Contacts of the helix formed by residues 325 - 342 (chain A) in PDB entry 3EIJ
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 ASN 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A VAL* 1.3 89.0 - - - +
326A HIS* 1.3 68.7 + - - +
327A LEU* 3.6 10.1 - - - +
328A VAL* 3.1 45.9 - - + +
329A LYS* 3.1 18.4 + - - +
362A GLU* 5.3 1.6 + - - +
325B ASN* 3.6 53.1 + - + +
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Residues in contact with HIS 326 (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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324A VAL* 4.5 22.3 - - + +
325A ASN* 1.3 73.6 - - - +
327A LEU* 1.3 67.3 + - - +
329A LYS* 3.3 14.3 + - - +
330A GLU* 3.2 25.7 + - + +
359B PHE* 3.9 17.0 - - + -
361B HIS* 3.7 12.1 - + + +
362B GLU* 3.5 28.4 + - - +
403B ARG* 3.1 30.1 + - - +
407B ARG* 3.3 30.2 + - + -
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN* 3.3 9.1 - - - +
326A HIS* 1.3 78.3 - - - +
328A VAL* 1.3 64.2 + - - +
330A GLU* 3.0 16.0 + - + +
331A ILE* 3.1 25.5 + - + +
354A LEU* 5.0 2.7 - - + -
356A VAL* 4.2 20.0 - - + -
359A PHE* 3.7 35.7 - - + +
362A GLU* 4.7 11.4 - - + +
327B LEU* 4.0 30.5 - - + +
359B PHE* 3.5 33.6 - - + -
362B GLU* 5.3 1.0 + - - -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL 5.9 0.2 - - - +
325A ASN* 3.1 39.0 - - + +
327A LEU* 1.3 75.7 - - + +
329A LYS* 1.3 54.6 + - - +
331A ILE* 3.1 9.7 + - - +
332A ASP* 2.7 36.7 + - + +
362A GLU* 3.7 31.9 - - + +
366A GLU* 3.6 28.0 - - + +
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Residues in contact with LYS 329 (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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324A VAL* 4.9 12.8 - - + +
325A ASN 3.1 14.5 + - - +
326A HIS* 3.4 16.6 - - - +
327A LEU 3.1 0.2 - - - -
328A VAL* 1.3 78.8 - - - +
330A GLU* 1.3 65.3 + - + +
332A ASP* 3.5 8.4 + - + +
333A MET* 3.1 49.4 + - + +
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Residues in contact with GLU 330 (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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326A HIS 3.4 14.1 - - - +
327A LEU* 3.0 9.2 + - + +
329A LYS* 1.3 76.9 - - - +
331A ILE* 1.3 61.7 + - - +
333A MET* 3.5 24.6 + - - +
334A LEU* 2.9 29.7 + - - +
354A LEU* 3.8 34.6 - - + +
359B PHE* 4.3 13.0 - - + -
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Residues in contact with ILE 331 (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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327A LEU* 3.1 24.6 + - + +
328A VAL* 3.1 10.3 + - - +
330A GLU* 1.3 72.8 - - - +
332A ASP* 1.3 64.7 + - - +
334A LEU* 3.2 5.7 + - + +
335A LEU* 2.9 34.1 + - + +
351A LEU* 4.1 17.3 - - + -
354A LEU* 3.9 23.8 - - + -
356A VAL* 5.5 3.4 - - + -
359A PHE 5.6 2.0 - - - +
360A HIS* 6.3 0.7 - - + -
362A GLU* 4.0 10.3 - - + +
363A LEU* 3.6 45.3 - - + +
366A GLU* 3.9 12.3 - - + -
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Residues in contact with ASP 332 (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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328A VAL* 2.7 24.6 + - + +
329A LYS* 3.5 11.2 - - - +
331A ILE* 1.3 75.2 - - - +
333A MET* 1.3 61.7 + - - +
335A LEU* 3.3 2.9 + - - +
336A LYS* 2.9 71.2 + - - +
366A GLU* 5.1 7.4 - - + +
370A MET* 3.5 18.2 - - - +
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Residues in contact with MET 333 (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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301A LEU* 5.5 5.8 - - + +
304A MET* 3.3 42.2 - - + +
305A SER* 5.7 8.3 - - - -
329A LYS* 3.1 39.9 + - + +
330A GLU* 3.8 31.2 - - - +
331A ILE 3.3 0.2 - - - -
332A ASP* 1.3 81.5 - - - +
334A LEU* 1.3 66.9 + - - +
336A LYS* 4.4 0.9 - - + -
337A GLU* 2.9 25.6 + - - +
