Contacts of the strand formed by residues 217 - 224 (chain C) in PDB entry 2ATW
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 217 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ARG* 3.9 0.2 - - - -
213C GLU* 2.9 30.4 + - - +
216C HIS* 1.3 82.6 + - - +
218C SER* 1.3 72.8 + - - +
219C LYS* 5.4 0.7 - - - +
253C GLU* 3.6 3.7 - - - +
254C LYS* 3.1 30.6 - - + +
256C ASP* 2.8 30.4 + - - -
274C PRO* 6.0 1.5 - - - +
308C GLN* 2.8 36.9 + - - +
309C ASN* 5.5 3.4 - - - +
312C LEU* 3.5 21.9 - - + +
3D A 3.0 32.7 + - - +
4D C 3.6 17.6 + - - -
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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
----------------------------------------------------------
189C VAL* 4.0 6.9 - - - +
210C VAL* 4.7 3.1 - - - -
211C ALA 3.1 10.5 - - - -
212C ARG* 3.3 20.5 - - - +
217C ARG* 1.3 79.3 - - - +
219C LYS* 1.3 65.6 + - - +
220C ILE* 4.7 8.1 - - - -
253C GLU* 2.8 25.1 + - - -
254C LYS 2.9 8.2 + - - -
255C ILE* 3.3 13.9 - - - +
256C ASP* 2.9 24.1 + - - -
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Residues in contact with LYS 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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210C VAL* 3.4 2.9 - - - +
211C ALA* 2.8 37.9 + - + +
218C SER* 1.3 75.2 - - - +
220C ILE* 1.3 63.2 + - - +
256C ASP* 2.8 37.5 + - + +
258C ILE* 4.4 4.9 - - + +
271C ALA 2.9 21.5 + - - +
273C SER 2.8 29.5 + - - -
309C ASN* 3.0 37.4 + - - +
312C LEU* 3.6 26.0 - - + +
313C ALA* 3.7 10.5 - - - +
316C LEU* 3.5 18.6 - - + +
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Residues in contact with ILE 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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189C VAL* 4.0 20.6 - - + -
193C PHE* 3.9 29.4 - - + -
207C ILE* 4.7 11.7 - - + -
209C ALA 3.3 7.4 - - - +
210C VAL* 3.9 20.2 - - + -
218C SER* 4.7 3.1 - - - -
219C LYS* 1.3 80.3 - - - +
221C ALA* 1.3 58.8 + - - +
222C VAL* 3.8 23.3 + - + -
235C CYS* 4.9 2.0 - - - -
255C ILE* 4.3 10.1 - - + -
256C ASP 3.0 8.5 + - - +
257C ILE* 3.9 25.1 - - + -
258C ILE* 2.8 29.6 + - - +
316C LEU* 4.3 1.1 - - - -
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Residues in contact with ALA 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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207C ILE* 3.5 4.7 - - - +
208C VAL* 2.8 32.5 + - + -
209C ALA* 2.9 18.1 + - + +
220C ILE* 1.3 74.1 - - - +
222C VAL* 1.3 61.3 + - - +
258C ILE* 3.2 7.9 - - + +
260C TYR* 4.5 4.3 - - + -
267C PHE* 3.8 33.2 - - + -
316C LEU* 3.8 14.3 - - + +
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Residues in contact with VAL 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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205C VAL* 4.1 7.2 - - + -
206C GLU 3.2 11.0 - - - +
207C ILE* 4.2 9.6 - - + -
208C VAL* 4.4 0.9 - - - -
220C ILE* 3.8 27.8 - - + -
221C ALA* 1.3 80.1 - - - +
223C ARG* 1.3 61.2 + - - +
231C ALA* 4.0 27.9 - - + +
232C LYS* 4.3 3.4 - - - +
235C CYS* 3.8 13.9 - - - -
257C ILE* 4.3 11.9 - - + -
258C ILE 2.9 19.1 + - - +
259C ASP* 3.8 6.3 - - - +
260C TYR* 2.9 24.7 + - - +
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Residues in contact with ARG 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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205C VAL* 3.3 2.4 - - - -
206C GLU* 2.7 66.6 + - + +
208C VAL* 3.9 20.9 - - + +
222C VAL* 1.3 77.1 - - - +
224C SER* 1.3 68.4 + - - +
225C ASN* 5.3 3.3 + - - +
231C ALA* 3.8 9.0 - - - -
260C TYR* 4.1 41.0 + - + +
262C ASP* 4.4 10.9 + - - -
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Residues in contact with SER 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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204C SER 3.5 4.9 - - - -
205C VAL* 4.4 0.7 - - - +
223C ARG* 1.3 81.7 - - - +
225C ASN* 1.3 61.4 + - - +
226C VAL 2.8 31.2 + - - -
229C LEU* 3.6 28.1 - - - +
231C ALA* 3.7 14.9 - - - +
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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