Contacts of the helix formed by residues 370 - 383 (chain A) in PDB entry 3AG2
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 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A VAL 3.4 24.5 - - - +
367A LEU* 2.6 18.3 + - - +
368A HIS 3.1 7.5 - - - +
369A ASP* 1.3 81.4 - - - +
371A TYR* 1.3 60.7 + - - +
372A TYR* 2.9 25.3 + - - +
373A VAL* 3.0 17.7 + - - +
374A VAL* 3.7 5.2 + - - +
432A GLY* 3.6 15.8 + - - +
435A GLY* 4.7 8.1 - - - +
436A MET 3.3 18.4 - - - +
437A PRO* 4.9 0.9 - - + -
438A ARG* 3.7 7.2 - - - +
166B PRO* 6.5 0.2 - - + -
171B LYS* 4.0 5.4 - - - +
197B SER* 6.0 0.2 - - - +
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 5.0 3.3 - - - +
38A ARG* 4.2 5.8 + - - -
41A LEU* 3.3 25.8 - - + +
54A TYR* 4.3 5.4 + - - -
370A THR* 1.3 74.5 - - - +
372A TYR* 1.3 57.2 + - - +
373A VAL 3.2 0.7 - - - -
374A VAL* 3.7 29.9 - - + +
375A ALA* 2.9 23.7 + - - +
428A GLN* 3.3 59.1 - - + +
431A LEU* 4.0 9.0 - - + -
432A GLY* 3.9 8.7 - - - +
436A MET* 3.0 37.2 + - + +
437A PRO 3.4 27.4 - - - -
438A ARG* 3.8 12.8 - - + -
439A ARG 4.7 3.3 + - - -
440A TYR 4.9 2.6 + - - -
451A ASN* 5.3 0.2 - - - -
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Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A THR* 3.6 45.6 - - + +
357A VAL* 3.6 31.7 - - + +
358A LEU* 3.8 19.3 - - + -
367A LEU* 3.9 18.2 - - + -
370A THR* 2.9 15.9 + - - +
371A TYR* 1.3 76.0 - - - +
373A VAL* 1.3 56.8 + - - +
375A ALA* 3.5 3.4 + - - +
376A HIS* 3.0 23.7 + - - +
428A GLN 4.3 2.9 - - - -
429A HIS* 3.9 27.5 - + + -
432A GLY* 3.3 8.7 - - - -
433A LEU* 3.9 36.6 - - + -
24B HIS* 4.8 5.4 + - - -
28B LEU* 5.7 4.0 - - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 3.9 31.4 - - + -
364A ASP* 4.9 1.8 - - - +
367A LEU 3.4 22.4 - - - +
368A HIS* 4.2 6.7 - - - +
369A ASP 4.2 9.4 - - - +
370A THR 3.0 7.4 + - - +
372A TYR* 1.3 75.0 - - - +
374A VAL* 1.3 59.4 + - - +
376A HIS* 3.2 5.9 + - + +
377A PHE* 2.9 42.7 + - + -
438A ARG* 3.7 26.9 - - - +
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Residues in contact with VAL 374 (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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370A THR 4.1 2.7 - - - +
371A TYR* 3.3 28.2 + - + +
373A VAL* 1.3 75.9 - - - +
375A ALA* 1.3 61.6 + - - +
377A PHE* 3.4 12.7 + - + -
378A HIS* 2.9 53.7 + - + +
428A GLN* 3.3 18.2 - - - +
438A ARG* 3.7 42.8 - - + +
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Residues in contact with ALA 375 (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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371A TYR 2.9 17.4 + - - +
372A TYR 3.7 4.5 - - - +
374A VAL* 1.3 75.0 - - - +
376A HIS* 1.3 67.3 + - - +
378A HIS* 3.9 0.9 - - - +
379A TYR* 3.1 29.1 + - - -
425A PHE* 3.8 15.5 - - - +
428A GLN* 3.9 9.1 + - + -
429A HIS* 3.7 40.2 - - + +
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Residues in contact with HIS 376 (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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351A GLY* 2.8 32.2 + - - -
352A GLY* 4.8 2.0 - - - -
354A THR* 3.4 17.0 - - - +
355A GLY* 3.2 21.8 + - - -
358A LEU* 3.8 24.9 - - + -
372A TYR 3.0 15.3 + - - +
373A VAL* 3.4 11.2 - - + +
375A ALA* 1.3 79.4 - - - +
377A PHE* 1.3 82.7 + + + +
