Contacts of the helix formed by residues 247 - 257 (chain B) in PDB entry 3KHU
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 ASP 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASN* 4.6 4.9 - - - +
215A SER* 2.8 14.9 + - - +
241B CYS* 3.5 2.5 - - - -
245B GLY 3.8 0.4 + - - +
246B ALA* 1.3 74.1 - - - +
248B VAL* 1.3 65.3 + - - +
249B GLU* 3.1 27.5 + - - +
250B GLU* 3.1 30.2 + - + +
251B VAL* 3.0 21.7 + - - +
443B ARG* 3.0 27.2 + - - -
463B GLY 3.5 4.1 - - - +
464B LYS* 4.3 12.2 + - + +
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Residues in contact with VAL 248 (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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234B ILE* 3.8 39.5 - - + +
237B ILE* 4.3 4.5 - - + -
238B SER* 3.9 11.7 - - - +
241B CYS* 3.3 11.3 - - - -
247B ASP* 1.3 72.7 - - - +
249B GLU* 1.3 64.2 + - + +
251B VAL* 4.4 1.8 - - - -
252B ALA* 2.8 28.9 + - + +
268B ALA* 4.0 20.9 - - + -
443B ARG* 3.7 14.1 - - - +
462B ILE 4.1 2.0 - - - +
463B GLY* 3.0 35.7 + - - -
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Residues in contact with GLU 249 (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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247B ASP* 3.1 10.7 + - - +
248B VAL* 1.3 79.3 - - + +
250B GLU* 1.3 65.0 + - - +
252B ALA* 3.9 3.4 - - - +
253B THR* 2.8 32.4 + - - +
266B LEU 4.6 2.9 - - - +
267B LYS* 4.6 6.5 - - - +
268B ALA 4.5 14.6 + - - -
443B ARG* 3.6 36.3 - - - +
446B ASP* 3.7 12.9 - - - +
607B EDO 3.3 22.3 + - - -
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Residues in contact with GLU 250 (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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209A LEU* 4.2 4.4 - - - +
210A THR 5.0 1.9 - - - +
211A THR* 3.2 18.1 - - + +
212A ASN* 2.9 32.7 + - - +
215A SER* 2.7 32.4 + - - +
219A SER* 4.7 1.3 - - - -
247B ASP* 3.1 26.7 + - - +
249B GLU* 1.3 77.0 - - + +
251B VAL* 1.3 61.3 + - - +
253B THR* 3.3 6.9 + - - -
254B ALA* 3.1 22.2 + - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 3.8 21.3 - - - +
218A LEU* 4.3 5.8 - - + -
219A SER* 3.4 30.3 - - - +
222A ALA* 4.3 4.7 - - + -
234B ILE* 4.9 0.4 - - + -
237B ILE* 3.7 24.2 - - + -
241B CYS* 4.1 14.4 - - - -
246B ALA* 4.2 2.9 - - + -
247B ASP 3.0 16.6 + - - +
248B VAL 3.8 3.6 - - - +
250B GLU* 1.3 72.0 - - - +
252B ALA* 1.3 60.0 + - - +
254B ALA* 3.2 2.6 + - - +
255B ILE* 2.9 45.1 + - + +
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Residues in contact with ALA 252 (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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234B ILE* 3.9 18.1 - - + +
248B VAL* 2.8 22.6 + - + +
249B GLU* 3.9 6.1 - - - +
250B GLU 3.4 0.2 - - - -
251B VAL* 1.3 72.5 - - - +
253B THR* 1.3 57.4 + - - +
255B ILE* 3.8 3.3 - - - +
256B GLY* 2.9 24.4 + - - -
266B LEU* 3.4 30.8 - - + +
607B EDO 3.6 22.9 + - - +
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Residues in contact with THR 253 (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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209A LEU* 3.9 27.6 - - + -
249B GLU* 2.8 24.0 + - - -
250B GLU* 3.6 5.8 - - - -
252B ALA* 1.3 76.3 - - - +
254B ALA* 1.3 62.8 + - - +
256B GLY* 3.3 1.4 + - - -
257B MET* 3.1 39.4 + - + +
607B EDO 3.8 21.3 + - - -
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Residues in contact with ALA 254 (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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177A ARG* 2.8 35.3 + - + +
179A LEU* 4.1 15.3 - - + -
209A LEU* 3.6 19.0 - - + +
211A THR* 5.4 0.2 - - + -
219A SER* 3.4 33.2 - - - +
250B GLU 3.1 10.6 + - - +
251B VAL 3.2 2.0 + - - +
253B THR* 1.3 78.3 - - - +
255B ILE* 1.3 62.1 + - - +
257B MET* 3.6 2.9 + - - -
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Residues in contact with ILE 255 (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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177A ARG* 4.2 5.8 - - - +
219A SER* 4.4 4.7 - - - +
222A ALA* 4.0 8.5 - - + -
223A ALA* 4.1 17.9 - - - +
226A PHE* 3.8 35.4 - - + -
234B ILE* 4.1 13.7 - - + -
237B ILE* 5.3 0.2 - - + -
251B VAL* 2.9 37.3 + - + +
252B ALA 3.8 3.1 - - - +
254B ALA* 1.3 76.1 - - - +
256B GLY* 1.3 64.0 - - - +
258B ASP* 3.1 23.9 + - - +
261B ILE* 3.7 34.3 - - + +
266B LEU* 4.2 7.9 - - + -
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Residues in contact with GLY 256 (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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252B ALA 2.9 16.0 + - - -
253B THR 3.3 1.5 + - - -
255B ILE* 1.3 79.1 - - - +
257B MET* 1.3 59.1 + - - +
258B ASP 3.2 4.0 + - - +
259B GLN* 5.2 0.3 - - - +
262B GLY* 3.3 37.6 - - - -
263B ASN* 3.5 16.5 + - - +
266B LEU* 3.7 7.4 - - - -
607B EDO 4.5 0.7 - - - -
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Residues in contact with MET 257 (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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176A ASP* 3.2 25.8 - - - +
177A ARG* 3.8 42.8 - - + +
206A GLU 3.6 23.3 - - - +
207A LYS* 4.0 11.9 - - + +
209A LEU* 4.3 24.2 - - + -
253B THR* 3.1 30.7 + - + +
255B ILE 3.1 1.0 + - - -
256B GLY* 1.3 74.8 - - - +
258B ASP* 1.3 62.1 + - - +
259B GLN* 3.3 7.1 + - - +
263B ASN* 6.3 0.4 - - + -
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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