Contacts of the helix formed by residues 325 - 344 (chain A) in PDB entry 5M4G
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 TRP 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A GLY 3.5 2.0 + - - -
324A VAL* 1.3 76.8 - - - +
326A TRP* 1.3 67.6 + - - +
327A PRO* 3.5 23.1 - - + +
328A ASP* 2.9 51.8 + - - +
329A MET 3.5 2.9 + - - -
389A ILE* 3.8 23.6 - - + -
400A ALA* 2.8 29.4 + - + -
401A ARG 3.8 2.2 - - - -
402A HIS* 3.4 39.2 - + + +
506A GOL 3.6 26.2 - - - -
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Residues in contact with TRP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 4.3 0.7 - - + -
320A MET* 3.7 36.6 - - + -
324A VAL 3.6 2.9 + - - -
325A TRP* 1.3 70.3 - - - +
327A PRO* 1.4 69.3 - - + +
329A MET* 2.9 40.2 + - + +
330A HIS* 3.1 10.4 + - - +
368A LEU* 3.8 21.3 - - + -
369A GLY* 2.9 31.3 + - - -
397A LEU* 3.7 17.9 - - + +
399A THR* 3.4 37.8 - - + +
401A ARG 3.1 20.3 + - - +
403A LEU* 4.1 14.4 - - + -
409A LEU* 3.7 19.7 - - + -
410A THR 3.6 24.9 - - - -
411A VAL* 4.2 4.7 - - + -
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Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TRP* 3.5 35.2 - - + +
326A TRP* 1.4 94.3 - - + +
328A ASP* 1.3 59.2 + - - +
330A HIS* 3.3 3.6 + - - +
331A ARG* 3.1 21.3 + - - +
389A ILE* 3.7 29.2 - - + -
394A LEU* 3.8 7.4 - - + +
397A LEU* 3.9 16.4 - - + -
400A ALA* 3.9 17.9 - - + -
506A GOL 3.6 16.0 + - - +
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 5.3 0.7 - - + -
325A TRP* 2.9 39.4 + - + +
327A PRO* 1.3 76.8 - - - +
329A MET* 1.3 68.2 + - + +
331A ARG* 3.4 3.6 + - - +
332A LEU* 2.9 27.7 + - - +
506A GOL 2.9 21.7 + - - -
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Residues in contact with MET 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.8 20.3 - - + +
319A ALA* 3.7 31.6 - - + +
320A MET* 4.3 4.7 - - + -
324A VAL* 3.6 33.2 - - + -
325A TRP 4.2 0.4 - - - +
326A TRP* 2.9 31.8 + - + +
328A ASP* 1.3 84.1 - - + +
330A HIS* 1.3 66.9 + - - +
332A LEU* 3.2 17.2 + - + +
333A ALA* 3.1 18.2 + - - +
368A LEU* 3.4 21.9 - - + +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A TRP 3.1 9.8 + - - +
327A PRO 3.5 8.5 - - - +
329A MET* 1.3 78.2 - - - +
331A ARG* 1.3 64.5 + - - +
333A ALA* 3.3 4.3 + - - +
334A ASP* 3.1 36.1 + - - -
364A MET* 3.6 17.2 + - + +
366A HIS 3.2 27.6 - - - -
367A GLY* 3.7 4.0 - - - -
368A LEU* 3.1 35.8 + - + +
393A GLY* 3.8 24.7 - - - -
394A LEU* 3.7 22.4 - - + -
397A LEU* 3.7 11.1 - - + +
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Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PRO 3.1 11.0 + - - +
328A ASP* 4.0 4.3 - - - +
330A HIS* 1.3 84.9 + - - +
332A LEU* 1.3 64.6 + - - +
334A ASP* 2.7 36.8 + - - +
335A ARG* 3.0 23.7 + - - +
355A VAL* 5.5 14.7 + - + +
358A HIS* 3.4 22.1 + - - +
361A ALA* 5.0 4.8 - - - +
391A GLU* 3.0 28.3 + - - +
392A PRO 3.0 28.7 + - - -
393A GLY* 4.5 0.6 - - - -
394A LEU* 3.5 14.3 - - + +
506A GOL 2.8 45.8 + - - +
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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
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315A ALA* 4.0 30.1 - - + +
316A VAL* 4.3 4.5 - - + +
319A ALA* 4.3 6.1 - - + -
328A ASP 2.9 18.2 + - - +
329A MET* 3.2 27.6 + - + +
331A ARG* 1.3 73.5 - - - +
333A ALA* 1.3 66.0 + - - +
335A ARG* 3.2 11.3 + - + +
336A ILE* 3.1 42.5 + - + +
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Residues in contact with ALA 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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312A SER* 4.0 22.9 - - - -
316A VAL* 4.3 5.6 - - + +
329A MET 3.1 11.2 + - - +
330A HIS 3.3 7.8 + - - +
332A LEU* 1.3 77.8 - - - +
334A ASP* 1.3 62.8 + - - +
336A ILE* 3.3 1.8 + - - +
337A HIS* 2.9 34.9 + - + -
364A MET* 4.3 9.4 - - + -
368A LEU* 4.1 22.4 - - + -
413A PRO* 4.3 0.9 - - + -
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Residues in contact with ASP 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 HIS* 3.1 18.2 + - - +
331A ARG* 2.7 49.5 + - - +
333A ALA* 1.3 77.0 - - - +
335A ARG* 1.3 62.1 + - - +
337A HIS* 3.3 7.4 + - - +
338A LEU* 2.9 32.7 + - + +
355A VAL* 5.7 3.4 - - + -
360A GLY* 3.5 33.8 - - - +
361A ALA* 4.8 0.2 - - - -
364A MET* 3.5 19.2 - - - +
