Contacts of the helix formed by residues 333 - 352 (chain A) in PDB entry 2J0M
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 SER 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 5.7 2.6 - - - +
312A ARG* 3.7 9.9 - - - -
313A LYS* 4.1 0.2 - - - +
314A GLY* 3.8 11.3 + - - -
331A ALA* 3.9 2.6 - - - +
332A PRO* 1.3 80.7 - - - +
334A LEU* 1.3 65.6 + - - +
335A THR* 3.4 10.8 + - - -
336A ILE* 3.3 36.0 + - - +
337A ALA 3.4 8.0 + - - -
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Residues in contact with LEU 334 (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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304A TYR* 4.6 8.5 - - + -
305A SER 3.5 29.2 - - - +
306A ASN* 4.4 11.2 - - + +
312A ARG* 3.1 25.8 + - + +
313A LYS 4.0 1.3 - - - +
314A GLY* 4.3 6.7 - - - -
333A SER* 1.3 72.9 - - - +
335A THR* 1.3 60.3 + - - +
337A ALA* 3.2 6.9 + - + +
338A GLU* 2.9 52.8 + - - +
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 4.8 17.4 - - + +
95A VAL 3.3 25.1 - - - +
96A HIS* 3.9 30.0 + - + +
333A SER* 3.2 9.6 + - - -
334A LEU* 1.3 79.0 - - - +
336A ILE* 1.3 57.9 + - + +
338A GLU* 3.2 13.5 + - + +
339A ASN* 2.8 37.3 + - - +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.9 7.4 - - + +
258A PHE* 4.3 22.2 - - + -
259A LYS 5.2 2.7 - - - +
331A ALA* 3.8 14.6 - - + -
332A PRO* 3.7 35.0 - - + -
333A SER* 3.3 24.1 + - - +
334A LEU 3.3 0.2 - - - -
335A THR* 1.3 76.3 - - + +
337A ALA* 1.3 51.4 + - - +
339A ASN* 3.2 10.7 + - - +
340A MET* 2.7 38.4 + - - +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 4.5 10.0 - - + +
305A SER 5.3 1.1 - - - +
314A GLY* 4.1 19.5 - - - +
315A MET 3.7 23.6 - - - +
316A LEU* 4.9 5.6 - - + +
331A ALA* 3.9 9.3 - - + +
333A SER 3.4 2.4 + - - +
334A LEU 3.2 9.5 + - - +
336A ILE* 1.3 75.5 - - - +
338A GLU* 1.3 55.9 + - - +
339A ASN 3.1 1.6 - - - -
340A MET* 3.7 7.2 - - - +
341A ALA* 2.7 37.0 + - - +
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Residues in contact with GLU 338 (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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96A HIS* 5.8 2.9 + - - -
97A TRP 4.9 6.1 - - - +
110A LYS* 5.6 4.2 + - - -
304A TYR* 3.3 45.8 + - + +
334A LEU* 2.9 44.2 + - - +
335A THR* 3.5 13.8 + - + +
337A ALA* 1.3 75.0 - - - +
339A ASN* 1.3 62.0 + - - +
341A ALA* 3.9 6.1 - - - +
342A ASP* 3.3 22.9 + - - +
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Residues in contact with ASN 339 (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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95A VAL* 2.8 38.2 + - - +
96A HIS* 4.1 1.0 - - - -
97A TRP* 3.4 31.4 + - + +
127A ARG* 3.2 20.0 + - - +
258A PHE* 5.1 7.4 - - + -
335A THR* 2.8 22.3 + - - +
336A ILE* 3.4 13.0 - - - +
338A GLU* 1.3 78.0 - - - +
340A MET* 1.3 66.1 + - - +
341A ALA 3.2 1.1 - - - -
342A ASP* 3.3 4.3 + - - -
343A LEU* 3.0 18.2 + - - +
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Residues in contact with MET 340 (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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258A PHE* 3.9 43.2 - - + -
260A CYS* 3.7 10.8 - - - -
272A LEU* 3.6 31.2 - - + -
274A ILE* 4.3 5.2 - - + -
316A LEU* 3.9 17.3 - - + -
329A VAL* 3.7 25.8 - - + -
331A ALA* 4.4 10.3 - - - -
