Contacts of the helix formed by residues 184 - 196 (chain B) in PDB entry 3AP1
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ARG* 1.3 70.8 - - - +
185B GLY* 1.3 60.1 + - - +
186B ARG* 2.8 57.3 + - - +
187B ALA* 2.9 26.4 + - + +
188B SER* 3.0 9.9 + - - -
239B GLU* 2.9 19.6 + - - +
301B TRP* 3.8 1.7 - - - -
320B LEU* 3.5 4.3 - - - +
325B TYR* 3.3 24.4 + - + -
332B PRO* 3.7 0.2 - - - +
334B TYR* 2.7 31.3 + - - +
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Residues in contact with GLY 185 (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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183B ARG 2.9 4.2 + - - -
184B ASP* 1.3 72.1 + - - +
186B ARG* 1.3 56.8 + - - +
188B SER* 3.8 1.1 - - - -
189B VAL* 2.9 35.7 + - - +
211B LEU* 3.6 6.3 - - - -
214B TRP* 3.2 45.9 - - - -
320B LEU* 3.6 6.1 - - - +
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Residues in contact with ARG 186 (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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184B ASP* 2.8 36.1 + - - +
185B GLY* 1.3 76.3 - - - +
187B ALA* 1.3 57.7 + - - +
189B VAL* 4.2 1.2 - - - +
190B HIS* 3.0 31.4 + - - +
211B LEU* 3.8 8.5 - - + +
301B TRP* 3.5 41.9 - - + +
305B ILE* 4.2 10.2 - - + +
313B MET* 3.7 39.0 - - + +
320B LEU* 4.1 6.8 - - + +
325B TYR* 4.2 5.9 - - - +
326B ASP 3.0 20.6 + - - -
327B PRO* 3.3 27.0 + - - +
329B ALA 3.0 19.0 + - - -
330B ASN* 4.4 4.6 - - - +
332B PRO* 3.3 13.7 - - - +
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Residues in contact with ALA 187 (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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1B A3P 4.7 0.3 + - - -
183B ARG* 3.4 35.3 + - + +
184B ASP* 2.9 15.1 + - + +
186B ARG* 1.3 77.0 - - - +
188B SER* 1.3 65.5 + - - +
190B HIS* 3.9 1.6 - - - +
191B SER* 3.0 24.9 + - - -
239B GLU* 5.0 0.7 - - - +
297B ALA 4.8 0.4 - - - +
298B LEU 4.2 6.3 - - - +
301B TRP* 3.4 28.3 - - + +
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 4.1 7.4 - - - -
78B ARG* 3.0 29.1 + - - +
79B SER* 3.1 17.1 + - - -
183B ARG* 3.6 15.4 + - - +
184B ASP 3.0 7.3 + - - -
185B GLY 3.4 6.3 + - - -
187B ALA* 1.3 76.3 - - - +
189B VAL* 1.3 61.3 + - - +
191B SER* 3.4 3.3 + - - -
192B MET* 3.1 29.4 + - - +
214B TRP* 4.1 17.4 + - - -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY 2.9 21.0 + - - +
186B ARG 4.2 1.8 - - - +
188B SER* 1.3 74.0 - - - +
190B HIS* 1.3 65.6 + - - +
192B MET* 3.3 12.3 - - + +
193B ILE* 3.0 36.7 + - + +
207B TYR* 3.7 21.5 - - + +
210B CYS* 3.5 49.1 - - + +
211B LEU* 3.6 15.7 - - + +
214B TRP* 4.1 10.3 - - + -
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Residues in contact with HIS 190 (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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1B A3P 6.1 0.9 - - - -
186B ARG 3.0 20.6 + - - +
187B ALA 3.9 1.8 - - - +
189B VAL* 1.3 76.5 - - - +
191B SER* 1.3 59.3 + - - +
193B ILE* 3.9 0.5 - - - +
194B THR* 2.9 64.5 + - + +
207B TYR* 2.7 36.6 + - + -
300B LYS* 3.7 20.7 + - + +
301B TRP* 3.5 28.5 - - + -
304B HIS* 3.5 33.2 + + - +
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Residues in contact with SER 191 (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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1B A3P 2.6 38.0 + - - -
78B ARG* 2.8 27.2 + - - +
183B ARG* 4.2 1.6 - - - -
187B ALA 3.0 18.1 + - - -
188B SER 3.4 5.8 - - - -
189B VAL 3.2 0.2 - - - -
190B HIS* 1.3 78.4 - - - +
192B MET* 1.3 57.9 + - - +
194B THR* 3.9 4.9 - - - -
195B ARG* 2.9 37.6 + - - +
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Residues in contact with MET 192 (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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76B VAL* 4.4 7.2 - - + -
77B PRO 4.1 13.7 - - - +
78B ARG* 3.9 12.3 - - + -
188B SER* 3.1 24.0 + - - +
189B VAL* 3.3 19.1 - - + +
191B SER* 1.3 79.2 + - - +
193B ILE* 1.3 59.7 + - + +
196B LYS* 2.9 23.9 + - - -
197B VAL* 3.0 28.3 + - + +
199B ILE* 3.9 23.8 - - + -
202B PHE* 3.6 34.3 - - + -
204B LEU* 3.8 16.0 - - + +
210B CYS* 4.2 13.0 - - - -
214B TRP* 5.5 0.7 - - + -
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Residues in contact with ILE 193 (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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189B VAL* 3.0 35.1 + - + +
190B HIS 4.0 2.2 - - - +
192B MET* 1.3 77.0 - - - +
194B THR* 1.3 64.1 + - + +
196B LYS* 3.4 19.4 + - - +
204B LEU* 3.5 40.7 - - + +
205B SER 5.3 0.2 - - - -
206B SER 3.9 4.7 - - - +
207B TYR* 3.7 55.6 - - + +
210B CYS* 4.2 8.1 - - - -
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Residues in contact with THR 194 (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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190B HIS* 2.9 64.7 + - + +
191B SER* 3.5 6.1 + - - -
193B ILE* 1.3 76.9 - - + +
195B ARG* 1.3 68.8 + - - +
196B LYS* 3.7 9.5 + - - +
207B TYR* 4.2 5.6 - - - +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A3P 2.7 39.0 + - - -
78B ARG* 3.4 19.8 - - - +
191B SER* 2.9 18.1 + - - +
194B THR* 1.3 82.6 - - - +
196B LYS* 1.3 68.5 + - - +
197B VAL* 3.9 11.7 - - + -
284B ARG* 2.8 35.5 + - - +
287B ASP* 4.5 7.3 + - - -
288B GLN* 3.6 30.1 + - - +
300B LYS* 3.6 13.4 - - - +
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Residues in contact with LYS 196 (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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192B MET 2.9 11.8 + - - -
193B ILE 3.4 11.9 + - - +
194B THR 3.4 8.0 - - - +
195B ARG* 1.3 79.3 - - - +
197B VAL* 1.3 62.2 + - - +
198B THR* 3.6 10.9 + - + +
204B LEU* 3.9 14.6 - - + -
284B ARG* 2.9 14.1 + - - +
1005T ASP* 3.9 1.7 - - - +
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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