Contacts of the helix formed by residues 219 - 229 (chain B) in PDB entry 7KAC
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 HIS 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ASP 3.9 2.0 + - - -
218B VAL* 1.3 75.9 - - - +
220B PRO* 1.4 82.4 - - + +
221B ASP* 3.2 47.3 + - + +
222B ARG* 3.0 22.9 + - + +
223B VAL* 3.0 10.4 + - - +
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Residues in contact with PRO 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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175A THR* 5.5 0.7 - - - +
176A PRO* 3.5 36.3 - - + +
177A TYR* 3.4 20.2 - - + +
218B VAL 4.0 0.2 - - - +
219B HIS* 1.4 101.7 - - + +
221B ASP* 1.3 66.1 + - - +
223B VAL* 3.3 2.8 + - + -
224B LEU* 3.2 22.1 + - - +
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Residues in contact with ASP 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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219B HIS* 3.2 26.1 + - - +
220B PRO* 1.3 81.8 - - - +
222B ARG* 1.3 60.2 + - - +
224B LEU* 3.5 12.3 + - - +
225B GLU* 2.6 34.3 + - - +
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Residues in contact with ARG 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 VAL* 3.6 20.2 - - + -
219B HIS* 3.0 19.6 + - + +
221B ASP* 1.3 80.3 - - - +
223B VAL* 1.4 55.7 + - - +
224B LEU 3.4 0.2 - - - -
225B GLU* 3.5 17.1 + - - +
226B LEU* 3.1 62.0 + - + +
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Residues in contact with VAL 223 (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 PRO* 4.2 16.2 - - + -
177A TYR* 3.7 30.5 - - + -
215B LEU* 3.9 17.7 - - + +
218B VAL* 3.7 20.2 - - + -
219B HIS 3.0 13.8 + - - +
220B PRO 3.3 7.4 + - - +
222B ARG* 1.4 74.3 - - - +
224B LEU* 1.3 63.3 + - - +
226B LEU* 3.4 7.0 + - - +
227B MET* 3.1 50.6 + - + +
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Residues in contact with LEU 224 (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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172A PHE* 5.5 8.7 - - + -
176A PRO* 3.7 11.2 - - + -
179A MET* 3.4 33.0 - - + -
184A ALA* 4.3 15.3 - - + +
187A ALA* 4.5 8.3 - - + +
188A LEU* 4.0 28.0 - - + +
220B PRO 3.2 15.5 + - - +
221B ASP* 3.7 11.9 - - - +
222B ARG 3.4 0.2 - - - -
223B VAL* 1.3 75.9 - - - +
225B GLU* 1.3 69.6 + - - +
227B MET* 3.6 4.6 + - - +
228B THR* 2.8 30.1 + - - -
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Residues in contact with GLU 225 (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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188A LEU* 3.6 35.7 - - + +
221B ASP* 2.6 29.5 + - - +
222B ARG* 3.7 19.3 - - - +
223B VAL 3.3 0.6 - - - -
224B LEU* 1.3 73.8 - - - +
226B LEU* 1.3 64.6 + - - +
228B THR* 3.3 2.7 + - - -
229B LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 226 (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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215B LEU* 4.6 20.0 - - + -
218B VAL* 4.3 21.3 - - + -
222B ARG* 3.1 52.1 + - + +
223B VAL* 3.4 7.6 + - - +
225B GLU* 1.3 75.7 - - - +
227B MET* 1.3 61.6 + - - +
229B LYS* 3.2 21.5 + - + +
232B TYR* 3.4 25.7 - - + +
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Residues in contact with MET 227 (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 PRO* 3.7 20.2 - - - +
177A TYR* 4.1 11.7 - - - +
179A MET 3.7 21.5 - - - +
180A ALA 4.9 1.8 - - - +
181A PRO* 4.1 18.8 - - + +
184A ALA* 4.0 22.9 - - + -
199B TRP* 5.5 4.9 - - + +
203B ILE* 6.0 1.8 - - + -
214B PRO 6.0 1.3 - - - +
215B LEU* 4.8 5.4 - - + -
223B VAL* 3.1 38.0 + - + +
224B LEU* 4.0 3.4 - - - +
226B LEU* 1.3 76.1 - - + +
228B THR* 1.3 59.7 + - - +
229B LYS 3.9 1.0 - - - +
232B TYR* 3.7 51.9 - - + +
257B LYS* 6.0 0.3 - - - +
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Residues in contact with THR 228 (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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181A PRO 5.5 2.0 - - - -
184A ALA* 4.0 2.8 - - - +
185A ALA* 3.9 30.5 + - + +
188A LEU* 3.7 20.5 - - + +
189A LYS* 4.5 16.2 - - + -
224B LEU 2.8 19.8 + - - -
225B GLU 3.9 4.0 - - - -
226B LEU 3.3 0.2 - - - -
227B MET* 1.3 73.0 - - - +
229B LYS* 1.4 65.9 + - - +
230B SER* 3.6 1.6 + - - -
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Residues in contact with LYS 229 (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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225B GLU 3.0 12.6 + - - +
226B LEU* 3.2 17.6 + - + +
227B MET 3.9 0.9 - - - +
228B THR* 1.4 79.6 - - - +
230B SER* 1.3 67.0 + - - +
231B GLY 3.4 4.5 - - - +
232B TYR* 3.3 17.8 + - - +
257B LYS* 5.3 0.2 + - - -
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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