336A ILE* 2.7 31.5 + - - +
337A ALA* 3.2 5.1 + - - +
339A ASN* 1.3 71.3 - - - +
341A ALA* 1.3 65.6 + - - +
343A LEU* 3.2 9.0 + - - +
344A ILE* 3.1 27.7 + - + +
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Residues in contact with ALA 341 (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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302A ILE* 4.2 21.1 - - + +
304A TYR* 3.8 29.8 - - + -
316A LEU* 4.4 6.2 - - + +
337A ALA 2.7 20.6 + - - +
338A GLU 3.9 4.9 - - - +
340A MET* 1.3 70.7 - - - +
342A ASP* 1.3 68.9 + - - +
343A LEU 2.8 1.0 + - - -
344A ILE* 3.1 2.0 + - - +
345A ASP* 2.7 26.9 + - - +
359A ILE* 4.5 5.2 - - + -
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Residues in contact with ASP 342 (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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97A TRP* 3.5 27.7 - - + +
98A LEU 4.2 15.6 - - - +
99A HIS* 4.9 4.3 - - - +
100A LEU 5.6 0.5 + - - -
127A ARG* 2.8 24.7 + - - +
128A TYR* 2.5 27.7 + - - -
338A GLU 3.3 12.2 + - - +
339A ASN 3.3 5.0 + - - +
341A ALA* 1.3 77.4 - - - +
343A LEU* 1.3 52.4 + - - +
345A ASP* 3.4 9.4 - - - +
346A GLY* 2.6 31.9 + - - -
349A ARG* 4.5 8.0 + - - -
359A ILE* 5.0 3.1 - - - +
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Residues in contact with LEU 343 (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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127A ARG* 3.3 46.4 - - + +
128A TYR* 3.9 4.4 - - + -
256A GLU* 3.9 17.3 - - + +
258A PHE* 3.5 31.0 - - + -
274A ILE* 3.6 30.5 - - + +
339A ASN 3.0 8.0 + - - +
340A MET 3.4 8.3 - - - +
341A ALA 2.8 4.6 + - - -
342A ASP* 1.3 71.6 - - - +
344A ILE* 1.3 65.9 + - + +
346A GLY* 3.2 2.3 + - - -
347A TYR* 3.1 45.2 + - + -
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Residues in contact with ILE 344 (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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272A LEU* 6.1 1.3 - - + -
274A ILE* 4.5 20.6 - - + -
280A ILE* 4.0 32.5 - - + -
296A PHE* 4.3 8.5 - - + -
299A VAL* 4.4 7.4 - - + -
302A ILE* 3.9 12.8 - - + -
316A LEU* 4.0 17.5 - - + -
318A LEU* 3.8 25.8 - - + -
340A MET* 3.1 17.2 + - + +
341A ALA* 4.1 0.7 - - - +
343A LEU* 1.3 71.6 - - - +
345A ASP* 1.3 60.8 + - - +
347A TYR* 3.3 5.2 + - - +
348A CYS* 2.9 51.3 + - - -
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Residues in contact with ASP 345 (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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99A HIS* 4.4 5.5 + - - -
302A ILE* 3.6 9.2 - - + +
341A ALA 2.7 25.9 + - - +
342A ASP* 3.4 9.2 - - - +
344A ILE* 1.3 73.9 - - - +
346A GLY* 1.3 61.9 + - - +
348A CYS* 3.5 2.7 + - - +
349A ARG* 2.7 49.2 + - - -
357A SER* 3.2 15.4 - - - -
358A PHE* 2.9 31.2 + - - +
359A ILE* 3.6 23.4 + - + +
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Residues in contact with GLY 346 (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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81A ALA 4.5 1.9 - - - +
128A TYR* 3.4 33.5 - - - +
342A ASP 2.6 16.3 + - - -
343A LEU 3.2 0.2 + - - -
344A ILE 3.2 0.4 - - - -
345A ASP* 1.3 76.1 - - - +
347A TYR* 1.3 59.3 + - - +
349A ARG* 3.5 20.0 + - - +
350A LEU* 3.2 21.5 + - - +
