Contacts of the helix formed by residues 215 - 227 (chain B) in PDB entry 2PK9
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 ASN 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ASP* 3.5 27.2 + - - +
210B PRO* 2.6 39.9 + - - +
211B LYS* 3.3 29.4 + - - +
213B GLY* 3.3 4.0 + - - -
214B TYR* 1.3 81.5 - - - +
216B VAL* 1.3 63.6 + - - +
217B LEU 3.6 1.6 - - - -
218B ASP* 4.0 9.5 + - - +
219B LYS* 3.3 23.9 + - - +
222B ARG* 4.9 1.2 + - - -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR* 3.7 36.6 - - + -
172B PRO* 3.8 16.2 - - + +
173B ARG* 3.2 43.1 - - - +
174B ASP* 3.4 12.8 - - - +
213B GLY 4.3 0.2 - - - +
214B TYR 3.6 1.6 - - - -
215B ASN* 1.3 75.8 - - - +
217B LEU* 1.3 62.4 + - + +
219B LYS* 3.1 12.5 + - + +
220B TYR* 3.0 40.9 + - + -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 4.5 9.9 - - + -
161A PRO* 5.3 3.1 - - + -
27B PHE* 3.6 28.3 - - + -
93B CYS* 3.8 29.8 - - + +
96B MET* 3.7 15.8 - - + +
97B THR* 3.6 35.9 - - - +
100B TYR* 4.8 6.5 - - + -
172B PRO* 3.8 28.0 - - + +
214B TYR 5.5 0.6 - - - -
215B ASN 3.6 0.2 - - - -
216B VAL* 1.3 79.9 - - + +
218B ASP* 1.3 59.6 + - - +
220B TYR* 3.5 5.4 + - + +
221B TYR* 2.9 26.9 + - - +
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Residues in contact with ASP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 5.1 7.3 - - - +
26B ASP* 5.6 2.6 - - - +
27B PHE* 3.9 21.2 - - + -
211B LYS* 3.5 27.7 + - - -
214B TYR 4.2 5.5 - - - +
215B ASN* 4.2 6.1 - - - +
216B VAL 3.3 0.2 - - - -
217B LEU* 1.3 74.7 + - - +
219B LYS* 1.3 58.7 + - - +
221B TYR* 3.0 9.4 + - + +
222B ARG* 2.8 54.9 + - + +
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASP* 6.1 1.6 - - - +
215B ASN 3.3 13.4 + - - +
216B VAL* 3.1 17.2 + - + +
218B ASP* 1.3 79.8 - - - +
220B TYR* 1.3 65.9 + - + +
222B ARG* 3.2 27.0 + - - +
223B ARG* 3.1 27.3 + - - +
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Residues in contact with TYR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET* 3.5 20.2 - - + +
99B LEU* 3.8 24.5 - - + -
100B TYR* 3.5 46.3 - + + -
103B ASP* 2.8 40.1 + - - +
177B ILE* 4.5 3.6 - - - +
216B VAL* 3.0 34.2 + - + +
217B LEU* 3.7 5.4 - - - +
219B LYS* 1.3 85.2 - - + +
221B TYR* 1.3 65.4 + - - +
223B ARG* 3.2 8.5 + - + +
224B ILE* 3.1 28.6 + - + +
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Residues in contact with TYR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.1 23.0 - - + +
24B PRO* 3.0 33.5 + - - +
25B ALA 3.5 16.8 - - - -
27B PHE* 3.6 34.3 - + + -
30B CYS* 4.0 6.0 - - - +
35B LEU* 3.7 27.6 - - + -
38B LEU* 4.5 7.0 - - + -
96B MET* 3.4 10.9 - - + +
217B LEU 2.9 15.8 + - - +
218B ASP* 3.0 11.9 + - - +
220B TYR* 1.3 77.6 - - - +
222B ARG* 1.3 68.7 + - + +
224B ILE* 3.3 17.7 - - + +
225B VAL* 3.3 24.9 - - + +
245B LEU* 3.7 15.3 - - + -
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Residues in contact with ARG 222 (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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25B ALA 5.7 1.8 - - - +
215B ASN 4.9 1.2 + - - -
218B ASP* 2.8 50.7 + - + +
219B LYS* 3.2 28.7 + - - +
221B TYR* 1.3 77.1 - - + +
223B ARG* 1.3 60.8 + - - +
225B VAL* 3.6 3.5 + - - +
226B GLN* 3.1 25.7 + - - +
245B LEU* 3.8 28.3 - - + +
248B ASN 5.4 7.2 - - - -
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Residues in contact with ARG 223 (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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42B MET* 5.2 0.7 - - + -
219B LYS 3.1 19.8 + - - +
220B TYR* 3.2 10.7 + - + +
222B ARG* 1.3 76.7 - - - +
224B ILE* 1.3 61.7 + - + +
226B GLN* 2.5 46.9 + - - +
227B LEU* 2.8 59.4 + - + +
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Residues in contact with ILE 224 (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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35B LEU* 5.2 1.6 - - + -
38B LEU* 3.4 41.4 - - + +
39B ILE* 4.2 14.6 - - + -
42B MET* 3.6 32.8 - - + -
96B MET* 4.6 10.8 - - + -
99B LEU* 3.5 24.7 - - + -
220B TYR* 3.1 12.7 + - + +
221B TYR* 3.3 18.6 - - + +
223B ARG* 1.3 77.7 - - + +
225B VAL* 1.3 60.8 + - - +
226B GLN 3.2 0.2 - - - -
228B VAL* 3.1 17.1 + - + +
229B GLY* 3.0 21.7 + - - -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.8 11.2 - - + -
38B LEU* 3.8 25.6 - - + -
221B TYR* 3.3 21.3 + - + +
222B ARG 3.9 4.5 - - - +
223B ARG 3.3 0.2 - - - -
224B ILE* 1.3 77.2 - - - +
226B GLN* 1.3 60.7 + - - +
229B GLY* 3.2 19.6 - - - -
230B SER 4.6 0.5 + - - -
243B TYR* 3.7 24.1 - - + +
244B VAL 4.0 6.7 - - - +
245B LEU* 3.7 38.6 - - + +
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Residues in contact with GLN 226 (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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222B ARG* 3.1 12.7 + - - +
223B ARG* 2.5 56.3 + - - +
225B VAL* 1.3 77.5 - - - +
227B LEU* 1.3 68.1 + - + +
230B SER 5.8 0.2 + - - -
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Residues in contact with LEU 227 (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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42B MET* 3.5 31.6 - - + -
223B ARG* 2.8 62.3 + - + +
226B GLN* 1.3 84.4 - - + +
228B VAL* 1.3 62.6 + - + +
229B GLY 3.3 5.1 + - - -
230B SER* 4.4 7.1 + - - -
232B ASN 5.1 4.3 - - - +
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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