Contacts of the helix formed by residues 298 - 314 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A TYR* 3.9 5.3 - - - -
297A ARG* 1.3 79.4 - - - +
299A LEU* 1.3 59.2 + - - +
300A ALA* 3.1 22.8 + - - +
301A ASP* 2.9 34.9 + - - +
302A PHE* 3.1 10.9 + - - +
489A ALA* 4.1 14.8 - - + +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A THR* 1.3 75.8 - - - +
300A ALA* 1.3 62.4 + - - +
302A PHE* 3.8 27.6 - - + -
303A ARG* 2.9 25.6 + - - +
488A ASN 3.9 7.4 - - - +
489A ALA 3.6 16.7 + - - +
490A ASP 3.5 33.7 - - - +
491A VAL 3.7 3.1 - - - +
492A TYR* 3.6 39.7 - - + +
509A PHE* 3.9 29.6 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.1 12.0 + - - +
299A LEU* 1.3 79.3 - - - +
301A ASP* 1.3 64.5 + - - +
303A ARG* 3.5 5.2 - - - +
304A GLN* 3.0 47.6 + - - +
486A PRO 4.0 6.7 - - - +
487A SER* 4.0 19.1 - - - +
488A ASN 4.0 1.8 - - - +
489A ALA* 3.9 10.6 - - + +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A TYR* 4.0 16.2 - - + -
297A ARG* 3.5 22.3 + - + -
298A THR* 2.9 36.4 + - - +
300A ALA* 1.3 77.6 - - - +
302A PHE* 1.3 57.5 + - - +
304A GLN* 3.4 10.2 + - - +
305A THR* 2.9 36.6 + - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LEU* 3.4 21.1 - - + +
285A TYR* 3.6 20.8 - + + +
298A THR 3.1 5.4 + - - +
299A LEU* 3.4 26.5 - - + +
301A ASP* 1.3 80.8 - - - +
303A ARG* 1.3 65.8 - - - +
305A THR* 3.3 3.3 + - - -
306A ILE* 3.1 49.1 + - + +
323A LEU* 4.1 18.8 - - + -
335A PHE* 3.5 41.3 - + + -
350A LEU* 5.4 0.9 - - + -
353A VAL* 4.4 9.6 - - + -
492A TYR* 3.9 15.9 - + - -
509A PHE* 4.1 21.8 - + - -
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LEU* 2.9 25.4 + - + +
300A ALA* 3.5 5.6 - - - +
302A PHE* 1.3 75.0 - - - +
304A GLN* 1.3 64.4 + - - +
306A ILE* 3.3 8.3 + - - +
307A ASP* 2.9 27.7 + - - +
481A TYR* 4.7 0.7 + - - -
483A ASP* 2.9 39.6 + - - +
485A ASP* 2.9 17.0 + - - +
486A PRO* 3.5 15.7 - - + +
488A ASN* 2.7 45.5 + - - +
491A VAL 2.9 24.4 + - - -
492A TYR* 3.6 24.8 - - + +
493A ALA* 3.2 28.9 + - - +
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Residues in contact with GLN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ALA* 3.0 32.4 + - - +
301A ASP* 3.9 9.5 - - - +
303A ARG* 1.3 74.2 - - - +
305A THR* 1.3 66.6 + - - +
307A ASP* 3.3 8.4 + - - +
308A LYS* 3.1 36.7 + - - +
486A PRO* 2.8 42.1 + - + +
487A SER* 4.1 5.3 - - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 6.1 0.4 - - + -
281A ASP* 3.6 20.2 - - + +
282A LEU* 3.6 38.1 - - + +
285A TYR* 4.3 9.5 - - - +
301A ASP* 2.9 22.7 + - - +
302A PHE* 3.6 5.2 - - - -
303A ARG 3.2 0.2 - - - -
304A GLN* 1.3 77.0 - - - +
306A ILE* 1.3 62.8 + - - +
308A LYS* 3.1 16.9 + - + +
309A VAL* 3.0 21.2 + - + +
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LEU* 3.9 23.1 - - + -
302A PHE* 3.1 47.7 + - + +
303A ARG 3.6 7.4 - - - +
305A THR* 1.3 76.3 - - - +
