Contacts of the strand formed by residues 214 - 221 (chain C) in PDB entry 3MY0
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 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C GLY 3.0 32.5 + - - +
212C ARG 3.2 2.0 + - - -
213C TYR* 1.3 83.9 - - - +
215C GLU* 1.3 69.1 + - - +
230C ILE 3.4 9.4 - - - -
231C PHE 4.2 0.2 - - - -
232C SER* 3.7 14.4 - - - -
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Residues in contact with GLU 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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207C CYS* 4.4 8.4 - - - -
209C GLY 3.4 13.7 - - - +
210C LYS* 4.3 11.1 - - + +
213C TYR* 3.9 4.7 - - - -
214C GLY* 1.3 80.0 - - - +
216C VAL* 1.3 64.5 + - - +
217C TRP* 3.1 32.3 + - + +
228C VAL 3.8 0.7 - - - +
229C LYS* 3.4 3.5 - - - +
230C ILE* 2.8 42.7 + - + +
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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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207C CYS* 3.8 4.0 - - - -
208C VAL* 3.1 38.3 + - + -
209C GLY* 3.0 18.5 + - - +
213C TYR* 4.1 15.7 - - + +
215C GLU* 1.3 78.6 - - - +
217C TRP* 1.3 69.6 + - - +
227C ALA* 4.5 16.2 - - + -
228C VAL 3.6 6.3 - - - +
229C LYS* 3.9 24.0 - - + +
279C TYR* 5.9 1.3 - - + -
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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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204C LEU* 3.9 44.4 - - + -
205C VAL 4.0 7.6 - - - -
206C GLU* 3.3 35.2 - - - -
207C CYS* 3.6 26.4 - - + +
208C VAL* 4.4 2.2 - - - +
215C GLU* 3.1 28.5 + - + +
216C VAL* 1.3 83.3 - - - +
218C ARG* 1.3 60.2 + - - +
227C ALA* 3.5 5.4 - - - +
228C VAL 2.9 35.5 + - - +
230C ILE* 3.6 28.8 - - + +
279C TYR* 4.9 0.4 - - - -
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Residues in contact with ARG 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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204C LEU* 3.9 1.7 - - - -
205C VAL* 2.9 54.4 + - - +
206C GLU* 2.6 62.4 + - - +
208C VAL* 4.3 5.3 - - + +
217C TRP* 1.3 72.4 - - - +
219C GLY* 1.3 65.5 + - - +
220C LEU* 5.8 5.1 - - - +
225C SER* 4.4 11.5 + - - +
226C VAL 3.7 3.1 - - - +
279C TYR* 3.4 53.4 - - + +
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Residues in contact with GLY 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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202C VAL* 4.3 5.4 - - - -
203C ALA 3.2 13.0 - - - -
204C LEU* 4.4 4.7 - - - -
205C VAL* 4.4 1.8 - - - -
217C TRP 3.7 1.0 + - - -
218C ARG* 1.3 77.3 - - - +
220C LEU* 1.3 60.9 - - - -
225C SER* 3.4 7.8 + - - -
226C VAL* 2.7 52.2 + - - -
228C VAL* 4.8 0.9 - - - +
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Residues in contact with LEU 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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201C GLN 4.3 1.9 - - - +
202C VAL* 3.6 3.2 - - - -
203C ALA* 2.8 41.1 + - + +
205C VAL* 3.9 23.3 - - + +
218C ARG* 5.8 5.4 - - - +
219C GLY* 1.3 73.2 - - - -
221C TRP* 1.3 59.8 + - - +
222C HIS 4.2 0.4 - - - -
223C GLY* 3.5 32.3 - - - +
224C GLU 3.5 8.5 - - - +
225C SER* 4.7 7.2 - - - +
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Residues in contact with TRP 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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0C MET* 5.2 4.3 - - + -
197C THR* 4.0 3.6 + - + -
198C VAL* 3.5 46.9 - - + -
201C GLN* 2.6 45.2 + - + +
202C VAL* 3.9 16.2 - - + -
219C GLY 4.1 1.0 + - - -
220C LEU* 1.3 74.9 - - - +
222C HIS* 1.3 89.3 + + + +
223C GLY 3.3 0.7 - - - -
224C GLU* 3.0 27.1 + - + +
226C VAL* 4.4 21.3 - - + +
260C ILE* 4.1 15.3 - - + -
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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