Contacts of the helix formed by residues 221 - 232 (chain A) in PDB entry 4KPF
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ILE 4.1 0.8 + - - -
220A GLN* 1.3 73.3 - - - +
222A ARG* 1.3 64.6 + - - -
223A ASP* 3.0 5.3 + - - -
224A GLU* 3.1 9.0 + - - -
225A ILE* 3.0 28.4 + - - +
236A VAL* 3.9 4.4 - - - +
483A GLU 3.0 11.3 + - - -
484A ASP* 4.1 7.7 - - - +
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Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A MET* 4.4 8.8 - - + +
221A GLY* 1.3 74.1 - - - +
223A ASP* 1.3 63.0 + - - +
225A ILE* 3.4 13.5 + - - +
226A LYS* 3.1 21.5 + - - +
483A GLU 3.9 4.3 + - - +
484A ASP* 3.4 23.8 - - + +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLY* 3.0 1.4 - - - -
222A ARG* 1.3 77.7 - - - +
224A GLU* 1.3 59.3 + - + +
226A LYS* 3.1 10.5 + - - +
227A LYS* 2.9 25.1 + - - +
484A ASP* 5.0 1.6 - - - +
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLY* 3.1 10.6 + - - +
223A ASP* 1.3 75.5 - - + +
225A ILE* 1.3 61.2 + - - +
227A LYS* 3.6 24.6 - - - +
228A ALA* 2.8 30.8 + - - +
234A GLY* 3.2 12.2 - - - -
235A ARG* 2.7 53.9 + - - +
236A VAL* 4.7 3.8 - - + -
327A PHE* 5.6 1.1 - - - -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A MET* 4.3 4.7 - - + -
209A PRO 3.7 20.0 - - - +
210A GLY* 4.1 1.8 - - - -
211A PRO* 4.2 18.6 - - + -
219A ILE* 4.3 15.5 - - + +
221A GLY 3.0 20.2 + - - +
222A ARG* 3.6 11.4 - - - +
224A GLU* 1.3 74.3 - - - +
226A LYS* 1.3 58.3 + - - +
228A ALA* 3.2 6.2 + - - +
229A TYR* 2.8 61.7 + - + -
236A VAL* 3.7 13.9 - - + +
327A PHE* 4.9 6.3 - - + -
482A LEU* 4.3 11.9 - - + -
483A GLU 5.8 0.7 - - - +
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 4.5 3.3 - - + +
202A ASP* 4.3 17.5 - - - +
205A MET* 3.8 23.3 - - + -
222A ARG 3.1 11.8 + - - +
223A ASP* 3.1 12.9 + - - +
225A ILE* 1.3 73.5 - - - +
227A LYS* 1.3 65.8 - - - +
229A TYR* 3.0 4.2 + - - +
230A GLU* 2.9 47.0 + - - +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ASP 2.9 13.5 + - - +
224A GLU* 3.2 36.3 + - - +
226A LYS* 1.3 74.2 - - - +
228A ALA* 1.3 57.6 + - - +
230A GLU* 3.1 14.0 + - - +
231A THR* 2.9 42.2 + - + +
233A LYS 3.7 11.2 - - - +
234A GLY* 4.9 1.1 - - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU 2.8 16.4 + - - +
225A ILE 3.6 3.8 - - - +
227A LYS* 1.3 74.6 - - - +
229A TYR* 1.3 60.8 + - - +
230A GLU 2.9 4.3 - - - -
232A GLY* 2.6 31.7 + - - -
233A LYS 3.0 17.9 - - - +
234A GLY* 4.0 0.7 - - - -
327A PHE* 3.5 44.4 - - + -
329A MET* 3.7 3.5 - - - +
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Residues in contact with TYR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A HIS* 2.9 31.5 + + - -
201A ILE* 4.1 17.0 - - + +
205A MET* 3.7 25.4 - - + -
208A LEU* 3.5 25.5 - - + +
210A GLY* 3.1 21.7 - - - -
211A PRO* 3.4 1.1 - - + -
225A ILE* 2.8 33.3 + - + +
226A LYS 3.0 4.0 + - - +
228A ALA* 1.3 78.3 - - - +
230A GLU* 1.3 58.5 + - - +
327A PHE* 4.1 17.5 - + - -
329A MET* 4.3 5.4 - - + -
341A GLY* 3.3 3.3 - - - -
342A ILE* 2.7 66.9 + - + +
343A VAL* 4.3 1.6 + - - +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ILE* 3.9 32.1 - - + +
202A ASP* 5.4 1.6 - - - +
226A LYS* 2.9 31.3 + - - +
227A LYS* 3.4 14.5 - - - +
228A ALA 2.9 0.2 - - - -
229A TYR* 1.3 80.9 - - - +
231A THR* 1.3 66.6 + - + +
232A GLY 3.6 0.4 - - - -
341A GLY* 4.3 6.5 + - - -
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Residues in contact with THR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 2.9 25.8 + - + +
230A GLU* 1.3 82.0 - - + +
232A GLY* 1.3 56.7 + - - +
233A LYS* 3.2 18.8 + - - +
339A GLN* 2.8 33.6 + - - +
340A VAL 4.6 0.7 + - - -
341A GLY 4.6 4.3 - - - -
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA* 2.6 25.6 + - - -
230A GLU 3.6 1.0 - - - -
231A THR* 1.3 71.8 - - - +
233A LYS* 1.3 59.6 + - - +
327A PHE* 3.8 1.0 - - - -
328A ASN* 3.5 5.0 + - - -
329A MET* 2.9 35.0 + - - +
339A GLN* 4.2 4.0 - - - +
340A VAL 3.3 24.0 - - - -
341A GLY* 3.9 1.8 - - - -
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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