Contacts of the helix formed by residues 214 - 222 (chain C) in PDB entry 4EOZ
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 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ALA* 3.5 22.4 - - + +
193C LEU* 3.7 28.6 - - + +
194C TRP* 5.0 1.1 - - - -
198C ARG 2.8 23.4 + - - -
199C PHE 3.4 18.8 - - - -
200C THR* 3.2 24.9 - - + +
201C ASP* 3.3 10.8 - - - +
202C CYS* 4.2 2.0 - - - -
212C GLN 5.5 0.2 - - - -
213C ALA* 1.3 76.0 - - - +
215C LYS* 1.3 69.3 + - - +
216C ALA* 3.2 2.9 - - + +
217C ILE* 3.0 27.9 + - + +
218C LEU* 3.2 13.4 + - - +
259C TYR* 2.8 27.3 + - - +
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Residues in contact with LYS 215 (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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199A PHE* 4.7 17.0 - - + -
201C ASP* 2.7 41.7 + - - +
202C CYS* 3.7 7.6 - - - -
214C HIS* 1.3 71.0 - - - +
216C ALA* 1.3 64.0 + - - +
218C LEU* 3.1 2.1 + - - +
219C ALA* 2.9 26.3 + - - +
229C PHE* 3.5 58.9 - - + +
236C SER* 5.9 2.0 - - - -
239C ASN* 2.5 35.4 + - - +
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Residues in contact with ALA 216 (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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193A LEU* 3.3 23.1 - - + +
198A ARG 4.4 0.2 - - - +
199A PHE* 3.8 24.4 - - + +
201A ASP* 6.0 0.2 - - - +
214A HIS* 3.4 34.5 - - + -
217A ILE* 5.3 0.7 - - + -
201C ASP* 5.0 1.8 + - - +
214C HIS* 3.1 3.3 + - + +
215C LYS* 1.3 78.2 - - - +
217C ILE* 1.3 60.0 + - + +
219C ALA* 3.8 1.0 - - - +
220C ALA 3.0 21.3 + - - -
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Residues in contact with ILE 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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186A LEU* 6.2 0.2 - - + -
190A LEU* 5.0 10.3 - - + -
193A LEU* 4.7 4.0 - - + -
216A ALA* 5.5 0.7 - - + -
217A ILE* 4.1 27.1 - - + -
190C LEU* 5.0 11.7 - - + -
193C LEU* 4.0 22.4 - - + -
214C HIS* 3.0 19.3 + - + +
216C ALA* 1.3 79.3 - - + +
218C LEU* 1.3 63.4 + - - +
219C ALA 3.2 1.1 - - - -
220C ALA* 3.6 2.1 + - - +
221C ARG* 3.1 29.1 + - + +
258C ILE* 4.1 15.8 - - + +
259C TYR* 4.0 39.0 - - + -
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Residues in contact with LEU 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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202C CYS* 4.6 2.0 - - - -
204C LEU* 4.3 27.1 - - + -
213C ALA* 4.4 6.3 - - + -
214C HIS 3.2 12.5 + - - +
215C LYS 3.1 5.3 + - - +
217C ILE* 1.3 76.6 - - - +
219C ALA* 1.3 59.1 + - - +
221C ARG* 3.3 0.9 + - - +
222C SER* 2.9 36.2 + - - +
225C PHE* 3.8 28.0 - - + -
229C PHE* 4.1 19.5 - - + -
255C MET* 3.9 24.7 - - + -
258C ILE* 3.7 29.6 - - + -
259C TYR* 4.4 6.1 - - + +
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Residues in contact with ALA 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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198A ARG* 3.5 8.5 + - - +
199A PHE* 3.5 36.6 - - + -
215C LYS 2.9 16.4 + - - +
216C ALA 3.8 1.8 - - - +
218C LEU* 1.3 76.4 - - - +
220C ALA* 1.3 61.7 + - - +
221C ARG 3.1 5.9 + - - -
222C SER 3.6 6.2 + - - +
223C PRO* 4.5 0.3 - - - +
225C PHE 4.7 1.1 - - - +
226C SER* 3.3 37.2 - - - +
229C PHE* 5.0 1.6 - - + -
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Residues in contact with ALA 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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189A GLU* 3.2 46.1 - - - +
190A LEU* 4.5 4.7 - - + +
193A LEU* 3.5 31.8 - - + +
198A ARG* 4.2 10.1 + - - +
216C ALA 3.0 11.7 + - - +
217C ILE 3.6 4.9 + - - +
218C LEU 3.4 0.4 - - - -
219C ALA* 1.3 75.0 - - - +
221C ARG* 1.3 61.8 + - + +
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Residues in contact with ARG 221 (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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184A CYS* 5.7 0.4 - - - -
185A ARG* 4.0 7.5 - - - +
186A LEU* 3.4 37.0 - - - +
189A GLU* 2.7 51.7 + - - +
190A LEU* 4.3 9.9 - - + -
217C ILE* 3.1 20.4 - - + +
218C LEU 3.3 2.8 + - - +
219C ALA 3.1 0.4 - - - -
220C ALA* 1.3 81.7 - - - +
222C SER* 1.3 57.3 + - - +
223C PRO* 4.3 4.0 - - - +
257C PHE* 2.8 47.8 + - - -
258C ILE* 2.6 38.3 + - + +
261C GLY* 3.7 16.4 - - - +
281C ALA 4.6 2.3 - - - +
282C LEU* 3.2 15.3 - - + +
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Residues in contact with SER 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 LEU 2.9 14.5 + - - +
219C ALA 3.9 2.9 - - - -
221C ARG* 1.3 80.8 - - - +
223C PRO* 1.3 63.3 - - - +
224C VAL* 3.4 3.1 + - - +
225C PHE* 3.3 32.3 + - - -
226C SER* 2.8 25.3 + - - -
258C ILE* 5.3 0.9 - - - -
280C TYR* 2.6 26.1 + - - +
282C LEU* 3.9 8.7 - - - -
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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