Contacts of the helix formed by residues 298 - 314 (chain B) in PDB entry 1ZJA
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 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR* 3.9 6.2 - - - -
297B ARG* 1.3 79.2 - - - +
299B LEU* 1.3 64.8 + - - +
300B ALA* 3.1 24.2 + - - +
301B ASP* 2.9 25.3 + - - +
302B PHE* 3.2 10.3 + - - +
489B ALA* 4.1 14.7 - - + +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 1.3 76.1 - - - +
300B ALA* 1.3 62.7 + - - +
302B PHE* 3.1 29.6 + - + -
303B ARG* 2.9 29.3 + - - +
488B ASN 3.9 8.3 - - - +
489B ALA 3.5 17.7 + - - +
490B ASP 3.6 33.4 - - - +
491B VAL 3.7 2.9 - - - +
492B TYR* 3.7 37.5 - - + +
509B PHE* 4.1 26.9 - - + -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 3.1 12.7 + - - +
299B LEU* 1.3 78.7 - - - +
301B ASP* 1.3 59.5 + - - +
303B ARG* 3.4 10.6 - - - +
304B GLN* 3.0 52.1 + - - +
486B PRO 4.0 2.5 - - - +
487B SER 4.0 18.4 - - - +
488B ASN 4.2 1.1 - - - -
489B ALA* 4.0 9.3 - - + +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TYR* 4.0 16.4 - - + -
297B ARG* 3.5 21.3 + - + -
298B THR* 2.9 34.0 + - - +
300B ALA* 1.3 79.3 - - - +
302B PHE* 1.3 54.3 + - - +
304B GLN* 3.9 9.4 - - - +
305B THR* 2.8 39.3 + - - +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.6 21.2 - - + +
285B TYR* 3.7 17.8 - + + +
298B THR 3.2 4.2 + - - +
299B LEU* 3.1 31.6 + - + +
301B ASP* 1.3 80.5 - - - +
303B ARG* 1.3 60.2 + - - +
305B THR* 3.3 3.5 + - - -
306B ILE* 3.0 51.8 + - + +
323B LEU* 4.2 17.5 - - + -
335B PHE* 3.5 41.3 - + + -
350B LEU* 5.3 1.1 - - + -
353B VAL* 4.5 7.4 - - + -
492B TYR* 4.0 16.2 - + - -
509B PHE* 4.0 22.2 - + - -
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 2.9 25.5 + - + +
300B ALA* 3.4 6.7 - - - +
302B PHE* 1.3 75.1 - - - +
304B GLN* 1.3 63.6 + - - +
306B ILE* 3.1 7.9 + - - +
307B ASP* 2.8 29.1 + - - +
481B TYR* 4.9 0.7 + - - -
483B ASP* 2.9 42.1 + - - +
485B ASP* 2.9 17.6 + - - +
486B PRO* 3.5 16.4 - - + +
488B ASN* 2.8 43.7 + - - +
491B VAL 2.8 24.8 + - - -
492B TYR* 3.7 24.8 - - + +
493B ALA* 3.2 29.1 + - - +
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Residues in contact with GLN 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.0 33.8 + - - +
301B ASP* 3.9 9.1 - - - +
303B ARG* 1.3 76.5 - - - +
305B THR* 1.3 62.7 + - - +
307B ASP* 3.4 7.6 + - - +
308B LYS* 3.1 38.8 + - - +
486B PRO* 2.8 40.5 + - + +
487B SER* 4.2 4.6 - - - +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 6.2 0.4 - - + -
281B ASP* 3.7 20.0 - - + +
282B LEU* 3.6 39.5 - - + +
285B TYR* 4.3 9.4 - - - +
301B ASP* 2.8 23.9 + - - +
302B PHE 3.6 4.3 - - - -
304B GLN* 1.3 77.2 - - - +
306B ILE* 1.3 63.1 + - - +
308B LYS* 3.1 12.7 + - + +
309B VAL* 2.9 23.0 + - + +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.7 26.7 - - + -
302B PHE* 3.0 47.1 + - + +
303B ARG 3.1 6.9 + - - +
305B THR* 1.3 74.6 - - - +
307B ASP* 1.3 59.1 + - - +
309B VAL* 3.2 8.2 + - - +