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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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330A GLU 2.9 16.8 + - - +
331A ILE* 3.4 9.2 - - + +
333A MET* 1.3 77.0 - - - +
335A LEU* 1.3 64.3 + - + +
337A GLU* 3.5 7.8 + - - +
338A TYR* 3.1 24.7 + - + +
347A ALA* 3.9 26.0 - - + +
350A CYS* 3.3 36.1 - - - -
351A LEU* 3.6 34.8 - - + -
354A LEU* 4.1 11.2 - - + -
363A LEU* 4.0 18.2 - - + -
386A LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 2.9 33.7 + - + +
332A ASP 3.7 3.4 - - - +
334A LEU* 1.3 78.0 - - + +
336A LYS* 1.3 59.3 + - - +
338A TYR* 3.0 9.0 + - + +
339A LEU* 2.9 34.7 + - + +
363A LEU* 3.8 21.3 - - + +
366A GLU* 3.9 7.4 - - + -
367A ALA* 3.5 41.5 - - + +
370A MET* 3.8 21.1 - - + -
383A ILE* 6.1 2.7 - - + -
386A LEU* 3.9 24.5 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 3.8 34.9 + - + +
306A LYS* 6.1 2.2 - - - +
332A ASP* 2.9 53.4 + - - +
333A MET* 4.9 0.7 - - + -
335A LEU* 1.3 72.4 - - - +
337A GLU* 1.3 62.6 + - - +
339A LEU* 3.3 11.6 + - + +
340A LEU* 3.2 30.6 + - + +
370A MET* 3.9 12.1 - - + -
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Residues in contact with GLU 337 (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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297A LYS* 3.0 44.5 + - - +
300A VAL* 3.8 29.6 - - + +
301A LEU* 4.0 13.2 - - - +
304A MET* 4.0 5.2 - - - -
333A MET 2.9 18.1 + - - +
334A LEU* 3.7 6.6 - - - +
336A LYS* 1.3 75.7 - - - +
338A TYR* 1.3 62.6 + - - +
340A LEU* 3.2 6.4 + - - +
341A SER* 3.1 28.7 + - - +
346A GLU* 4.3 15.8 - - + +
350A CYS* 6.0 2.4 - - - -
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Residues in contact with TYR 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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334A LEU* 3.1 14.1 + - + +
335A LEU* 3.0 15.7 + - + +
337A GLU* 1.3 75.8 - - - +
339A LEU* 1.3 65.8 + - + +
341A SER* 4.3 4.9 - - - -
342A GLY* 2.7 43.9 + - - -
343A ASP 3.4 20.2 - - - -
344A ILE* 3.6 41.0 - - + +
347A ALA* 4.1 19.1 - - + -
382A MET* 3.1 44.5 + - + +
383A ILE* 4.6 1.8 - - + -
385A ASP* 3.9 3.5 + - - +
386A LEU* 3.7 29.5 + - + -
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Residues in contact with LEU 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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335A LEU* 2.9 17.4 + - + +
336A LYS* 3.7 10.8 - - + +
337A GLU 3.3 0.2 - - - -
338A TYR* 1.3 86.7 - - + +
340A LEU* 1.3 61.3 + - + +
341A SER 3.7 0.2 + - - -
342A GLY 4.5 0.5 + - - -
370A MET* 3.8 29.4 - - + -
379A THR* 4.1 31.0 - - + +
382A MET* 3.4 51.3 - - + +
383A ILE* 4.7 7.4 - - + -
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Residues in contact with LEU 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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300A VAL* 4.1 29.2 - - + +
303A SER* 5.0 6.5 - - - +
304A MET* 4.7 15.0 - - + -
336A LYS* 3.2 21.1 + - + +
337A GLU* 3.2 7.0 + - - +
339A LEU* 1.3 81.1 - - + +
341A SER* 1.3 58.9 + - - +
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Residues in contact with SER 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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300A VAL* 6.2 4.3 - - - -
337A GLU* 3.1 21.0 + - - +
338A TYR* 4.1 2.8 + - - -
339A LEU 4.9 0.2 - - - -
340A LEU* 1.3 80.0 - - - +
342A GLY* 1.3 63.8 + - - +
343A ASP* 3.1 24.2 + - - +
346A GLU* 5.6 0.9 - - - +
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Residues in contact with GLY 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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338A TYR* 2.7 32.1 + - - -
339A LEU 4.5 0.6 - - - -
340A LEU 3.8 0.4 - - - -
341A SER* 1.3 73.2 + - - +
343A ASP* 1.3 58.2 + - - +
344A ILE* 3.3 19.3 + - - +
382A MET* 4.9 10.8 - - - -
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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