Contacts of the helix formed by residues 216 - 228 (chain C) in PDB entry 4K9P
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 ALA 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C VAL* 2.9 21.2 + - + +
214C ALA* 4.4 3.8 - - + +
215C ASN* 1.3 75.9 - - - +
217C ASN* 1.3 63.1 + - - +
218C ALA 3.3 2.7 - - - -
219C ASP* 3.2 13.6 + - + +
220C CYS* 2.9 23.2 + - - +
318C ILE* 4.4 4.5 - - + +
319C GLY* 4.3 17.7 - - - -
322C ALA* 3.8 24.7 - - + -
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Residues in contact with ASN 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C VAL* 3.5 4.2 - - - +
212C ASP* 3.2 40.2 + - - +
215C ASN* 3.3 8.1 - - - +
216C ALA* 1.3 81.4 + - - +
218C ALA* 1.3 63.3 + - - +
220C CYS* 3.1 4.7 + - - +
221C VAL* 2.9 26.9 + - - +
240C CYS 3.4 5.5 + - - -
241C PRO* 3.3 38.3 + - - +
242C PHE* 4.0 3.2 - - - +
243C PRO* 5.4 4.5 - - + +
391C ASN 5.1 0.8 + - - -
392C PRO* 3.8 30.1 - - + +
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Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ASN* 4.9 4.1 + - - +
216C ALA 3.3 0.2 - - - -
217C ASN* 1.3 77.9 - - - +
219C ASP* 1.3 64.2 + - - +
221C VAL* 3.1 11.9 + - - +
222C MET* 3.0 22.1 + - - +
392C PRO* 5.6 1.4 - - + +
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Residues in contact with ASP 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ASN 5.2 1.4 - - - +
216C ALA* 3.2 17.5 + - - +
218C ALA* 1.3 81.9 - - - +
220C CYS* 1.3 57.6 + - - +
222C MET* 3.3 7.0 + - - +
223C LEU* 2.9 24.1 + - - +
319C GLY 4.4 3.1 - - - +
322C ALA* 3.9 21.1 - - + +
323C SER* 3.5 33.4 + - - -
326C ALA* 3.2 17.8 - - + +
327C ASN* 4.7 4.5 + - - -
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Residues in contact with CYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ILE* 5.2 2.0 - - + +
207C LEU* 3.7 37.6 - - + +
211C VAL* 3.6 25.8 - - + -
216C ALA 2.9 14.8 + - - +
217C ASN* 3.1 9.8 + - - +
219C ASP* 1.3 74.4 - - - +
221C VAL* 1.3 60.3 + - - +
223C LEU* 3.6 9.1 - - - +
224C ALA* 2.8 30.0 + - - +
242C PHE* 4.0 4.6 - - + -
273C ILE* 4.5 11.9 - - - -
322C ALA* 4.5 12.1 - - - -
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Residues in contact with VAL 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C ASN 2.9 17.7 + - - +
218C ALA* 3.1 11.9 + - - +
220C CYS* 1.3 76.9 - - - +
222C MET* 1.3 64.1 + - - +
224C ALA* 3.2 2.8 + - - +
225C GLU* 2.9 47.6 + - - +
242C PHE* 3.6 23.3 - - + -
243C PRO* 3.7 27.8 - - + -
246C HIS* 3.9 9.6 - - + +
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ALA 3.0 12.2 + - - +
219C ASP* 3.5 13.0 - - - +
221C VAL* 1.3 78.4 - - - +
223C LEU* 1.3 63.5 + - - +
225C GLU* 3.3 10.6 + - - +
226C ARG* 2.9 62.0 + - + +
326C ALA* 3.4 23.1 - - + +
327C ASN* 3.4 20.9 - - - +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C LEU* 5.3 1.1 - - + -
205C ILE* 4.2 13.5 - - + -
219C ASP 2.9 14.0 + - - +
220C CYS* 3.6 13.0 - - - +
222C MET* 1.3 75.8 - - - +
224C ALA* 1.3 64.0 + - - +
226C ARG* 3.3 3.3 + - - +
227C LEU* 3.1 37.3 + - + +
271C LEU* 3.9 15.7 - - + -
273C ILE* 3.8 28.0 - - + -
322C ALA* 5.3 3.8 - - + +
325C LEU* 4.0 25.1 - - + +
326C ALA* 4.0 9.6 - - + +
329C VAL* 3.7 28.7 - - + -
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ILE* 3.9 12.5 - - + +
220C CYS 2.8 17.4 + - - +
221C VAL 3.2 4.2 + - - +
223C LEU* 1.3 77.3 - - - +
225C GLU* 1.3 54.1 + - + +
227C LEU 3.5 0.2 + - - -
228C LYS* 2.8 30.5 + - - -
229C ALA 3.1 14.2 + - - +
231C VAL* 3.7 29.8 - - + -
242C PHE* 4.0 11.4 - - + -
248C CYS* 4.2 7.4 - - - -
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C VAL* 2.9 32.3 + - - +
222C MET* 3.8 8.8 - - - +
224C ALA* 1.3 71.7 - - - +
226C ARG* 1.3 67.0 + - + +
228C LYS* 2.8 29.3 + - - +
246C HIS* 3.0 35.1 + - + +
331C GLU* 4.6 1.1 - - - -
336C LEU* 4.2 16.6 - - + +
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Residues in contact with ARG 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C MET* 2.9 45.1 + - + +
223C LEU 3.6 4.3 - - - +
225C GLU* 1.3 81.2 - - + +
227C LEU* 1.3 60.3 + - - +
228C LYS* 3.1 6.0 + - - +
326C ALA 3.0 25.3 + - - +
327C ASN* 3.4 22.8 + - - +
328C LEU 3.8 0.4 - - - +
329C VAL* 2.6 49.9 + - + -
330C GLU 4.0 2.2 - - - +
331C GLU* 4.1 24.5 + - + +
332C SER* 2.8 30.1 + - - -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 4.1 42.0 - - + +
198C ASN* 4.8 2.7 - - - +
203C PRO* 4.3 11.2 - - + +
205C ILE* 4.2 17.3 - - + -
223C LEU* 3.1 35.7 + - + +
226C ARG* 1.3 79.0 - - - +
228C LYS* 1.3 71.2 + - - +
229C ALA* 3.3 13.3 + - + +
271C LEU* 5.3 1.8 - - + -
329C VAL* 4.2 22.9 - - + -
330C GLU 4.6 5.6 - - - +
332C SER* 4.2 2.2 - - - -
334C ARG* 2.5 35.3 + - - +
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PRO* 5.8 0.3 - - - +
224C ALA 2.8 12.2 + - - -
225C GLU 2.8 19.9 + - - +
226C ARG 3.1 6.9 + - - +
227C LEU* 1.3 79.8 - - - +
229C ALA* 1.3 56.8 + - - +
230C PRO* 4.2 2.1 - - - +
331C GLU* 1.9 37.5 + - - -
332C SER* 3.3 22.6 + - - +
334C ARG* 3.3 39.3 + - + +
335C GLN 4.0 8.6 - - - +
336C LEU* 3.9 25.1 - - + +
337C PRO* 3.7 20.8 - - - +
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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