310B ASP* 2.8 30.2 + - + +
321B PHE* 3.9 17.5 - - + -
357B GLN* 3.3 22.4 - - - +
481B TYR* 3.8 13.7 - - + +
492B TYR* 3.7 22.2 - - + +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG 2.8 16.2 + - - +
304B GLN* 3.5 9.6 - - - +
305B THR 3.2 0.2 - - - -
306B ILE* 1.3 78.4 - - - +
308B LYS* 1.3 64.1 + - + +
310B ASP* 3.2 4.7 + - - +
311B ALA* 2.9 24.3 + - - +
481B TYR* 3.7 22.4 - - + -
483B ASP* 4.4 13.9 + - - +
486B PRO* 4.1 19.2 - - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 3.8 18.4 - - + -
304B GLN* 3.1 26.1 + - - +
305B THR* 3.1 10.7 + - + +
307B ASP* 1.3 81.0 - - + +
309B VAL* 1.3 61.4 + - - +
311B ALA* 3.3 14.2 + - - +
312B ILE* 3.3 19.2 + - - +
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Residues in contact with VAL 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.0 28.0 - - + -
279B THR* 3.7 22.0 - - - +
281B ASP* 4.1 15.9 - - + -
282B LEU* 5.0 5.2 - - + +
305B THR* 2.9 23.2 + - + +
306B ILE* 3.7 7.2 - - - +
308B LYS* 1.3 75.9 - - - +
310B ASP* 1.3 64.5 + - - +
312B ILE* 3.1 16.3 + - + +
319B ASN* 3.1 36.2 + - + +
320B THR 5.7 1.6 - - - +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ILE* 2.8 18.6 + - + +
307B ASP* 3.7 5.0 - - - +
309B VAL* 1.3 78.9 - - - +
311B ALA* 1.3 63.2 + - - +
313B ALA* 3.2 15.8 + - - +
314B GLY 4.1 1.9 + - - -
319B ASN* 3.9 8.8 + - - +
358B ARG* 3.0 47.3 + - - +
481B TYR* 3.6 41.1 + - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ASP 2.9 17.2 + - - +
308B LYS* 3.6 8.3 - - - +
309B VAL 3.2 0.2 - - - -
310B ASP* 1.3 78.4 - - - +
312B ILE* 1.3 65.1 + - + +
314B GLY* 3.3 13.3 + - - -
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Residues in contact with ILE 312 (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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260B LEU* 3.5 32.8 - - + +
261B ASN* 4.3 10.8 - - - -
263B VAL* 3.7 21.3 - - + -
264B PRO* 3.2 48.4 - - + +
267B ILE* 4.8 2.2 - - + +
308B LYS 3.4 13.7 - - - +
309B VAL* 3.1 8.9 + - + +
310B ASP 3.1 1.0 - - - -
311B ALA* 1.3 79.6 - - + +
313B ALA* 1.3 63.0 + - - +
314B GLY* 3.2 1.4 + - - -
317B GLY* 5.5 0.2 - - - -
319B ASN* 5.6 1.1 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 4.4 6.3 - - - -
309B VAL 3.7 2.4 + - - -
310B ASP 3.2 10.8 + - - +
312B ILE* 1.3 78.1 - - - +
314B GLY* 1.3 61.7 + - - +
317B GLY* 2.7 52.4 + - - +
318B TRP* 4.2 4.9 - - + +
319B ASN* 3.6 24.2 - - + +
358B ARG* 3.9 16.2 - - - +
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Residues in contact with GLY 314 (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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310B ASP 4.1 1.8 + - - -
311B ALA 3.3 12.6 + - - -
312B ILE 3.1 5.7 - - - -
313B ALA* 1.3 83.5 - - - +
315B GLU* 1.3 58.6 + - - -
316B TYR 4.4 0.2 - - - -
317B GLY 4.5 0.9 - - - +
358B ARG* 3.7 21.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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