Contacts of the helix formed by residues 204 - 214 (chain B) in PDB entry 4KMH
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 CYS 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B ARG* 3.7 39.3 - - + -
174B ILE* 4.3 4.9 - - - -
176B HIS* 4.1 1.1 - - - -
203B VAL* 1.3 72.6 - - - +
205B THR* 1.3 57.5 + - - +
206B GLU* 3.7 15.0 - - - +
207B GLU* 2.7 49.9 + - - +
208B LEU* 3.0 8.7 + - - +
240B ARG* 3.6 26.0 - - - -
242B GLU 5.2 0.2 - - - -
243B THR* 3.8 14.4 - - + -
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Residues in contact with THR 205 (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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164B HIS* 4.9 9.2 - - + +
175B GLN* 2.8 29.9 + - - +
176B HIS* 3.2 30.7 + - + -
204B CYS* 1.3 70.9 - - - +
206B GLU* 1.3 69.5 + - - +
208B LEU* 3.4 2.9 + - - +
209B HIS* 3.1 51.7 + - + +
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Residues in contact with GLU 206 (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 ARG* 3.8 24.0 + - - +
204B CYS* 2.9 16.1 + - - +
205B THR* 1.3 79.7 + - + +
207B GLU* 1.3 56.0 + - - +
209B HIS* 3.3 13.4 + - + +
210B SER* 2.8 31.0 + - - -
243B THR* 3.8 15.7 - - + +
245B PHE* 4.4 10.5 - - + -
246B GLU* 5.5 1.1 - - - +
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Residues in contact with GLU 207 (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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178B LEU* 5.2 0.7 - - - +
203B VAL* 3.4 19.1 - - + +
204B CYS* 2.7 46.5 + - - +
206B GLU* 1.3 69.8 - - - +
208B LEU* 1.3 63.0 + - - +
210B SER* 3.3 10.6 + - - -
211B ALA* 3.2 20.1 + - - +
219B ILE* 4.0 13.8 - - + +
223B LEU* 5.0 2.7 - - + -
240B ARG* 2.9 36.0 + - - -
243B THR* 3.4 7.2 - - - -
244B ILE* 3.2 40.8 + - + +
245B PHE* 3.9 7.9 - - + -
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Residues in contact with LEU 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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160B HIS* 3.7 40.2 - - + -
161B VAL 4.2 14.1 - - - +
162B SER* 4.3 12.1 - - - +
164B HIS* 4.8 4.3 - - + -
176B HIS* 3.6 46.4 - - + +
177B MET 4.8 2.5 - - - +
178B LEU* 5.1 2.9 - - + -
203B VAL* 4.5 6.5 - - + +
204B CYS 3.0 9.5 + - - +
205B THR 3.4 9.0 - - - +
207B GLU* 1.3 76.7 - - - +
209B HIS* 1.3 69.8 + - + +
211B ALA* 3.2 8.5 + - - +
212B GLN* 3.1 33.9 + - - +
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Residues in contact with HIS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B HIS* 5.5 6.1 - + - -
205B THR* 3.1 44.9 + - + +
206B GLU* 3.3 11.6 + - + +
208B LEU* 1.3 82.8 - - + +
210B SER* 1.3 57.7 + - - +
212B GLN* 3.1 21.2 + - - +
213B GLN* 3.0 47.2 + - - +
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Residues in contact with SER 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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206B GLU 2.8 17.0 + - - -
207B GLU* 3.5 8.0 - - - -
208B LEU 3.2 0.4 - - - -
209B HIS* 1.3 77.0 - - - +
211B ALA* 1.3 57.3 + - - +
213B GLN* 3.5 10.2 + - - +
214B TRP* 2.9 32.2 + - - +
219B ILE* 3.6 22.2 - - - +
245B PHE* 3.1 26.5 - - - -
252B GLN* 5.8 1.1 + - - -
255B VAL* 4.6 9.0 - - - +
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Residues in contact with ALA 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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160B HIS* 5.1 7.0 + - + +
178B LEU* 4.0 26.0 - - + -
207B GLU 3.2 8.7 + - - +
208B LEU 3.2 9.0 + - - +
210B SER* 1.3 77.0 - - - +
212B GLN* 1.3 65.2 + - - +
214B TRP 3.4 1.2 - - - +
215B ASN* 3.3 32.0 - - - +
216B GLY* 3.7 7.7 + - - -
219B ILE* 3.6 18.6 - - + +
265B ASN* 4.1 3.3 + - - -
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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
----------------------------------------------------------
160B HIS* 3.6 40.5 + - + +
162B SER* 4.8 5.7 + - - -
208B LEU* 3.1 21.4 + - - +
209B HIS* 3.1 39.6 + - - +
211B ALA* 1.3 77.4 - - - +
213B GLN* 1.3 62.4 + - + +
265B ASN* 3.4 12.5 - - - +
266B LEU* 3.3 34.7 + - + +
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Residues in contact with GLN 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 HIS* 3.0 34.7 + - - +
210B SER* 3.8 7.8 - - - +
212B GLN* 1.3 78.5 - - + +
214B TRP* 1.3 57.6 + - - +
252B GLN* 5.5 4.0 + - - -
255B VAL* 5.3 4.3 - - + +
256B ASP* 5.7 0.7 - - - +
259B ILE* 4.2 15.1 - - + +
264B SER* 2.5 36.4 + - - -
266B LEU* 4.2 12.8 - - + +
380B LEU* 4.3 13.4 - - - +
383B LEU* 3.8 27.9 - - + +
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Residues in contact with TRP 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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210B SER 2.9 14.8 + - - +
211B ALA 3.4 2.4 - - - +
213B GLN* 1.3 74.4 - - - +
215B ASN* 1.3 81.2 + - - +
218B GLY* 3.6 37.0 - - - -
219B ILE* 3.9 15.5 - - + -
222B LEU* 4.0 17.0 - - + -
254B ARG* 3.9 19.3 - - + -
255B VAL* 3.9 19.5 - - + -
258B GLY* 3.3 30.8 + - - -
259B ILE* 3.8 15.5 - - + -
262B ASP* 2.9 28.6 + - - -
263B GLY 3.8 11.6 - - - +
264B SER 4.0 0.2 - - - -
265B ASN* 3.1 33.1 + - - +
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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