379A TYR* 3.2 11.5 + - - +
380A VAL* 3.3 22.6 + - + +
429A HIS* 4.5 2.3 + - - -
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Residues in contact with PHE 377 (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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126A TRP* 6.2 1.6 - + - -
373A VAL* 2.9 36.8 + - + -
374A VAL* 3.6 25.4 - - + -
376A HIS* 1.3 86.8 - + + +
378A HIS* 1.3 90.5 + + - +
380A VAL* 3.4 12.0 - - + +
381A LEU* 2.8 50.8 + - + +
438A ARG* 3.8 34.1 - - - -
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Residues in contact with HIS 378 (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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61A HIS* 4.0 23.5 + + - -
374A VAL* 2.9 44.3 + - + +
375A ALA 4.2 0.9 - - - +
377A PHE* 1.3 101.3 - + - +
379A TYR* 1.3 63.9 + - - +
381A LEU* 5.5 2.9 - - + -
382A SER* 2.8 37.5 + - - +
383A MET* 3.2 8.7 + - - +
425A PHE* 3.2 51.5 - + + -
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Residues in contact with TYR 379 (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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347A LEU* 3.8 29.3 - - + +
350A VAL* 3.9 19.7 - - + -
351A GLY* 3.6 20.9 - - - +
375A ALA 3.1 23.3 + - - +
376A HIS* 3.2 3.8 + - - +
378A HIS* 1.3 78.8 - - - +
380A VAL* 1.3 63.4 + - - +
383A MET* 3.3 45.8 - - + +
384A GLY* 3.2 15.6 + - - -
422A ASN* 2.9 21.0 + - - -
425A PHE* 3.8 14.1 - - + -
426A PHE* 3.3 34.6 + + - +
429A HIS* 3.6 25.1 - + - -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.7 10.9 - - + +
348A PHE* 3.9 29.6 - - + +
351A GLY* 3.6 31.6 - - - +
352A GLY* 3.6 6.7 - - - +
376A HIS* 3.3 18.7 + - + +
377A PHE* 3.4 21.3 - - + +
379A TYR* 1.3 79.0 - - - +
381A LEU* 1.3 64.7 + - + +
384A GLY* 3.1 6.7 - - - +
385A ALA* 3.1 18.0 + - - +
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Residues in contact with LEU 381 (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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66A ILE* 5.3 13.5 - - + -
70A VAL* 5.3 6.3 - - + -
243A VAL* 6.1 6.1 - - + -
246A LEU* 4.0 34.8 - - + -
247A ILE* 6.1 0.7 - - + -
377A PHE* 2.8 42.0 + - + +
378A HIS* 4.5 4.7 - - + -
380A VAL* 1.3 83.6 - - + +
382A SER* 1.3 61.7 + - - +
383A MET 3.3 1.3 - - - -
385A ALA* 3.2 21.5 + - + +
386A VAL* 3.0 30.9 + - - +
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Residues in contact with SER 382 (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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378A HIS* 2.8 27.8 + - - -
381A LEU* 1.3 76.5 - - - +
383A MET* 1.3 60.8 + - - +
386A VAL* 3.5 27.1 - - - +
387A PHE* 3.6 10.7 - - - -
417A MET* 5.1 3.6 - - - +
421A VAL* 4.1 12.9 - - - +
425A PHE* 4.0 25.2 - - - -
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Residues in contact with MET 383 (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 PHE* 4.0 6.8 - - - -
347A LEU* 3.6 38.5 - - + +
348A PHE 4.4 1.4 + - - -
378A HIS 3.2 6.7 + - - +
379A TYR* 3.3 66.9 - - + +
382A SER* 1.3 78.3 - - - +
384A GLY* 1.3 58.2 + - - +
387A PHE* 3.5 25.2 - - - +
421A VAL* 3.2 51.8 - - + +
422A ASN* 3.7 5.4 - - - +
425A PHE* 3.9 9.0 - - + -
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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