Contacts of the strand formed by residues 322 - 330 (chain B) 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 LEU 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 3.7 35.6 - - + +
38B ASN* 3.7 4.7 - - - +
39B SER* 3.5 20.4 - - - +
314B GLU* 3.8 28.7 - - + +
315B LEU 3.6 7.4 - - - +
316B HIS* 3.8 4.0 - - + -
320B GLY 3.3 4.4 + - - -
321B THR* 1.3 83.1 - - - +
323B ILE* 1.4 62.8 + - - +
324B GLU 3.5 29.2 - - - +
325B ALA* 4.6 1.8 - - + -
8406B DMS 4.4 9.9 - - - -
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 3.3 17.8 + - - +
218B PRO* 3.8 16.1 - - + +
220B THR* 3.3 33.0 - - + +
253B TYR* 5.7 0.2 - - + -
254B LEU* 3.6 30.7 - - + -
315B LEU* 2.8 27.1 + - + +
316B HIS* 4.1 16.2 - - - -
317B THR* 4.1 10.3 - - + -
321B THR* 3.6 4.7 + - + +
322B LEU* 1.4 75.8 - - - +
324B GLU* 1.4 62.1 + - - +
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 2.6 35.9 + - - +
36B TRP 3.4 13.5 - - - +
37B ARG* 3.9 1.6 - - - +
217B LYS* 2.7 31.9 + - - -
218B PRO* 3.4 21.2 - - + +
221B GLN* 3.2 5.2 - - - +
222B ILE* 2.7 32.4 + - + +
315B LEU* 2.8 40.0 + - + +
322B LEU* 3.5 9.6 - - - +
323B ILE* 1.4 81.6 - - - +
325B ALA* 1.3 59.2 + - - +
326B GLU* 4.4 2.5 - - - -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B SER* 4.0 0.5 - - - -
36B TRP* 3.0 40.2 + - + +
39B SER* 4.5 12.1 - - - +
42B ALA* 4.1 20.0 - - + -
222B ILE* 4.4 0.4 - - - -
312B VAL* 4.5 1.3 - - + -
313B VAL 3.2 10.8 - - - +
314B GLU* 4.3 15.5 - - + -
322B LEU* 4.6 4.0 - - + -
324B GLU* 1.3 76.4 - - - +
326B GLU* 1.3 69.6 + - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO 4.3 1.1 - - - +
33B PHE* 3.1 23.1 - - + +
34B ALA* 2.7 25.2 + - - +
35B SER* 2.9 26.0 + - - -
36B TRP* 4.3 4.8 - - - -
42B ALA* 4.8 0.2 - - - -
217B LYS* 2.9 28.4 + - - +
222B ILE* 4.0 21.7 - - + +
225B PHE* 3.7 22.2 - - + -
312B VAL* 3.8 3.8 - - - +
313B VAL* 2.9 32.3 + - + +
324B GLU* 4.7 1.1 - - - +
325B ALA* 1.3 76.1 - - - +
327B ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO 4.5 2.0 + - - +
36B TRP* 4.0 9.3 - - + -
42B ALA* 3.6 17.5 - - + +
225B PHE* 3.9 13.4 - - - -
310B ARG* 3.6 23.3 - - - +
311B ALA 3.2 15.7 - - - +
312B VAL* 4.2 3.4 - - + -
313B VAL* 4.6 1.1 - - - +
326B GLU* 1.3 79.9 + - - +
328B CYS* 1.3 66.6 + - - +
8404B DMS 3.1 21.5 - - - +
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Residues in contact with CYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B PHE* 4.0 22.0 - - + -
227B VAL* 4.1 14.6 - - - -
310B ARG* 3.6 13.8 - - - +
311B ALA* 2.9 35.5 + - - +
327B ALA* 1.3 77.8 - - - +
329B ASP* 1.3 75.5 + - - +
330B VAL* 4.0 13.5 - - - -
449B ASN* 4.3 18.4 - - + +
8404B DMS 4.7 2.9 - - + -
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Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LEU* 4.2 22.4 - - + +
309B TYR 3.5 6.8 - - - +
310B ARG* 3.0 28.8 + - - +
328B CYS* 1.3 85.5 - - - +
330B VAL* 1.3 59.2 + - - +
400B THR* 4.4 5.4 + - - +
403B ASP* 4.5 13.6 - - - +
404B ARG* 2.9 39.4 + - - +
449B ASN 4.0 12.3 - - - +
450B HIS* 6.5 0.2 - - + -
451B PRO* 4.0 5.7 - - - +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B VAL* 4.3 12.1 - - + -
229B THR* 4.1 11.2 - - + -
240B LEU* 4.1 11.4 - - + -
260B LEU* 4.4 4.5 - - + -
308B LEU* 3.4 8.8 - - - -
309B TYR* 2.7 44.9 + - + +
311B ALA* 3.6 33.7 - - + +
328B CYS* 4.0 8.3 - - - +
329B ASP* 1.3 79.2 - - - +
331B GLY* 1.3 60.7 + - - +
332B PHE* 4.0 24.2 - - + -
8401B DMS 3.7 10.3 - - - +
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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