Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 2PHA
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 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B VAL 2.8 24.8 + - - -
204B ASP 4.8 2.2 - - - -
205B ARG 3.5 1.4 - - - -
206B LEU* 1.3 79.6 - - - +
208B ILE* 1.3 66.4 + - - -
209B GLY 3.1 4.6 + - - -
210B LYS 3.3 0.4 + - - -
211B VAL* 3.2 18.6 + - - +
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Residues in contact with ILE 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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177B ILE* 4.6 2.0 - - + -
203B VAL* 3.7 23.5 + - + +
207B GLY* 1.3 71.0 - - - -
209B GLY* 1.3 62.7 + - - +
210B LYS 3.5 0.2 - - - -
211B VAL* 3.4 14.8 - - + +
212B MET* 3.2 17.0 + - - +
252B LEU* 4.1 13.7 - - + -
256B GLU* 3.8 35.9 + - + +
259B TYR* 3.7 29.0 - - + -
260B ILE* 3.3 33.7 - - + -
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLY 3.1 1.4 - - - -
208B ILE* 1.3 79.3 - - - +
210B LYS* 1.3 64.2 + - - +
211B VAL 3.0 1.6 - - - -
212B MET* 3.3 4.0 + - - +
213B GLU* 3.2 22.3 + - - +
259B TYR* 3.6 25.0 + - - -
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Residues in contact with LYS 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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62A SER* 3.5 17.4 - - - -
63A PRO* 4.8 2.8 + - - +
206B LEU* 3.3 44.2 + - + +
207B GLY 3.3 1.6 + - - -
209B GLY* 1.3 74.2 - - - +
211B VAL* 1.3 56.7 + - - +
213B GLU* 2.9 36.1 + - - +
214B GLU* 2.7 68.1 + - - +
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Residues in contact with VAL 211 (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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177B ILE* 4.3 13.0 - - + -
198B PHE* 3.9 34.7 - - + -
202B GLU 4.1 5.2 - - - +
203B VAL* 3.9 25.6 - - + -
206B LEU* 4.3 2.9 - - + -
207B GLY 3.2 15.5 + - - +
208B ILE* 3.4 26.7 - - + +
209B GLY 3.0 0.6 - - - -
210B LYS* 1.3 76.2 - - - +
212B MET* 1.3 63.0 + - - +
214B GLU* 3.4 1.4 + - - +
215B THR* 2.8 46.7 + - + +
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Residues in contact with MET 212 (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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121B ILE* 4.9 2.0 - - + -
177B ILE* 4.0 11.4 - - - -
208B ILE 3.2 13.0 + - - +
209B GLY 3.3 1.1 + - - +
211B VAL* 1.3 76.9 - - - +
213B GLU* 1.3 60.5 + - - +
215B THR* 2.6 30.8 + - - +
216B LEU* 2.8 34.9 + - + +
259B TYR* 3.8 26.2 - - + +
260B ILE* 3.2 57.9 - - + +
263B GLU* 4.0 16.6 - - + +
264B ILE* 3.3 24.2 - - + -
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Residues in contact with GLU 213 (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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209B GLY 3.2 16.5 + - - +
210B LYS* 2.9 46.9 + - - +
212B MET* 1.3 77.9 - - - +
214B GLU* 1.3 59.6 + - - +
216B LEU* 3.9 3.8 - - - +
217B SER* 2.9 34.5 + - - -
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Residues in contact with GLU 214 (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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62A SER* 3.0 17.1 + - - -
63A PRO* 3.9 24.1 - - + +
196B LYS* 4.1 9.8 + - - +
198B PHE* 3.3 28.9 - - + -
206B LEU* 3.3 16.4 - - - +
210B LYS* 2.7 48.4 + - - +
213B GLU* 1.3 79.5 - - - +
215B THR* 1.3 61.2 + - - +
217B SER* 2.9 17.9 + - - -
218B TYR* 3.0 20.1 + - - +
