Contacts of the helix formed by residues 328 - 349 (chain A) in PDB entry 4GSA
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 328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LEU 3.7 6.4 + - - -
323A LEU* 3.0 48.4 + - + +
325A GLN* 2.8 23.7 + - - +
326A PRO 3.3 2.1 + - - -
327A GLY* 1.3 80.8 - - - +
329A TYR* 1.3 79.3 + - + +
330A GLU* 3.8 0.8 + - - -
331A TYR* 3.4 0.6 + - - +
332A LEU* 3.2 23.7 + - + +
412A LEU* 3.6 26.3 - - + +
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Residues in contact with TYR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.7 0.7 - - + -
251A PHE 2.6 31.1 + - - -
252A ARG 3.3 21.3 - - - -
253A ILE 4.4 1.8 - - - +
254A ALA* 3.8 13.7 - - + -
255A TYR* 3.5 37.2 - + + -
323A LEU* 3.7 27.3 - - + +
328A THR* 1.3 93.0 - - + +
330A GLU* 1.3 67.7 + - - +
332A LEU* 3.8 16.9 - - + +
333A ASP* 3.0 28.9 + - - +
360A SER* 3.8 12.1 + - - +
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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
----------------------------------------------------------
327A GLY* 3.5 26.3 + - - +
328A THR 3.2 0.7 + - - -
329A TYR* 1.3 85.6 + - - +
331A TYR* 1.3 65.1 + - - +
333A ASP* 3.2 6.4 + - - +
334A GLN* 3.0 26.0 + - - +
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Residues in contact with TYR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY 3.0 17.6 + - - +
328A THR* 3.8 4.0 - - - +
330A GLU* 1.3 76.7 - - - +
332A LEU* 1.3 63.6 + - - +
334A GLN* 3.3 16.5 + - - +
335A ILE* 3.1 56.4 + - + +
411A SER 4.4 1.8 - - - -
412A LEU* 4.2 28.5 - - + -
414A HIS 2.8 29.3 + - - -
415A THR* 3.4 16.1 - - - +
416A GLU* 3.9 12.7 + - - -
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.0 23.1 - - + -
252A ARG 4.6 0.9 - - - +
328A THR* 3.2 20.9 + - + +
329A TYR* 3.8 27.1 - - + +
331A TYR* 1.3 79.6 - - + +
333A ASP* 1.3 59.7 + - - +
335A ILE* 3.8 3.7 - - - +
336A THR* 2.4 32.4 + - - -
360A SER* 3.7 13.6 - - - +
361A GLY* 4.1 6.5 - - - +
410A THR* 3.3 39.0 - - + +
411A SER* 3.9 16.8 - - - +
412A LEU* 3.7 13.9 - - + -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A TYR 3.0 18.1 + - - +
330A GLU* 3.6 6.1 - - - +
332A LEU* 1.3 76.8 - - - +
334A GLN* 1.3 56.7 + - - +
337A LYS* 2.9 40.1 + - - +
358A GLN* 3.2 16.9 + - - +
359A VAL* 4.4 1.2 - - - -
360A SER* 3.1 30.2 + - - +
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Residues in contact with GLN 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 3.0 16.9 + - - +
331A TYR* 3.5 19.1 - - - +
333A ASP* 1.3 77.1 - - - +
335A ILE* 1.3 62.6 + - - +
337A LYS* 3.4 6.1 + - - +
338A ARG* 3.3 29.2 + - - +
416A GLU* 3.6 20.3 - - - +
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Residues in contact with ILE 335 (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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331A TYR* 3.1 59.8 + - + +
332A LEU* 3.8 5.6 - - - +
334A GLN* 1.3 78.4 - - + +
336A THR* 1.3 65.8 + - - +
338A ARG* 3.8 10.0 + - - +
339A LEU* 3.4 20.1 + - - +
410A THR* 3.8 23.1 - - + +
411A SER 3.8 9.2 - - - +
414A HIS* 3.8 18.2 - - + +
416A GLU* 4.1 21.1 - - + +
419A ILE* 3.8 23.2 - - + +
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Residues in contact with THR 336 (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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332A LEU 2.4 27.9 + - - -
335A ILE* 1.3 75.0 - - - +
337A LYS* 1.3 60.5 + - - +
339A LEU* 3.6 5.6 - - + +
340A SER* 2.9 30.0 + - - -
358A GLN* 3.7 18.8 - - + -
360A SER 3.2 22.2 + - - +
361A GLY 4.5 1.1 - - - -
362A MET 4.3 4.7 - - - +
363A PHE* 4.0 26.0 - - + -
410A THR* 3.3 24.2 - - - +
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Residues in contact with LYS 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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333A ASP* 2.9 24.5 + - - +
334A GLN* 3.6 7.4 - - - +
335A ILE 3.3 0.2 - - - -
336A THR* 1.3 77.8 - - - +
338A ARG* 1.3 59.1 + - + +
340A SER* 3.7 0.5 - - - -
341A ASP* 2.9 63.4 + - - +
358A GLN* 3.7 25.3 + - + +
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Residues in contact with ARG 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 GLN* 3.3 20.4 + - + +
335A ILE* 3.9 8.5 - - - +
337A LYS* 1.3 75.9 - - + +
339A LEU* 1.3 54.6 + - - +
341A ASP* 4.1 4.0 - - - +
342A GLY* 2.8 31.9 + - - -
416A GLU* 3.5 41.1 + - - +
419A ILE* 3.4 34.6 - - + +
420A ASP* 2.8 29.7 + - - -
423A LEU* 4.0 9.8 - - + +
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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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63A TYR* 4.0 20.9 - - + +
