Contacts of the helix formed by residues 213 - 224 (chain C) in PDB entry 5J63
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 PRO 213 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C HIS 4.8 0.4 - - - +
212C LYS* 1.4 95.7 - - + +
214C ALA* 1.3 56.3 + - - +
215C SER* 4.2 10.3 - - - +
216C VAL* 2.7 49.2 + - + +
217C LEU* 2.9 13.8 + - - +
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Residues in contact with ALA 214 (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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212C LYS 3.5 3.6 + - - -
213C PRO* 1.3 69.9 - - - +
215C SER* 1.3 56.3 + - - +
217C LEU* 3.7 16.2 - - + +
218C HIS* 2.9 29.3 + - - +
247C VAL* 4.1 11.4 - - + +
248C HIS 5.5 5.6 - - - +
268C ALA 5.6 7.9 - - - -
274C LEU* 3.8 34.7 - - + +
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Residues in contact with SER 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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213C PRO* 4.2 10.3 - - - +
214C ALA* 1.3 78.0 - - - +
216C VAL* 1.3 71.5 + - - +
218C HIS* 3.5 3.3 + - - +
219C ASN* 3.3 30.4 + - - +
247C VAL* 4.5 16.0 - - - +
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Residues in contact with VAL 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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122C VAL* 4.8 8.6 - - + +
212C LYS* 4.7 23.6 - - + +
213C PRO* 2.7 33.5 + - + +
215C SER* 1.3 85.2 + - - +
217C LEU* 1.3 64.3 + - + +
218C HIS 3.4 0.2 - - - -
219C ASN* 3.7 10.7 + - - +
220C MET* 3.3 19.9 + - - +
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Residues in contact with LEU 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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208C LEU* 4.0 19.3 - - + +
209C GLU 3.5 28.7 - - - +
210C TRP* 3.4 45.8 - - + +
212C LYS* 3.7 15.3 - - + +
213C PRO 2.9 19.6 + - - +
214C ALA* 3.7 17.7 - - + +
215C SER 3.3 0.2 - - - -
216C VAL* 1.3 79.2 - - + +
218C HIS* 1.3 64.4 + - - +
220C MET* 3.1 9.0 + - + +
221C VAL* 3.0 26.9 + - - +
268C ALA 6.2 0.7 - - - -
274C LEU* 4.4 8.7 - - + -
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Residues in contact with HIS 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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154C PRO 4.7 6.3 - - - -
155C ASP* 6.1 1.1 - - - -
214C ALA 2.9 18.1 + - - +
215C SER 3.6 6.5 - - - +
216C VAL 3.4 0.2 - - - -
217C LEU* 1.3 76.3 - - - +
219C ASN* 1.3 65.9 + - - +
221C VAL* 3.1 4.0 + - - +
222C ARG* 3.1 60.3 + - + +
245C SER* 2.6 59.4 + - - -
246C ARG* 3.7 9.1 - - - -
247C VAL* 3.8 16.0 - - + +
274C LEU* 4.1 4.2 - - + +
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Residues in contact with ASN 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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121C LEU 3.3 22.8 - - - +
122C VAL* 3.8 11.6 + - - +
123C ASN 4.5 0.2 - - - -
124C GLY* 3.2 29.1 - - - +
215C SER* 3.3 16.8 + - - +
216C VAL* 3.8 11.5 - - - +
217C LEU 3.3 0.4 - - - -
218C HIS* 1.3 82.1 + - - +
220C MET* 1.3 56.5 + - - +
222C ARG* 3.4 28.8 + - - +
223C ALA* 2.9 24.1 + - - +
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Residues in contact with MET 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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122C VAL* 3.9 27.5 - - + +
201C ARG* 3.5 31.2 - - - +
205C ASP 3.7 11.4 - - - +
206C SER* 3.8 30.3 - - - +
207C PHE 5.2 3.4 - - - +
208C LEU* 4.5 10.8 - - + -
216C VAL* 3.3 12.3 + - + +
217C LEU* 3.1 14.2 + - + +
219C ASN* 1.3 77.8 - - - +
221C VAL* 1.3 65.5 + - - +
223C ALA* 3.4 10.1 + - - -
224C VAL* 3.5 11.3 + - - +
231C ALA* 4.6 1.1 - - + -
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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
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208C LEU* 4.4 4.7 - - + -
217C LEU 3.0 16.1 + - - +
218C HIS 3.1 3.1 + - - +
220C MET* 1.3 76.2 - - - +
222C ARG* 1.3 66.4 + - + +
224C VAL* 3.2 2.6 + - - +
225C ALA* 3.2 22.2 + - - +
231C ALA* 3.8 21.8 + - + +
242C VAL* 3.7 30.7 - - + +
243C TRP 3.8 20.4 - - - +
244C SER* 3.9 1.8 - - - +
245C SER* 3.2 35.2 - - - +
274C LEU* 4.2 8.5 - - + -
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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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121C LEU* 3.3 30.3 + - + +
124C GLY* 5.2 4.4 - - - -
125C GLU 5.4 2.6 + - - -
152C ILE* 3.9 7.3 - - - +
153C ALA 3.5 12.9 + - - -
154C PRO* 3.2 24.0 + - - +
155C ASP 4.8 0.6 - - - -
156C ASP 2.9 31.7 + - - +
157C ILE* 3.5 18.6 - - + +
158C ALA 3.1 24.3 + - - -
218C HIS* 3.1 50.2 + - + +
219C ASN* 3.4 31.9 + - - +
221C VAL* 1.3 78.9 - - + +
223C ALA* 1.3 62.0 + - - +
224C VAL 3.3 0.7 + - - -
225C ALA* 3.7 3.4 + - - -
245C SER 6.3 0.2 - - - +
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Residues in contact with ALA 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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118C ASN* 3.0 36.6 + - + +
121C LEU* 3.9 13.4 - - + +
122C VAL* 3.4 32.8 - - + -
158C ALA* 3.5 7.0 - - - +
219C ASN 2.9 15.5 + - - +
220C MET* 3.5 9.2 - - - +
221C VAL 3.3 0.4 - - - -
222C ARG* 1.3 77.9 - - - +
224C VAL* 1.3 62.9 + - + +
225C ALA 3.7 0.4 - - - -
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Residues in contact with VAL 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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201C ARG* 4.5 2.7 - - - +
206C SER* 3.4 28.7 - - - +
220C MET 3.5 16.2 - - - +
221C VAL 3.2 2.4 + - - +
222C ARG 3.2 0.4 - - - -
223C ALA* 1.3 85.1 - - + +
225C ALA* 1.3 66.0 + - - +
228C TRP* 3.2 14.5 - - + -
229C PRO* 4.2 4.7 - - + -
230C GLY* 2.9 30.2 + - - +
231C ALA 3.5 22.2 - - - +
401C G3N 3.2 33.9 - - + +
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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