Contacts of the helix formed by residues 213 - 222 (chain B) in PDB entry 3K72
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 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B PHE* 5.7 0.2 - - - +
150B VAL 3.3 7.3 + - - -
151B ASP* 3.0 30.0 + - - -
152B LYS 5.3 0.9 + - - -
181B ALA* 5.5 4.3 - - - +
212B GLU* 1.3 74.8 - - - +
214B GLY* 1.3 62.8 + - - +
215B LEU 3.2 4.4 + - - -
216B ASP* 3.5 18.2 + - - +
217B ALA* 4.1 2.4 + - - +
246B HIS* 4.3 1.1 - - - -
279B TYR* 3.6 19.4 - - - -
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Residues in contact with GLY 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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149B PHE* 3.6 31.9 - - - -
212B GLU* 3.4 7.5 + - - +
213B GLY* 1.3 75.2 - - - +
215B LEU* 1.3 63.3 + - - +
216B ASP 3.3 0.2 - - - -
217B ALA* 3.2 15.7 + - - +
218B MET* 3.2 18.8 + - - +
239B PHE* 4.0 13.0 - - - -
245B PHE* 5.1 2.0 - - - +
246B HIS 5.0 0.8 - - - +
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Residues in contact with LEU 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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213B GLY 3.2 1.2 - - - -
214B GLY* 1.3 76.0 - - - +
216B ASP* 1.3 65.5 + - - +
218B MET* 3.1 26.3 + - + +
219B MET 3.6 0.9 + - - -
239B PHE* 5.0 4.5 - - + -
245B PHE* 4.1 30.7 - - + +
246B HIS 3.1 29.6 - - - +
247B PHE* 3.6 22.7 - - + -
280B PRO* 3.3 28.1 - - + +
281B SER 5.4 0.2 - - - +
282B VAL* 5.3 7.9 - - + -
285B LEU* 4.0 23.4 - - + +
311B LEU* 6.2 3.6 - - + -
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Residues in contact with ASP 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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152B LYS* 5.9 0.9 - - - +
181B ALA* 6.3 2.7 - - + -
213B GLY 3.5 11.5 + - - +
214B GLY 3.3 0.4 - - - -
215B LEU* 1.3 79.5 - - - +
217B ALA* 1.3 62.1 + - - +
219B MET* 3.7 3.1 + - - +
220B GLN* 3.1 38.6 + - - +
274B SER* 3.2 26.4 - - - +
277B PHE* 3.1 35.1 - - - +
278B ASP 4.8 0.7 - - - +
279B TYR* 4.4 16.8 - - + -
280B PRO* 3.5 15.5 - - + +
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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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110B LEU* 5.4 2.0 - - + -
149B PHE* 3.7 33.7 - - + -
181B ALA 4.1 5.2 - - - +
182B PHE* 3.8 18.1 - - + -
213B GLY 4.1 1.7 + - - +
214B GLY* 3.2 13.3 + - - +
215B LEU 3.1 0.4 - - - -
216B ASP* 1.3 78.0 - - - +
218B MET* 1.3 69.5 + - - +
220B GLN* 3.4 9.4 + - - +
221B VAL* 3.1 27.5 + - + +
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Residues in contact with MET 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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110B LEU* 3.1 35.9 - - + -
214B GLY 3.3 13.7 - - - +
215B LEU* 3.2 26.2 - - + +
217B ALA* 1.3 79.5 - - - +
219B MET* 1.3 65.5 + - - +
221B VAL* 3.2 17.9 + - - +
222B ALA* 3.4 7.1 + - - +
237B LEU* 4.4 8.6 - - + +
239B PHE* 3.7 23.3 - - + -
285B LEU* 4.1 21.1 - - + -
289B LEU* 5.4 9.1 - - + +
296B PRO* 3.7 32.5 - - + -
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Residues in contact with MET 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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499A TRP* 5.6 0.4 - - + -
215B LEU 3.6 1.6 + - - -
216B ASP* 4.1 6.1 - - - +
217B ALA 3.4 0.2 - - - -
218B MET* 1.3 79.0 - - - +
220B GLN* 1.3 65.8 + - + +
221B VAL 2.8 1.9 + - - -
222B ALA* 3.1 12.4 + - - +
223B ALA* 3.0 20.2 + - - +
260B ASN* 3.7 13.0 - - - +
262B GLY* 3.4 40.1 - - - +
277B PHE* 5.7 0.7 - - + -
280B PRO* 3.6 28.3 - - + -
284B GLN* 3.5 23.1 - - + +
285B LEU* 3.4 25.4 - - + -
288B LYS* 3.6 27.6 - - + +
289B LEU 5.4 0.4 - - - -
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Residues in contact with GLN 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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181B ALA* 5.9 0.3 - - - +
182B PHE* 3.4 37.9 - - + +
216B ASP* 3.1 33.9 + - - +
217B ALA* 3.4 6.5 + - - +
219B MET* 1.3 78.9 - - + +
221B VAL* 1.3 63.1 + - - +
223B ALA* 3.8 0.6 - - - +
228B ILE* 3.8 5.5 - - - +
264B CYS* 3.2 46.5 - - + +
266B LEU* 6.3 0.2 - - + -
271B TYR* 3.5 17.3 - - - +
273B ARG* 5.0 5.1 - - - +
274B SER* 3.8 26.7 - - - +
277B PHE* 4.9 5.5 - - + -
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Residues in contact with VAL 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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108B TYR* 4.2 13.0 - - + -
110B LEU* 3.9 18.6 - - + -
182B PHE* 3.1 37.2 - - + -
217B ALA 3.1 14.1 + - - +
218B MET* 3.2 10.5 - - - +
219B MET 2.8 1.4 + - - -
220B GLN* 1.3 79.3 - - - +
222B ALA* 1.3 62.5 + - + +
223B ALA 3.1 6.0 + - - -
224B CYS 4.3 2.1 + - - -
225B PRO* 4.9 1.2 - - - +
228B ILE* 3.4 18.8 - - + +
230B TRP* 4.1 32.3 + - + +
237B LEU* 4.1 17.0 - - + -
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Residues in contact with ALA 222 (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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218B MET 3.4 6.1 + - - +
219B MET* 3.1 9.0 + - - +
221B VAL* 1.3 77.9 - - + +
223B ALA* 1.3 56.5 + - - +
225B PRO* 4.9 5.6 - - - -
230B TRP* 5.0 3.6 - - - +
237B LEU* 5.9 0.7 - - + -
288B LYS* 3.9 12.5 + - + +
289B LEU* 4.9 13.2 - - + -
292B ASN* 3.1 25.5 + - + +
294B ILE* 3.1 35.2 - - + -
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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