335A ILE 3.4 12.3 + - - +
336A THR* 3.3 9.1 + - + +
337A LYS 3.2 0.4 - - - -
338A ARG* 1.3 77.1 - - - +
340A SER* 1.3 58.9 + - - +
342A GLY* 3.7 0.3 - - - -
343A LEU* 2.8 48.0 + - + +
363A PHE* 3.7 41.3 - - + -
410A THR* 5.0 3.6 - - - +
419A ILE* 4.1 20.4 - - + +
422A THR* 4.4 18.6 - - + -
423A LEU* 3.9 15.9 - - + -
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A THR 2.9 20.5 + - - -
337A LYS 3.7 1.1 - - - -
339A LEU* 1.3 72.5 - - - +
341A ASP* 1.3 66.1 + - - +
343A LEU* 3.2 12.0 + - - +
344A LEU* 3.0 32.8 + - - +
357A GLY* 3.5 31.3 + - - -
358A GLN* 3.6 19.7 - - - -
363A PHE* 4.7 8.7 - - - +
364A GLY 4.8 2.4 + - - -
365A PHE* 5.4 0.4 - - - -
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Residues in contact with ASP 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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337A LYS* 2.9 55.7 + - - +
338A ARG* 4.1 4.1 - - - +
340A SER* 1.3 74.1 + - - +
342A GLY* 1.3 58.3 + - - +
344A LEU* 3.0 15.0 + - - +
345A ALA* 2.8 30.9 + - - +
358A GLN* 6.1 0.2 - - - +
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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 ARG 2.8 23.7 + - - -
339A LEU 3.7 0.7 - - - -
341A ASP* 1.3 74.6 - - - +
343A LEU* 1.3 55.6 + - - +
345A ALA* 3.3 7.9 + - - +
346A ILE* 3.0 34.6 + - - +
423A LEU* 3.8 19.7 - - - -
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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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339A LEU* 2.8 48.4 + - + +
340A SER* 3.5 6.7 - - - +
342A GLY* 1.3 72.2 - - - +
344A LEU* 1.3 62.8 + - - +
346A ILE* 3.5 3.2 + - - -
347A ALA 3.1 17.0 + - - -
363A PHE* 4.2 23.6 - - + -
365A PHE* 3.6 34.3 - - + -
389A PHE* 4.8 12.1 - - + -
393A MET* 5.3 4.3 - - + -
400A LEU* 6.5 0.9 - - + -
422A THR* 5.6 2.5 - - + -
423A LEU* 3.8 4.4 - - + +
426A ALA* 3.8 27.8 - - + -
430A MET* 3.6 12.0 - - + +
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Residues in contact with LEU 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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340A SER* 3.0 23.7 + - - +
341A ASP* 3.5 13.9 - - - +
343A LEU* 1.3 74.3 - - - +
345A ALA* 1.3 64.9 + - - +
347A ALA* 3.1 11.2 + - - +
348A GLN* 3.1 31.2 + - - +
354A ALA* 4.1 7.0 - - + +
355A CYS* 3.7 35.4 - - - +
356A GLY* 3.8 22.4 - - - +
357A GLY* 5.3 0.9 - - - -
365A PHE* 3.8 20.2 - - + -
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Residues in contact with ALA 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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341A ASP 2.8 16.1 + - - +
342A GLY* 3.6 11.7 - - - +
344A LEU* 1.3 71.7 - - - +
346A ILE* 1.3 58.1 + - + +
348A GLN* 3.3 7.7 + - - +
349A GLU* 2.9 34.4 + - - +
427A ARG* 6.2 0.9 - - - +
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Residues in contact with ILE 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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342A GLY* 3.0 21.4 + - - +
343A LEU* 3.9 0.9 - - - +
344A LEU 3.3 0.4 - - - -
345A ALA* 1.3 77.2 - - + +
347A ALA* 1.3 55.6 + - - +
349A GLU* 3.8 5.1 - - - -
350A THR* 2.6 40.9 + - + +
423A LEU* 3.4 39.5 - - + +
426A ALA* 3.9 8.7 - - + +
427A ARG* 3.5 59.9 - - + +
430A MET* 3.5 26.5 - - + -
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Residues in contact with ALA 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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343A LEU 3.1 13.3 + - - +
344A LEU 3.1 10.1 + - - +
346A ILE* 1.3 78.3 - - - +
348A GLN* 1.3 59.0 + - - +
350A THR* 3.4 5.8 + - - -
351A GLY 3.1 5.9 + - - -
352A HIS* 2.8 39.6 + - + +
354A ALA* 3.7 30.1 - - + -
365A PHE* 4.0 8.7 - - + -
430A MET* 3.8 10.3 - - - +
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Residues in contact with GLN 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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344A LEU* 3.1 36.3 + - - +
345A ALA* 3.7 9.3 - - - +
347A ALA* 1.3 77.9 - - - +
349A GLU* 1.3 56.5 + - - +
351A GLY* 3.0 19.9 + - - +
352A HIS 3.3 24.4 - - - +
353A ALA* 4.9 0.7 - - - -
354A ALA 4.0 19.2 + - - +
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Residues in contact with GLU 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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345A ALA* 2.9 20.0 + - - +
346A ILE 3.8 3.8 - - - +
348A GLN* 1.3 78.0 - - - +
350A THR* 1.3 62.6 + - + +
351A GLY 3.3 1.2 + - - -
427A ARG* 2.7 34.9 + - - +
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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