE* 3.5 33.7 - + - -
204B THR* 3.2 41.5 - - + -
205B GLU 2.9 4.7 + - - +
207B LEU* 1.3 77.7 - - + +
209B SER* 1.3 64.9 + - - +
210B GLU 3.5 5.9 - - - +
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B GLU* 2.7 21.9 + - - -
206B ARG* 3.9 8.9 + - - +
208B PHE* 1.3 77.6 - - - +
210B GLU* 1.3 65.9 + - - +
211B PRO* 4.0 1.6 - - - +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PHE* 5.9 1.7 - - - -
181B LYS* 2.8 32.0 + - - +
206B ARG* 3.0 50.9 + - + +
207B LEU* 4.1 11.7 - - - +
208B PHE 3.8 8.5 - - - +
209B SER* 1.3 84.7 + - - +
211B PRO* 1.3 81.1 - - + +
212B LEU* 3.4 2.3 + - - -
214B HIS* 3.0 24.3 - - + +
215B ARG* 4.4 2.1 - - - -
216B GLY 4.2 8.3 + - - -
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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