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Residues in contact with THR 215 (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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121B ILE* 5.4 2.9 - - - +
175B VAL* 3.8 15.2 - - + +
177B ILE* 3.7 23.1 - - + -
198B PHE* 3.2 30.1 - - + -
211B VAL* 2.8 25.1 + - + +
212B MET* 2.6 26.3 + - - +
214B GLU* 1.3 76.1 - - - +
216B LEU* 1.3 65.7 + - - +
218B TYR* 3.0 7.0 + - - +
219B LEU* 2.8 42.5 + - - +
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Residues in contact with LEU 216 (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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121B ILE* 4.3 17.3 - - + -
212B MET* 2.8 38.1 + - + +
213B GLU* 4.2 3.1 - - - +
215B THR* 1.3 82.4 + - - +
217B SER* 1.3 57.8 + - - +
219B LEU* 4.4 4.9 - - + -
220B LEU* 2.8 43.6 + - + +
227B ILE* 5.5 3.8 - - + -
263B GLU* 3.5 25.1 - - + +
264B ILE* 4.5 3.8 - - + -
267B THR* 3.5 35.2 - - + -
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Residues in contact with SER 217 (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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63A PRO* 5.8 3.6 - - - +
65A GLN 6.2 0.2 - - - -
213B GLU* 2.9 21.7 + - - -
214B GLU* 2.9 18.2 + - - +
216B LEU* 1.3 74.6 - - - +
218B TYR* 1.3 64.4 + - - +
219B LEU 3.1 0.4 - - - -
221B GLY* 2.9 31.5 + - - +
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Residues in contact with TYR 218 (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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20A PRO* 5.9 1.7 - - - +
68A LYS* 4.7 28.3 - - + -
171B ALA 4.8 0.7 + - - -
172B LYS* 3.6 32.8 + - - +
173B ASP* 5.5 0.2 - - - -
174B ILE 4.6 4.3 - - - -
175B VAL* 4.1 14.4 - - + -
194B GLY 4.3 7.8 + - - -
196B LYS* 3.5 56.3 + - + +
214B GLU 3.0 16.8 + - - +
215B THR* 3.4 3.8 - - - +
217B SER* 1.3 83.0 + - - +
219B LEU* 1.3 62.7 + - + +
221B GLY 4.8 0.9 + - - -
225B ARG* 5.1 1.7 + - - -
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Residues in contact with LEU 219 (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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119B GLY* 3.5 26.5 - - - -
120B VAL 3.9 5.2 - - - +
121B ILE* 3.7 31.0 - - + -
173B ASP 4.1 7.9 - - - +
175B VAL* 3.3 33.7 - - + -
215B THR* 2.8 16.5 + - - +
216B LEU* 4.2 3.4 - - + +
218B TYR* 1.3 82.7 - - + +
220B LEU* 1.3 65.5 + - + +
221B GLY 3.5 0.4 - - - -
222B ARG 5.6 0.2 + - - -
223B LYS 3.8 3.3 + - - +
225B ARG* 3.1 53.3 + - - +
227B ILE* 4.3 7.2 - - + -
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Residues in contact with LEU 220 (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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216B LEU* 2.8 31.8 + - + +
217B SER* 5.1 0.2 - - - -
219B LEU* 1.3 79.5 - - + +
221B GLY* 1.3 66.6 + - - +
222B ARG 3.6 0.4 - - - -
223B LYS 3.4 14.0 - - - +
224B LYS* 2.8 40.9 + - - +
225B ARG* 3.6 13.5 - - - +
227B ILE* 3.6 21.1 - - + -
267B THR* 3.9 30.7 - - + +
269B LEU* 3.3 34.3 - - + -
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Residues in contact with GLY 221 (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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66A ILE* 6.3 3.4 - - - -
217B SER* 2.9 24.0 + - - +
218B TYR 4.6 1.0 + - - -
219B LEU 3.5 2.2 - - - -
220B LEU* 1.3 81.5 - - - +
222B ARG* 1.3 61.7 + - - +
224B LYS* 3.7 11.5 + - - +
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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