Contacts of the strand formed by residues 309 - 317 (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 TYR 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.8 30.3 - - + -
261D TRP 3.2 20.6 - - - +
262D GLN* 3.8 34.5 + - + -
267D VAL* 4.3 11.7 - - + -
295D VAL* 4.8 4.6 - - + +
297D ASN 4.7 0.5 + - - -
298D PRO* 3.6 8.8 - - + +
299D LYS* 2.9 53.9 + - + +
307D ASN* 5.1 1.3 - - + -
308D LEU* 1.3 86.0 - - - +
310D ARG* 1.3 58.3 + - - +
329D ASP* 3.4 6.4 - - - +
330D VAL* 2.7 36.7 + - + +
332D PHE* 3.5 28.0 - + + -
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Residues in contact with ARG 310 (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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36D TRP* 3.6 12.9 - - - -
42D ALA 2.9 26.9 + - - -
43D ARG* 3.2 21.6 + - + +
45D ASP* 2.9 42.3 + - - +
260D LEU* 3.4 5.9 - - - -
261D TRP* 2.8 51.2 + - + +
263D GLY 6.2 0.4 - - - +
309D TYR* 1.3 72.8 - - - +
311D ALA* 1.4 59.5 + - - +
312D VAL* 4.0 13.9 - - + -
327D ALA* 3.6 12.9 - - - +
328D CYS* 3.6 11.4 - - - +
329D ASP* 2.8 43.6 + - - +
404D ARG* 4.1 1.6 - - - +
8404D DMS 4.0 5.1 - - - +
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Residues in contact with ALA 311 (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* 5.0 7.4 - - + -
240D LEU* 5.1 2.7 - - + -
258D VAL* 4.7 13.0 - - + -
259D SER 3.3 7.6 - - - +
260D LEU* 4.4 7.2 - - + -
310D ARG* 1.4 71.4 - - - +
312D VAL* 1.3 62.3 + - - +
313D VAL* 4.1 4.6 - - + +
327D ALA* 3.2 7.3 - - - +
328D CYS* 2.9 40.5 + - - +
330D VAL* 3.6 25.2 - - + +
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Residues in contact with VAL 312 (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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39D SER* 4.3 14.4 - - - +
42D ALA* 4.4 7.9 - - + -
43D ARG* 3.7 35.2 - - + +
257D THR 3.6 2.3 - - - +
258D VAL* 3.4 5.0 - - - +
259D SER* 2.9 35.5 + - - +
261D TRP* 4.2 15.0 - - + +
310D ARG* 4.1 8.7 - - + -
311D ALA* 1.3 78.6 - - - +
313D VAL* 1.3 63.9 + - - +
314D GLU* 3.9 25.7 + - + +
325D ALA* 4.6 2.2 - - + -
326D GLU 3.7 7.9 - - - +
327D ALA* 4.3 4.0 - - + -
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Residues in contact with VAL 313 (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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222D ILE* 3.6 18.1 - - + +
225D PHE* 4.0 33.7 - - + -
227D VAL* 5.9 1.3 - - + -
242D ALA* 5.8 2.7 - - + -
244D VAL* 3.9 31.9 - - + -
256D VAL* 4.2 7.0 - - + -
257D THR 3.8 2.5 - - - -
258D VAL* 4.4 14.6 - - + -
311D ALA* 4.8 7.2 - - + +
312D VAL* 1.3 76.2 - - - +
314D GLU* 1.3 62.5 + - - +
325D ALA* 3.2 4.0 - - - +
326D GLU* 2.8 48.1 + - + +
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Residues in contact with GLU 314 (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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39D SER* 2.5 36.2 + - - +
222D ILE* 4.6 2.0 - - - -
256D VAL* 3.2 10.0 - - - +
257D THR* 3.0 57.1 + - - +
259D SER* 4.5 4.9 + - - -
312D VAL* 3.9 17.2 - - + +
313D VAL* 1.3 74.9 - - - +
315D LEU* 1.3 59.0 + - - +
316D HIS* 3.5 9.8 - - + -
322D LEU* 3.6 13.0 - - + -
324D GLU 3.8 3.6 - - - -
325D ALA* 4.5 1.8 - - + -
8406D DMS 3.2 22.9 - - - +
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Residues in contact with LEU 315 (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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220D THR* 3.6 15.9 - - + +
221D GLN* 3.5 42.0 - - - +
222D ILE* 3.8 15.6 - - + +
246D MET* 5.0 3.4 - - + -
254D LEU* 4.3 14.6 - - + -
255D ARG 3.6 8.3 - - - +
256D VAL* 4.5 2.7 - - + +
274D PHE* 3.6 34.5 - - + -
314D GLU* 1.3 69.8 - - - +
316D HIS* 1.3 62.4 + - - +
322D LEU* 3.5 1.2 - - - +
323D ILE* 2.9 36.8 + - + +
324D GLU* 2.9 19.3 + - + +
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Residues in contact with HIS 316 (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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254D LEU* 3.6 8.0 - - - +
255D ARG* 2.8 60.2 + - + +
257D THR* 2.7 32.8 + - - -
271D THR* 4.2 5.4 - - + -
314D GLU* 3.5 22.9 - - + -
315D LEU* 1.3 74.0 - - - +
317D THR* 1.3 83.7 + - - +
318D ALA* 5.0 2.7 - - - -
321D THR 3.2 15.7 - - - +
322D LEU* 3.8 4.9 - - + -
323D ILE* 4.1 4.9 - - - +
8406D DMS 3.1 31.1 + - + +
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Residues in contact with THR 317 (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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253D TYR* 3.3 35.2 - - + -
255D ARG* 4.3 1.1 - - - -
316D HIS* 1.3 96.6 + - - +
318D ALA* 1.3 65.5 + - - +
319D ASP* 3.5 6.8 + - - +
320D GLY 2.9 13.7 + - - -
321D THR* 2.8 44.4 + - + +
323D ILE* 4.1 12.3 - - + -
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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