Contacts of the strand formed by residues 221 - 231 (chain D) in PDB entry 1JZ3
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 GLN 221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D GLN* 3.2 28.6 + - - +
140D ARG* 4.0 13.0 + - - -
217D LYS* 3.6 15.5 - - - +
218D PRO 2.9 29.9 + - - +
219D THR* 4.0 4.8 + - - +
220D THR* 1.3 74.0 - - - +
222D ILE* 1.3 62.3 - - - +
223D SER* 4.0 12.6 - - - -
246D MET* 3.1 26.3 - - - +
247D CYS* 2.9 30.8 + - + +
315D LEU* 3.5 10.3 - - - -
324D GLU* 3.4 13.7 - - - +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PHE* 3.6 4.4 - - + -
217D LYS* 2.7 34.0 + - - +
221D GLN* 1.3 69.8 - - - +
223D SER* 1.3 59.8 + - - +
224D ASP 3.9 19.3 - - - +
225D PHE* 4.2 18.2 - - + -
244D VAL* 4.4 14.6 - - + -
245D GLN 3.6 6.1 - - - +
246D MET* 4.5 0.9 - - + +
256D VAL* 6.1 0.4 - - + -
274D PHE* 6.2 0.7 - - + -
313D VAL* 3.6 34.3 - - + +
314D GLU 4.6 0.2 - - - -
315D LEU* 3.8 29.4 - - + +
324D GLU* 2.7 19.2 + - - +
325D ALA* 4.4 0.4 - - - -
326D GLU* 4.0 20.0 - - + +
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Residues in contact with SER 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA 5.2 0.3 - - - +
30D HIS* 3.7 10.9 - - - +
33D PHE* 3.5 16.2 - - - -
221D GLN* 3.4 13.6 + - - -
222D ILE* 1.3 73.2 - - - +
224D ASP* 1.3 64.1 + - - +
245D GLN* 2.9 22.9 + - - +
246D MET 3.3 13.5 + - - -
247D CYS* 3.7 26.5 - - - -
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8420A DMS 5.6 3.3 - - - +
29D ALA 5.3 2.6 - - - +
30D HIS* 4.9 3.8 - - - -
31D PRO* 3.1 22.7 - - - +
33D PHE* 4.2 7.6 - - - -
222D ILE* 3.6 4.7 - - - +
223D SER* 1.3 84.5 + - - +
225D PHE* 1.3 78.4 + - - +
226D HIS* 2.9 31.7 + - - -
244D VAL* 3.6 0.5 - - - -
245D GLN* 2.8 52.0 + - - +
445D GLN* 4.8 11.8 + - - +
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Residues in contact with PHE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PRO* 3.5 15.3 - - + +
32D PRO 4.7 3.4 - - - -
33D PHE* 3.9 17.5 - + - -
222D ILE* 4.2 12.6 - - + -
224D ASP* 1.3 81.9 + - - +
226D HIS* 1.3 70.3 + - - +
227D VAL* 4.2 10.8 - - + -
242D ALA* 6.0 1.3 - - + -
243D GLU 3.1 12.1 - - - +
244D VAL* 4.2 16.2 - - + -
245D GLN* 5.6 0.2 - - - -
313D VAL* 4.0 21.8 - - + -
326D GLU* 3.6 21.8 - - + -
327D ALA 4.0 24.0 - - - -
328D CYS* 4.0 20.6 - - + -
449D ASN* 3.0 38.3 + - - -
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Residues in contact with HIS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8420A DMS 4.5 12.7 + - + +
224D ASP* 2.9 30.2 + - - -
225D PHE* 1.3 82.8 - - - +
227D VAL* 1.3 64.0 + - - +
241D GLU 3.5 1.9 - - - +
242D ALA* 3.1 7.3 - - - +
243D GLU* 2.8 64.7 + - + +
245D GLN* 4.0 6.5 + - - -
445D GLN* 6.4 0.2 - - - -
448D ARG* 3.2 57.6 + - - +
449D ASN* 3.5 4.5 - - - -
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D PHE* 4.2 12.6 - - + -
226D HIS* 1.3 80.2 - - - +
228D ALA* 1.3 65.9 + - - +
229D THR* 4.9 1.6 - - + -
240D LEU* 3.9 33.2 - - + -
241D GLU 3.7 2.0 - - - -
242D ALA* 4.7 9.6 - - + -
311D ALA* 5.0 8.1 - - + -
328D CYS* 4.1 23.8 - - - -
330D VAL* 4.3 15.3 - - + -
448D ARG 4.7 2.3 - - - +
449D ASN* 2.8 20.9 + - + +
8401D DMS 4.1 21.2 - - + +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D HIS* 6.4 0.4 - - + -
227D VAL* 1.3 74.1 - - - +
229D THR* 1.3 66.4 + - - +
230D ARG* 4.3 8.3 - - + +
239D VAL 4.4 0.2 - - - -
240D LEU* 3.4 5.9 - - - +
241D GLU* 2.8 46.8 + - + +
481D SER* 6.2 4.3 - - - -
8401D DMS 4.7 2.0 - - - -
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Residues in contact with THR 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D VAL* 4.9 0.7 - - + -
228D ALA* 1.3 80.9 - - - +
230D ARG* 1.3 62.3 + - - +
231D PHE* 3.3 23.4 - - - -
239D VAL 3.4 4.0 - - - -
240D LEU* 4.4 6.5 - - + -
330D VAL* 4.3 8.5 - - + -
332D PHE* 3.4 44.2 - - + -
333D ARG 3.5 9.9 + - - +
334D GLU* 5.5 1.6 - - - +
8401D DMS 3.3 29.0 - - + +
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Residues in contact with ARG 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D ALA* 4.3 7.2 - - + -
229D THR* 1.3 74.6 - - - +
231D PHE* 1.4 65.7 + - - +
238D ALA* 3.1 6.6 - - - +
239D VAL* 2.8 69.2 + - - +
241D GLU* 3.1 31.1 + - - +
292D ARG* 5.1 2.2 - - - +
8409D DMS 5.8 7.9 - - + +
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Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D THR* 3.3 38.4 - - - -
230D ARG* 1.4 76.4 - - - +
232D ASN* 1.4 67.9 - - - +
235D PHE* 3.5 29.8 - + + -
237D ARG 3.4 7.2 - - - +
238D ALA* 3.8 23.1 - - + -
298D PRO* 4.2 2.9 - - + -
300D LEU* 3.9 20.9 - - + -
332D PHE* 3.7 10.1 - + + -
333D ARG* 3.6 33.4 - - - -
334D GLU* 3.8 22.0 + - + +
8417D DMS 3.1 22.8 - - - +
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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