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Residues in contact with ARG 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 ARG 3.0 13.6 + - - +
332A LEU* 3.2 11.9 + - + +
334A ASP* 1.3 80.2 - - - +
336A ILE* 1.3 59.8 + - + +
338A LEU* 3.3 4.3 + - - +
339A GLU* 2.9 51.3 + - - +
351A VAL* 3.9 19.8 - - + +
352A ASP* 2.9 31.9 + - - +
355A VAL* 3.7 39.8 - - + +
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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
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308A ALA 4.0 6.5 - - - +
311A ARG* 3.7 48.5 - - - +
312A SER* 3.8 26.2 - - - +
315A ALA* 3.3 33.9 - - + -
332A LEU* 3.1 32.0 + - + +
333A ALA* 3.3 4.2 + - - +
335A ARG* 1.3 74.1 - - + +
337A HIS* 1.3 66.8 + - - +
339A GLU* 3.3 6.8 + - - +
340A GLU* 3.0 23.6 + - + +
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA 4.0 8.3 - - - -
309A VAL* 4.3 4.2 - - - -
312A SER* 2.8 31.4 + - - -
333A ALA 2.9 24.0 + - - +
334A ASP* 3.6 8.1 + - - +
336A ILE* 1.3 76.8 - - - +
338A LEU* 1.3 58.6 + - + +
340A GLU* 3.2 4.9 + - - +
341A LEU* 2.9 39.5 + - + +
360A GLY* 5.6 3.5 + - - +
363A PHE* 5.6 3.5 - - + +
364A MET* 3.9 17.1 + - - +
413A PRO* 3.7 18.1 - - + +
414A GLY 3.3 27.1 + - - -
415A ILE* 3.7 29.0 - - + +
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Residues in contact with LEU 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 ASP* 2.9 23.3 + - + +
335A ARG 3.3 4.0 + - - +
337A HIS* 1.3 77.0 - - + +
339A GLU* 1.3 63.6 + - - +
341A LEU* 3.4 1.4 + - + -
342A ALA* 2.9 25.7 + - - +
347A LEU* 3.7 26.6 - - + +
351A VAL* 4.1 11.3 - - + +
354A MET* 4.0 17.8 - - + +
355A VAL* 3.8 30.7 - - + +
359A LEU* 3.9 16.8 - - + +
360A GLY* 3.8 33.0 - - - +
363A PHE* 4.6 6.7 - - + -
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Residues in contact with GLU 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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311A ARG* 2.9 36.2 + - - +
335A ARG* 2.9 37.6 + - - +
336A ILE* 3.3 9.8 + - - +
338A LEU* 1.3 75.6 - - - +
340A GLU* 1.3 57.8 + - - +
342A ALA* 3.3 3.9 + - - +
343A HIS* 2.9 43.3 + - + +
351A VAL* 4.2 24.0 - - + +
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Residues in contact with GLU 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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304A ALA 5.2 2.1 - - - +
307A GLU* 5.5 1.2 - - - +
308A ALA* 3.5 39.6 + - + +
311A ARG* 2.8 36.8 + - - +
336A ILE* 3.0 21.7 + - + +
337A HIS 3.8 2.0 - - - +
339A GLU* 1.3 73.7 - - - +
341A LEU* 1.3 61.4 + - - +
343A HIS* 3.2 21.8 + - - +
344A MET* 2.9 36.3 + - + +
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Residues in contact with LEU 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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305A VAL* 5.3 0.9 - - + -
337A HIS* 2.9 27.1 + - + +
338A LEU* 4.7 1.1 - - - +
340A GLU* 1.3 75.7 - - - +
342A ALA* 1.3 59.1 - - - +
344A MET* 3.4 19.2 - - + +
345A GLY 3.3 3.3 + - - -
346A ILE* 3.0 56.3 + - + +
347A LEU* 3.2 23.2 + - + -
363A PHE* 3.6 44.4 - - + -
415A ILE* 4.4 25.1 - - + -
417A PHE* 4.4 6.1 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.9 + - - +
339A GLU* 3.5 7.0 - - - +
341A LEU* 1.3 75.2 - - - +
343A HIS* 1.3 67.2 + - + +
345A GLY* 2.9 12.6 + - - -
347A LEU* 3.4 31.0 - - + +
348A SER* 5.3 1.3 - - - -
349A GLY 5.5 2.0 - - - +
351A VAL* 4.8 6.5 - - + -
354A MET* 4.6 10.3 - - + -
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG* 5.1 1.1 - - - -
339A GLU* 2.9 33.2 + - + +
340A GLU* 3.2 30.8 + - - +
342A ALA* 1.3 78.8 - - + +
344A MET* 1.3 59.9 + - - +
345A GLY 3.4 0.7 + - - -
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Residues in contact with MET 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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304A ALA* 3.6 47.6 - - + +
305A VAL* 4.1 15.5 - - - +
308A ALA* 4.3 2.9 - - + -
340A GLU* 2.9 35.8 + - + +
341A LEU* 3.4 25.6 - - + +
343A HIS* 1.3 78.0 - - + +
345A GLY* 1.3 57.8 + - - +
346A ILE* 3.7 24.1 + - + +
439A VAL* 4.2 8.7 - - - +
442A ARG* 4.9 7.4 + - - -
443A PHE* 4.7 7.7 - - + -
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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