Contacts of the helix formed by residues 215 - 224 (chain C) in PDB entry 4J44
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 ARG 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C LEU* 4.0 2.2 - - - -
183C GLU* 3.5 11.0 - - - +
210C TRP* 4.3 1.1 - - - -
213C GLY 3.6 8.3 + - - +
214C ASP* 1.3 77.9 - - - +
216C ALA* 1.3 65.8 + - - +
217C TRP* 4.6 2.9 - - + +
218C SER* 3.4 21.6 + - - +
219C GLU* 3.2 25.5 + - - +
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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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179C LEU* 3.4 14.7 - - + +
183C GLU* 3.0 33.2 + - + +
184C LEU* 3.9 14.1 - - + -
187C ALA* 3.7 20.9 - - + -
189C LEU* 4.2 2.9 - - + +
210C TRP* 3.9 9.4 - - - -
215C ARG* 1.3 71.8 - - - +
217C TRP* 1.3 64.0 + - + +
219C GLU* 3.4 1.9 + - - +
220C HIS* 3.0 24.1 + - - +
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Residues in contact with TRP 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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183C GLU* 4.8 3.1 + - + -
186C SER* 3.9 13.1 + - - -
187C ALA* 3.6 23.4 - - + +
215C ARG* 3.4 3.0 - - + +
216C ALA* 1.3 79.3 - - + +
218C SER* 1.3 63.0 + - - +
220C HIS* 3.3 11.8 + - + +
221C ARG* 2.9 33.2 + - + +
229C PHE* 3.1 43.7 - + - -
230C VAL* 4.1 23.6 - - + -
233C ARG* 3.5 75.8 - - + +
234C ASN* 5.9 0.4 - - - -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ARG* 3.4 26.9 + - - +
216C ALA 3.3 0.6 - - - -
217C TRP* 1.3 79.5 - - - +
219C GLU* 1.3 61.7 + - - +
221C ARG* 3.9 22.7 + - - +
222C ARG* 2.9 46.0 + - - +
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Residues in contact with GLU 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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151A GLY* 5.6 0.5 - - - -
152A THR* 2.8 38.9 + - + +
207C LEU* 4.3 3.5 - - + +
210C TRP* 3.5 31.9 - - + -
214C ASP* 4.1 20.5 - - + +
215C ARG 3.2 14.0 + - - +
218C SER* 1.3 76.8 + - - +
220C HIS* 1.3 67.8 + - - +
222C ARG* 3.3 28.6 + - - -
223C HIS* 3.1 41.1 + - - +
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Residues in contact with HIS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ALA 2.8 28.8 + - - -
189C LEU* 3.9 11.9 - - + +
200C CYS* 3.3 20.0 - - + +
207C LEU* 4.0 12.9 - - + +
216C ALA 3.0 17.6 + - - +
217C TRP* 3.3 11.0 + + + +
219C GLU* 1.3 76.2 - - - +
221C ARG* 1.3 57.9 + - - +
224C PHE* 3.0 42.4 + + + +
227C CYS* 3.7 1.4 - - - -
229C PHE* 4.2 11.2 - + - -
230C VAL* 3.5 14.9 - - + +
301C ZN 2.1 37.0 - - - -
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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
----------------------------------------------------------
217C TRP* 2.9 19.7 + - + +
218C SER* 4.0 23.9 + - - +
220C HIS* 1.3 74.2 - - - +
222C ARG* 1.3 67.5 + - - +
223C HIS 3.4 0.2 + - - -
225C PRO* 3.5 24.7 - - + +
230C VAL* 3.8 27.5 - - + +
233C ARG* 6.2 0.4 - - - +
234C ASN* 3.6 29.2 + - - +
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Residues in contact with ARG 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 SER* 2.9 33.1 + - - +
219C GLU* 3.3 33.2 + - - +
221C ARG* 1.3 79.8 - - - +
223C HIS* 1.3 83.9 + - + +
225C PRO* 3.8 7.4 - - - +
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Residues in contact with HIS 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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151A GLY* 5.5 2.6 - - - -
152A THR* 3.1 33.0 + - - -
153A ILE* 3.1 49.8 - - + +
228A PHE* 3.9 17.5 - - - +
231A LEU 4.7 0.2 - - - -
232A GLY* 4.7 1.0 + - - -
207C LEU* 3.9 5.2 - - + -
219C GLU* 3.1 32.4 + - - +
222C ARG* 1.3 100.4 + - - +
224C PHE* 1.3 78.2 + - + +
225C PRO* 3.3 10.7 - - - +
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Residues in contact with PHE 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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153A ILE* 4.0 11.2 - - + -
226A ASN 3.9 6.5 - - - -
228A PHE* 3.6 24.7 - - + -
231A LEU* 3.5 28.9 - - + -
189C LEU* 6.5 0.2 - - + -
200C CYS* 6.0 0.2 - - + -
203C CYS* 3.9 18.2 - - - -
205C GLY* 3.5 31.4 - - - -
206C LYS 3.5 16.2 - - - -
207C LEU* 3.6 28.3 - - + -
220C HIS* 3.0 31.6 + + + +
223C HIS* 1.3 85.8 - - + +
225C PRO* 1.3 64.0 - - - +
226C ASN 3.2 3.1 - - - -
227C CYS* 3.1 17.2 + - + +
230C VAL* 3.8 6.4 - - - +
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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