307A ASP* 1.3 58.5 + - - +
309A VAL* 3.8 7.8 - - + +
310A ASP* 2.9 30.2 + - + +
321A PHE* 4.1 10.5 - - + -
353A VAL* 5.1 0.2 - - + -
357A GLN* 3.2 27.6 - - - +
481A TYR* 4.0 11.4 - - + +
492A TYR* 3.6 21.1 - - + +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ARG 2.9 12.5 + - - +
304A GLN* 3.4 12.6 - - - +
305A THR 3.1 0.2 - - - -
306A ILE* 1.3 77.8 - - - +
308A LYS* 1.3 62.4 + - + +
310A ASP* 3.3 3.2 + - - +
311A ALA* 3.0 24.8 + - - +
481A TYR* 3.7 21.0 - - - -
483A ASP* 4.0 14.2 + - - +
486A PRO* 3.7 26.2 - - - +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.7 19.2 - - + +
304A GLN* 3.1 23.7 + - - +
305A THR* 3.1 15.6 + - + +
307A ASP* 1.3 78.6 - - + +
309A VAL* 1.3 61.1 + - - +
311A ALA* 3.4 7.2 + - - +
312A ILE* 3.3 26.7 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.1 25.6 - - + -
279A THR* 3.8 25.4 - - + +
281A ASP* 4.1 15.3 - - + -
282A LEU* 5.1 5.4 - - + +
305A THR* 3.0 22.2 + - + +
306A ILE* 3.8 7.9 - - + +
308A LYS* 1.3 73.4 - - - +
310A ASP* 1.3 67.1 + - - +
312A ILE* 3.3 14.4 + - - +
313A ALA 3.6 0.2 + - - -
319A ASN* 3.0 35.9 + - + +
320A THR 5.7 1.8 - - - +
321A PHE* 6.6 0.2 - - + -
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 2.9 20.9 + - + +
307A ASP* 3.8 4.7 - - - +
309A VAL* 1.3 76.9 - - - +
311A ALA* 1.3 64.8 + - - +
313A ALA* 3.2 10.4 + - - +
314A GLY 4.0 0.5 + - - -
319A ASN* 3.9 7.4 + - - +
358A ARG* 2.5 62.9 + - - +
481A TYR* 3.6 36.6 + - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ASP 3.0 18.0 + - - +
308A LYS* 3.7 8.5 - - - +
309A VAL 3.2 0.2 - - - -
310A ASP* 1.3 80.0 + - - +
312A ILE* 1.3 62.5 - - + +
314A GLY* 3.0 16.2 + - - -
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.6 33.4 - - + +
261A ASN* 4.2 10.8 - - + -
263A VAL* 3.7 22.0 - - + -
264A PRO* 3.3 48.1 - - + +
267A ILE* 4.8 2.2 - - + +
308A LYS 3.3 14.6 + - - +
309A VAL 3.6 8.5 - - - +
310A ASP 3.2 0.6 - - - -
311A ALA* 1.3 75.4 - - + +
313A ALA* 1.3 65.2 + - - +
314A GLY* 3.0 4.3 + - - -
317A GLY* 5.4 0.2 - - - -
319A ASN* 5.5 1.6 - - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 4.5 5.6 - - - -
309A VAL 3.6 2.6 + - - -
310A ASP 3.2 4.8 + - - +
312A ILE* 1.3 78.0 - - - +
314A GLY* 1.3 64.9 + - - +
315A GLU 3.3 0.2 + - - -
316A TYR 3.6 0.2 + - - -
317A GLY* 2.8 46.8 + - - +
318A TRP* 4.2 5.8 - - + +
319A ASN* 3.7 19.5 - - - +
358A ARG* 3.3 27.8 - - - +
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASP 4.0 1.2 + - - -
311A ALA 3.0 13.9 + - - -
312A ILE 3.0 5.7 - - - -
313A ALA* 1.3 82.7 - - - +
315A GLU* 1.3 58.9 + - - -
317A GLY 4.8 1.0 - - - +
358A ARG* 3.9 17.2 + - - -
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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
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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