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Residues in contact with TYR 347 (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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127A ARG 4.0 5.7 + - - -
128A TYR* 4.0 4.5 - + + -
129A LEU* 3.0 49.9 + - - +
255A LYS* 5.4 1.9 - - - -
274A ILE* 4.0 19.2 + - + -
275A GLY* 3.8 2.5 - - - -
276A PRO* 3.3 29.7 - - + +
296A PHE* 3.6 48.9 - + + -
343A LEU* 3.1 42.6 + - + +
344A ILE 3.8 1.3 - - - +
346A GLY* 1.3 72.8 - - - +
348A CYS* 1.3 61.1 + - - +
350A LEU* 3.3 12.5 + - + +
351A VAL* 2.9 38.7 + - + +
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Residues in contact with CYS 348 (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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296A PHE* 3.9 12.1 - - - -
299A VAL* 3.5 46.0 - - - -
302A ILE* 4.5 4.0 - - - -
344A ILE* 2.9 30.7 + - - +
345A ASP 3.8 3.1 - - - +
347A TYR* 1.3 72.9 - - - +
349A ARG* 1.3 65.9 + - - +
351A VAL* 4.5 0.2 - - - +
352A ASN* 2.7 36.5 + - - +
358A PHE* 3.7 24.9 - - + -
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Residues in contact with ARG 349 (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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81A ALA* 4.8 8.0 + - + +
83A TYR 4.8 2.2 + - - -
99A HIS* 5.6 0.2 + - - -
100A LEU* 3.6 43.6 - - - +
128A TYR* 3.9 27.1 + - - -
342A ASP* 4.5 8.5 + - - -
345A ASP* 2.7 58.1 + - - +
346A GLY* 3.5 14.0 - - - +
348A CYS* 1.3 79.7 - - - +
350A LEU* 1.3 63.2 + - - +
353A GLY* 3.5 4.5 + - - -
354A ALA* 3.3 42.3 + - - +
355A THR* 4.6 2.0 - - - +
356A GLN 3.9 15.9 - - - +
357A SER* 4.0 12.5 - - - +
358A PHE* 4.2 7.6 - - + -
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Residues in contact with LEU 350 (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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79A ASN* 6.1 0.4 - - - +
81A ALA* 3.9 31.8 - - + +
82A CYS* 4.7 7.4 - - - -
128A TYR* 3.7 17.0 - - + +
129A LEU 3.4 34.3 - - - +
130A PRO* 3.9 14.1 - - + -
136A GLN* 5.6 2.7 - - - +
346A GLY 3.2 13.1 + - - +
347A TYR* 3.3 13.9 + - + +
349A ARG* 1.3 79.8 - - - +
351A VAL* 1.3 69.3 + - + +
352A ASN 3.2 9.5 - - - +
353A GLY* 4.7 1.2 - - - -
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Residues in contact with VAL 351 (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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129A LEU 5.9 0.2 - - - +
130A PRO* 6.5 0.2 - - + -
131A LYS* 5.4 17.0 - - + +
296A PHE* 3.8 27.1 - - + +
297A ASN* 4.0 38.3 - - + +
347A TYR* 2.9 26.0 + - + +
348A CYS 4.5 1.1 - - - +
350A LEU* 1.3 79.5 - - + +
352A ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 352 (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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296A PHE 4.5 8.7 + - - -
297A ASN* 4.8 15.1 + - - +
299A VAL 5.3 3.6 + - - -
348A CYS* 2.7 32.2 + - - +
349A ARG 3.7 4.0 - - - +
350A LEU 3.2 5.9 - - - +
351A VAL* 1.3 83.8 - - - +
353A GLY* 1.3 60.5 + - - +
354A ALA* 4.1 9.6 - - + +
358A PHE* 3.5 25.4 - - + -
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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
------------------------------------------------------------
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