Contacts of the strand formed by residues 211 - 219 (chain C) in PDB entry 4J2X
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 THR 211 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C LYS* 4.6 20.6 - - - +
207C ILE* 4.1 9.7 - - - +
208C ALA* 2.6 43.5 + - + +
209C SER 4.5 1.3 - - - +
210C GLY* 1.3 81.6 - - - +
212C LYS* 1.3 68.0 + - - +
246C PHE 3.5 0.2 - - - +
247C TYR* 3.3 1.6 - - - -
248C ILE* 2.9 28.6 + - - +
358C SER* 4.6 3.9 + - - -
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Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 5.9 2.0 - - - +
80C LYS* 5.6 0.3 + - - -
211C THR* 1.3 75.3 + - - +
213C VAL* 1.3 65.7 + - - +
245C ALA* 3.8 16.2 - - + +
246C PHE 3.1 7.0 - - - +
247C TYR* 3.8 33.7 - - + +
279C SER* 3.9 24.2 + - - -
358C SER* 3.5 6.8 + - - -
359C THR* 3.1 60.4 + - - +
360C ASP* 4.1 24.5 + - - +
361C LYS* 4.4 18.0 - - - +
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 4.0 12.1 - - + -
211C THR* 5.2 0.4 - - - +
212C LYS* 1.3 79.2 - - - +
214C ALA* 1.3 60.0 + - - +
215C LEU* 4.4 8.7 - - + -
244C GLY 3.6 0.7 - - - +
245C ALA* 3.3 5.2 - - - -
246C PHE* 2.7 50.2 + - + +
248C ILE* 4.0 19.1 - - + -
276C LEU* 4.3 21.3 - - + -
356C ILE* 3.8 37.2 - - + -
357C ILE 3.4 11.4 - - - +
358C SER* 4.3 6.5 - - - +
359C THR* 4.2 5.2 - - - +
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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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95C PRO* 3.5 32.1 - - + -
213C VAL* 1.3 74.6 - - - +
215C LEU* 1.3 67.7 + - - +
216C PHE* 5.1 1.1 - - + -
228C TYR* 5.7 0.9 - - + -
243C TRP* 4.0 6.1 - - + -
244C GLY 3.8 14.1 - - - +
246C PHE* 4.8 0.4 - - - -
355C THR 3.6 3.0 - - - +
356C ILE* 3.6 0.7 - - - +
357C ILE* 2.9 33.0 + - + +
359C THR* 3.7 13.5 - - + -
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Residues in contact with LEU 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 VAL* 4.4 9.4 - - + -
214C ALA* 1.3 77.9 - - - +
216C PHE* 1.3 61.5 + - - +
228C TYR* 3.4 4.6 - - - +
229C LEU* 2.8 47.7 + - + +
244C GLY 5.0 0.6 + - - -
246C PHE* 5.1 7.6 - - + -
276C LEU* 3.8 34.5 - - + -
312C CYS* 4.7 0.2 - - - -
314C PHE* 3.7 31.0 - - + -
324C LEU* 6.0 0.7 - - + -
354C TRP* 3.8 25.5 - - + -
355C THR 3.4 1.1 - - - +
356C ILE* 3.7 32.3 - - + -
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Residues in contact with PHE 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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94C CYS* 3.9 28.7 - - + -
95C PRO* 4.7 2.7 - - + -
215C LEU* 1.3 76.6 - - - +
217C ASN* 1.4 61.5 + - - +
218C ARG* 3.8 29.2 - - + -
226C THR* 3.7 17.3 - - + -
227C ARG 3.3 11.4 - - - +
228C TYR* 3.4 30.3 - + + -
309C LEU* 4.8 7.0 - - + -
353C SER 4.2 0.2 - - - +
354C TRP* 3.5 8.5 - - - -
355C THR* 2.8 70.4 + - + -
357C ILE* 4.0 19.1 - - + -
8F G 5.6 0.9 - - - -
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Residues in contact with ASN 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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216C PHE* 1.4 74.4 - - - +
218C ARG* 1.3 70.7 + - - +
219C LEU* 4.4 7.3 + - - +
225C SER 3.7 4.0 - - - +
226C THR* 3.2 5.0 - - - +
227C ARG* 2.8 32.6 + - - +
326C LEU* 3.2 38.1 - - + +
350C ASP 2.8 26.3 + - - +
351C GLY* 3.4 13.2 - - - -
353C SER* 2.8 27.6 + - - +
354C TRP* 3.7 5.8 - - + -
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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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92C PHE 5.9 0.2 + - - -
94C CYS* 3.4 31.3 - - - +
216C PHE* 3.8 24.2 - - + -
217C ASN* 1.3 82.2 + - - +
219C LEU* 1.3 61.0 + - - +
220C ARG 4.3 0.5 + - - -
221C SER* 4.7 2.2 - - - -
222C GLN 3.3 34.8 - - - +
223C THR* 3.9 1.6 - - - +
225C SER* 3.9 4.5 - - - +
226C THR* 2.8 43.7 + - + +
350C ASP 4.9 2.1 - - - +
355C THR* 5.8 2.4 + - - +
7F T 3.5 27.1 + - - +
8F G 3.2 39.5 + - - +
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Residues in contact with LEU 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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217C ASN* 4.6 7.6 - - - +
218C ARG* 1.3 73.5 - - - +
220C ARG* 1.4 114.9 + - + +
221C SER 3.3 2.2 - - - -
222C GLN* 3.3 13.3 + - - +
225C SER* 2.8 34.2 + - - +
350C ASP* 3.5 39.9 - - + +
14E G 4.5 1.7 + - - -
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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