Contacts of the helix formed by residues 204 - 214 (chain A) in PDB entry 2PKG
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 GLU 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ARG* 3.1 33.0 + - + +
171A ARG* 2.9 33.9 + - - +
196A LEU* 5.0 4.9 - - + -
200A ASN* 2.7 48.0 + - + +
203A SER* 1.3 84.3 + - - +
205A ILE* 1.3 72.0 + - - +
207A PRO* 2.9 16.9 - - - +
208A MET* 2.9 26.5 + - + +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.3 13.9 - - + +
192A PHE* 4.5 5.6 - - + -
193A ALA* 3.3 44.9 - - + +
196A LEU* 3.6 20.4 - - + -
200A ASN 3.8 2.0 + - - -
201A VAL* 3.3 31.0 - - + +
204A GLU* 1.3 83.1 - - - +
206A ILE* 1.3 53.4 + - - +
208A MET* 2.7 20.1 + - + +
209A PHE* 2.6 32.4 + - + -
231A ILE* 3.8 27.6 - - + -
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL 2.9 22.2 - - - +
202A LYS 3.3 6.7 - - - +
205A ILE* 1.3 78.6 - - - +
207A PRO* 1.4 62.2 - - + +
209A PHE* 3.0 14.3 + - + +
210A SER* 2.7 37.8 + - - -
231A ILE* 4.1 17.0 - - + -
235A LEU* 3.9 13.7 - - + -
243A LEU* 3.4 68.2 - - + +
244A VAL* 4.7 2.2 - - + -
247A THR* 6.1 0.2 - - - +
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Residues in contact with PRO 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS 3.5 3.6 - - - +
203A SER* 3.8 9.2 - - - +
204A GLU* 2.9 39.5 - - - +
206A ILE* 1.4 90.7 - - + +
208A MET* 1.3 63.0 + - + +
210A SER* 3.1 6.8 + - - -
211A ASN* 2.9 36.3 + - - +
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Residues in contact with MET 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ARG* 5.3 7.9 - - + +
170A PHE* 3.5 25.6 - - + +
171A ARG* 4.2 24.7 - - + +
174A CYS* 3.4 36.1 - - + -
189A LEU* 3.8 9.0 - - + -
192A PHE* 5.4 3.4 - - + -
196A LEU* 5.5 1.3 - - + -
204A GLU* 2.9 35.8 + - + +
205A ILE* 2.7 30.6 + - + +
207A PRO* 1.3 74.0 - - + +
209A PHE* 1.3 61.9 + - - +
210A SER 3.1 0.2 + - - -
211A ASN* 3.8 7.3 - - - +
212A LEU* 2.9 32.4 + - - +
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.4 18.0 - - + +
205A ILE 2.6 15.2 + - - +
206A ILE* 3.2 24.2 - - + +
208A MET* 1.3 73.0 - - - +
210A SER* 1.3 59.5 + - - +
212A LEU* 4.1 0.7 - - - +
213A ALA* 3.0 27.8 + - + +
224A ALA* 4.0 17.5 - - - +
225A VAL* 4.7 2.7 - - + -
228A CYS* 3.8 44.0 - - + -
231A ILE* 3.2 30.5 - - + -
243A LEU 5.3 0.2 - - - -
244A VAL* 4.6 13.5 - - + -
247A THR* 3.1 44.0 - - + -
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 2.7 19.2 + - - -
207A PRO* 3.4 11.0 - - - -
208A MET 3.1 0.2 - - - -
209A PHE* 1.3 74.3 - - - +
211A ASN* 1.3 68.7 + - - +
212A LEU 3.1 1.3 - - - -
213A ALA* 2.7 15.9 + - - +
214A SER* 2.6 28.2 + - - -
247A THR* 4.3 14.1 + - - -
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Residues in contact with ASN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A CYS* 5.8 3.4 - - + +
207A PRO* 2.9 25.2 + - - +
208A MET* 3.8 5.8 - - - +
210A SER* 1.3 75.5 + - - +
212A LEU* 1.3 60.8 + - + +
214A SER* 2.9 9.8 + - - -
215A ASP* 2.8 27.8 + - - +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A CYS* 3.7 51.4 - - + +
182A ARG* 3.9 17.0 - - + +
186A ALA* 4.1 13.5 - - + +
189A LEU* 4.2 14.8 - - + -
208A MET 2.9 23.6 + - - +
209A PHE* 4.1 3.8 - - - +
211A ASN* 1.3 74.6 - - + +
213A ALA* 1.3 63.5 + - - +
214A SER 3.0 5.8 + - - -
215A ASP* 3.2 12.8 + - + +
220A VAL* 3.6 28.6 - - + +
221A ARG* 3.2 19.2 + - - -
224A ALA* 3.7 12.2 - - + +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.0 22.4 + - + +
210A SER 2.7 10.7 + - - +
212A LEU* 1.3 73.0 - - - +
214A SER* 1.3 58.3 + - - +
215A ASP 3.7 0.2 - - - -
221A ARG* 3.1 23.3 + - - +
224A ALA* 3.4 17.5 - - + +
225A VAL* 5.2 6.5 - - + +
247A THR* 3.5 27.8 - - + -
250A GLN* 5.7 4.4 - - - +
251A ALA* 6.6 0.2 - - + -
254A ASP* 4.3 3.8 - - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 2.6 24.1 + - - -
211A ASN* 3.2 7.1 + - - -
213A ALA* 1.3 79.7 - - - +
215A ASP* 1.3 65.8 + - - +
216A GLU* 3.7 1.0 + - - -
221A ARG* 3.5 6.1 - - - +
250A GLN* 6.1 5.4 - - - -
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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