Contacts of the helix formed by residues 371 - 381 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LYS 3.7 20.4 - - - -
364B SER* 3.4 18.5 + - - -
365B SER* 3.1 30.4 + - - +
369B ALA 4.4 0.4 - - - -
370B LEU* 1.2 80.7 - - - +
372B PRO* 1.3 77.2 - - + +
373B PHE* 3.1 36.5 - - + +
374B HIS* 3.0 23.5 + - + +
375B ALA 3.0 9.7 + - - -
399B TRP* 3.5 25.2 - + - -
545B ALA* 4.7 2.5 - - - -
548B PRO* 3.4 30.0 - - + +
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Residues in contact with PRO 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU 3.4 6.0 - - - +
371B HIS* 1.3 94.4 - - + +
373B PHE* 1.3 56.0 + - - +
375B ALA* 3.4 9.8 + - + +
376B SER* 3.0 31.2 + - - -
396B THR* 6.4 0.7 - - - -
399B TRP* 3.4 38.5 - - + +
473B MSE 5.3 4.2 - - + +
544B VAL* 3.6 16.2 - - + -
545B ALA* 3.5 22.9 - - + +
546B LEU 6.0 0.2 - - - +
548B PRO* 4.1 12.6 - - + +
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B TYR* 3.9 28.9 - + - -
360B ILE* 3.5 24.2 - - + -
361B ALA* 3.6 21.8 - - + -
364B SER* 3.6 19.5 - - - +
371B HIS* 3.1 22.4 - - + +
372B PRO* 1.3 74.4 - - - +
374B HIS* 1.3 66.6 + - - +
376B SER* 3.1 6.7 + - - -
377B GLN* 3.0 52.9 + - - +
399B TRP* 3.9 19.1 - + + -
402B GLU* 4.0 16.8 - - + -
403B VAL* 3.9 18.8 - - + -
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Residues in contact with HIS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ALA* 4.8 7.2 - - + -
364B SER* 3.1 38.3 + - - -
365B SER* 3.6 26.3 - - - -
366B SER* 4.6 2.0 + - - -
370B LEU* 3.6 15.7 - - + -
371B HIS* 3.0 17.0 + - + +
373B PHE* 1.3 79.7 - + - +
375B ALA* 1.3 61.3 + - - +
377B GLN* 3.3 22.7 + - - +
378B VAL* 3.2 26.1 + - - +
521B VAL* 4.1 13.1 - - + +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 4.0 12.6 - - + +
371B HIS 3.0 11.3 + - - +
372B PRO 3.4 9.4 - - - +
373B PHE 3.2 0.2 - - - -
374B HIS* 1.3 77.3 - - - +
376B SER* 1.3 60.5 + - - +
378B VAL* 3.2 9.3 + - - -
379B ILE* 3.3 10.6 + - - +
473B MSE 3.9 28.7 - - + -
524B PHE* 3.4 23.4 - - + -
542B VAL* 4.9 0.2 - - + -
544B VAL* 4.0 14.8 - - + -
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Residues in contact with SER 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO 3.0 14.6 + - - -
373B PHE* 3.1 9.6 + - - -
375B ALA* 1.3 72.9 - - - +
377B GLN* 1.3 59.7 + - - +
379B ILE* 3.2 8.2 + - - +
380B ALA 2.9 23.0 + - - -
396B THR 4.8 1.0 + - - -
399B TRP* 3.8 6.7 - - - +
400B LEU* 3.5 34.8 + - - +
403B VAL* 3.5 31.1 - - - +
473B MSE 4.5 5.5 - - - +
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Residues in contact with GLN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B TYR* 3.1 33.3 + - - +
361B ALA* 4.7 4.9 - - - +
373B PHE* 3.0 37.3 + - + +
374B HIS* 3.3 34.1 + - - +
375B ALA 3.3 0.2 - - - -
376B SER* 1.3 74.0 - - - +
378B VAL* 1.3 65.4 + - + +
380B ALA* 3.2 16.8 + - - +
381B LYS* 3.3 16.5 + - - +
403B VAL* 3.9 9.0 - - + -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 6.3 0.2 - - + -
374B HIS 3.2 15.4 + - - +
375B ALA* 3.2 10.6 + - - +
377B GLN* 1.3 76.6 - - + +
379B ILE* 1.3 61.4 + - - +
381B LYS* 3.3 17.4 - - - +
382B HIS* 3.1 22.5 - - - +
521B VAL* 4.3 30.5 - - + +
524B PHE* 3.6 26.5 - - + -
525B SER* 3.8 31.2 - - - +
528B LEU* 4.3 8.1 - - + -
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ALA 3.5 9.9 - - - +
376B SER* 3.2 7.3 + - - +
378B VAL* 1.3 76.6 - - - +
380B ALA* 1.3 64.9 + - - +
382B HIS* 2.9 18.6 + - + +
383B VAL* 3.4 17.3 - - + +
389B VAL* 5.4 3.8 - - + -
400B LEU* 4.6 11.4 - - + -
404B MSE 6.3 0.4 - - - -
443B ILE* 4.8 9.4 - - + -
445B VAL* 3.8 25.8 - - + -
471B ILE* 3.6 26.2 - - + -
473B MSE 3.3 31.2 - - + -
524B PHE* 3.7 13.9 - - + -
528B LEU* 4.0 7.6 - - + -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B TYR* 5.8 1.8 - - - +
376B SER 2.9 14.4 + - - +
377B GLN* 3.2 13.9 + - - +
379B ILE* 1.3 76.1 - - - +
381B LYS* 1.3 57.1 + - - +
383B VAL* 2.9 34.1 + - - +
403B VAL* 3.9 29.4 - - + +
404B MSE 6.1 0.9 - - - -
406B ARG* 6.2 0.9 - - + -
407B VAL* 3.6 18.3 - - + +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLN 3.3 8.3 + - - +
378B VAL* 3.3 30.7 - - - +
380B ALA* 1.3 76.1 - - - +
382B HIS* 1.3 72.8 + - + +
383B VAL 3.5 1.1 - - - -
407B VAL* 5.8 0.2 - - - -
521B VAL* 6.0 2.4 - - - +
525B SER* 2.9 28.0 + - - -
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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