Contacts of the helix formed by residues 207 - 218 (chain B) in PDB entry 1KPH
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 SER 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B THR* 4.6 1.6 - - - -
171B GLY 3.9 13.5 - - - +
173B HIS* 3.7 31.9 + - - -
205B LEU 4.2 0.2 + - - -
206B PRO* 1.3 76.3 - - - +
208B ILE* 1.3 64.9 + - - +
209B PRO* 3.4 11.5 - - - +
210B MET* 3.0 34.3 + - - +
211B VAL* 3.1 20.8 + - - +
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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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170B THR* 3.8 20.3 - - + +
206B PRO 4.3 0.2 + - - -
207B SER* 1.3 71.7 - - - +
209B PRO* 1.3 72.1 - - + +
211B VAL* 3.2 4.0 + - - +
212B GLN* 3.0 33.0 + - + +
225B VAL* 4.7 7.4 - - + -
279B ASP* 4.3 8.1 - - + +
281B ASN* 3.6 26.5 - - - +
283B PHE* 4.1 23.3 - - + -
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Residues in contact with PRO 209 (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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173B HIS* 6.0 0.9 - - + -
207B SER* 3.4 13.9 - - - +
208B ILE* 1.3 95.9 - - + +
210B MET* 1.3 55.6 + - - +
212B GLN* 3.2 8.6 + - + +
213B GLU* 2.9 32.5 + - - +
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Residues in contact with MET 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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144B HIS* 3.3 44.4 - - + +
147B TYR* 3.6 27.6 - - + -
173B HIS* 5.2 8.1 - - - +
206B PRO* 4.1 6.5 - - + -
207B SER* 3.0 34.6 + - - +
209B PRO* 1.3 77.8 - - - +
211B VAL* 1.3 62.3 + - - +
213B GLU* 3.4 4.5 + - - +
214B CYS* 3.1 33.2 + - - -
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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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139B PHE* 4.1 11.0 - - + -
151B PHE* 4.1 9.8 - - + -
166B LEU* 4.1 16.6 - - + -
168B THR* 4.6 2.7 - - + -
170B THR* 4.8 0.7 - - + -
206B PRO* 3.9 25.6 - - + -
207B SER 3.1 14.2 + - - +
208B ILE* 3.6 6.3 - - - +
210B MET* 1.3 76.8 - - - +
212B GLN* 1.3 64.3 + - - +
214B CYS* 3.8 4.6 - - - +
215B ALA* 3.1 24.5 + - + +
222B VAL* 5.9 0.4 - - + -
283B PHE* 3.8 47.6 - - + -
285B CYS* 5.9 0.2 - - - -
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Residues in contact with GLN 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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208B ILE* 3.0 30.9 + - + +
209B PRO* 3.2 11.6 + - + +
211B VAL* 1.3 77.1 - - - +
213B GLU* 1.3 62.3 + - - +
215B ALA* 4.0 1.6 - - - +
216B SER* 3.2 25.1 + - - -
222B VAL* 3.2 41.1 - - - +
225B VAL* 3.7 23.1 - - - +
283B PHE* 4.4 3.8 - - + -
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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 PRO 2.9 16.8 + - - +
210B MET* 4.0 4.6 - - - +
212B GLN* 1.3 73.6 - - - +
214B CYS* 1.3 60.7 + - - +
216B SER* 3.5 3.4 + - - -
217B ALA* 2.8 38.9 + - + +
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Residues in contact with CYS 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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147B TYR* 3.9 29.4 - - - +
148B ASP* 4.8 7.4 - - - -
151B PHE* 3.7 24.5 - - + -
210B MET* 3.1 28.5 + - - +
211B VAL* 3.8 1.1 - - - +
213B GLU* 1.3 77.8 - - - +
215B ALA* 1.3 60.9 + - - +
217B ALA* 3.4 3.3 + - - +
218B ASN* 2.8 35.3 + - - +
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Residues in contact with ALA 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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151B PHE* 3.6 30.4 - - + -
211B VAL* 3.1 18.5 + - + +
212B GLN 4.0 0.2 - - - +
214B CYS* 1.3 74.9 - - - +
216B SER* 1.3 61.6 + - - +
218B ASN* 3.1 9.7 + - - +
219B GLY 3.5 0.2 + - - -
220B PHE* 3.0 34.1 + - + +
222B VAL* 3.8 25.4 - - + -
285B CYS* 4.5 3.4 - - - -
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Residues in contact with SER 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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212B GLN 3.2 15.9 + - - -
213B GLU* 3.9 4.5 - - - -
215B ALA* 1.3 73.7 - - - +
217B ALA* 1.3 64.6 + - - +
218B ASN 2.9 5.6 + - - -
219B GLY* 3.1 12.6 + - - -
220B PHE 3.2 16.8 + - - +
222B VAL* 5.2 2.2 - - - +
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Residues in contact with ALA 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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148B ASP* 5.1 4.5 - - - +
213B GLU* 2.8 29.9 + - + +
214B CYS* 3.8 6.3 - - - +
216B SER* 1.3 72.1 - - - +
218B ASN* 1.3 65.6 + - - +
219B GLY 3.5 0.6 + - - -
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Residues in contact with ASN 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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148B ASP* 3.0 37.7 + - - +
151B PHE* 3.8 22.0 - - + +
152B SER* 3.5 29.2 - - - +
155B HIS* 3.2 26.0 + - - +
214B CYS* 2.8 25.2 + - - +
215B ALA 3.1 5.2 + - - +
216B SER 2.9 1.6 + - - -
217B ALA* 1.3 83.2 - - - +
219B GLY* 1.3 57.1 + - - +
220B PHE* 3.5 2.9 - - + -
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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