Contacts of the helix formed by residues 371 - 381 (chain A) in PDB entry 2AG1
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 HIS 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A LYS 3.7 19.7 + - - -
364A SER* 3.5 10.4 + - - -
365A SER* 3.1 38.0 + - - +
369A ALA 3.3 0.4 + - - -
370A LEU* 1.2 80.6 - - - +
372A PRO* 1.3 73.4 - - + +
373A PHE* 3.1 37.5 - - + -
374A HIS* 2.9 23.4 + - + +
375A ALA 2.9 9.9 + - - -
399A TRP* 3.4 24.2 - + - -
545A ALA* 4.7 2.7 - - - -
548A PRO* 3.4 31.4 - - + +
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Residues in contact with PRO 372 (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 LEU 3.4 5.8 - - - +
371A HIS* 1.3 93.4 - - + +
373A PHE* 1.3 55.6 + - - +
375A ALA* 3.3 10.5 + - + +
376A SER* 2.9 31.8 + - - -
396A THR* 6.4 0.4 - - - -
399A TRP* 3.4 38.3 - - + +
473A MSE 5.3 4.0 - - + +
544A VAL* 3.6 15.0 - - + -
545A ALA* 3.5 24.2 - - + +
546A LEU 6.1 0.2 - - - +
548A PRO* 4.1 12.8 - - + -
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Residues in contact with PHE 373 (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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357A TYR* 3.8 34.5 - + - -
360A ILE* 3.5 23.8 - - + -
361A ALA* 3.6 20.0 - - + -
364A SER* 3.6 17.7 - - - +
371A HIS* 3.1 23.0 - - + +
372A PRO* 1.3 73.5 - - - +
374A HIS* 1.3 69.5 + - - +
376A SER* 3.0 8.2 + - - -
377A GLN* 3.0 48.6 + - + +
399A TRP* 3.9 19.2 - + + -
402A GLU* 4.0 16.8 - - + -
403A VAL* 3.9 19.5 - - + -
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Residues in contact with HIS 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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361A ALA* 4.8 6.5 - - + -
364A SER* 3.1 37.5 + - - -
365A SER* 3.5 26.3 + - - -
366A SER* 4.5 2.9 + - - -
370A LEU* 3.6 16.4 - - + -
371A HIS* 2.9 15.9 + - + +
373A PHE* 1.3 79.6 - + - +
375A ALA* 1.3 63.4 + - - +
377A GLN* 3.3 25.2 + - - +
378A VAL* 3.2 26.3 + - - +
521A VAL* 4.1 13.0 - - + +
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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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370A LEU* 4.1 12.9 - - + +
371A HIS 2.9 10.2 + - - +
372A PRO 3.4 9.9 - - - +
374A HIS* 1.3 77.1 - - - +
376A SER* 1.3 61.7 + - - +
378A VAL* 3.2 10.5 + - - -
379A ILE* 3.3 9.7 + - - +
473A MSE 3.8 28.3 - - + -
524A PHE* 3.4 24.4 - - + -
542A VAL* 4.9 0.2 - - + -
544A VAL* 4.0 14.1 - - + -
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Residues in contact with SER 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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372A PRO 2.9 15.6 + - - -
373A PHE* 3.0 9.6 + - - -
375A ALA* 1.3 75.9 - - - +
377A GLN* 1.3 58.6 + - - +
379A ILE* 3.0 8.2 + - - +
380A ALA* 2.8 27.7 + - - +
396A THR 4.9 1.0 + - - -
399A TRP* 3.8 6.5 - - - +
400A LEU* 3.6 33.2 + - - +
403A VAL* 3.7 27.3 - - - +
473A MSE 4.8 6.3 - - - +
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Residues in contact with GLN 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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357A TYR* 3.0 34.5 + - - +
361A ALA* 4.7 4.6 - - - +
373A PHE* 3.0 35.7 + - + +
374A HIS* 3.3 33.8 + - - +
376A SER* 1.3 76.9 - - - +
378A VAL* 1.3 61.7 + - + +
380A ALA* 3.3 17.7 + - - +
381A LYS* 3.3 16.9 + - - +
403A VAL* 4.0 9.2 - - + -
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Residues in contact with VAL 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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374A HIS 3.2 14.5 + - - +
375A ALA* 3.2 9.9 + - - +
377A GLN* 1.3 77.3 - - + +
379A ILE* 1.3 59.8 + - - +
381A LYS* 3.3 21.0 - - - +
382A HIS* 3.1 22.2 - - - +
521A VAL* 4.2 33.0 - - + +
524A PHE* 3.6 26.2 - - + -
525A SER* 3.9 27.4 - - - +
528A LEU* 4.3 7.4 - - + -
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Residues in contact with ILE 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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375A ALA 3.6 10.3 - - - +
376A SER* 3.0 7.3 + - - +
378A VAL* 1.3 76.3 - - - +
380A ALA* 1.3 65.4 + - - +
382A HIS* 3.0 18.9 + - + +
383A VAL* 3.5 18.0 - - + +
389A VAL* 5.4 4.7 - - + -
400A LEU* 4.6 12.1 - - + -
443A ILE* 4.8 8.7 - - + -
445A VAL* 3.8 25.4 - - + -
471A ILE* 3.6 27.1 - - + -
473A MSE 3.3 31.6 - - + -
524A PHE* 3.7 15.3 - - + -
528A LEU* 4.0 8.1 - - + -
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Residues in contact with ALA 380 (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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357A TYR* 5.9 1.3 - - - +
376A SER 2.8 13.0 + - - +
377A GLN* 3.4 12.8 - - + +
379A ILE* 1.3 76.7 - - - +
381A LYS* 1.3 57.1 + - - +
383A VAL* 2.9 34.1 + - - +
403A VAL* 3.9 30.9 - - + +
404A MSE 6.2 0.2 - - - -
406A ARG* 6.2 0.9 - - + -
407A VAL* 3.5 18.7 - - + +
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Residues in contact with LYS 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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377A GLN 3.3 8.7 + - - +
378A VAL* 3.3 33.0 - - - +
380A ALA* 1.3 75.6 - - - +
382A HIS* 1.3 71.7 + - + +
383A VAL 5.2 0.8 - - - +
521A VAL* 5.9 2.4 - - - +
525A SER* 2.9 28.5 + - - -
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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