Contacts of the helix formed by residues 478 - 489 (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 TRP 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A MSE 4.7 13.0 - - + -
449A GLY* 3.4 39.3 - - - -
450A SER* 3.9 2.7 - - - -
453A TYR* 3.6 28.0 - + - -
477A SER* 1.3 66.6 - - - +
479A GLY* 1.3 59.5 + - - +
480A ALA 3.8 0.7 - - - -
481A THR* 2.9 23.4 - - + +
482A LEU* 2.9 28.2 + - - +
496A GLY 3.9 19.0 + - - -
497A THR 2.9 18.9 + - - +
498A ARG 4.9 0.2 - - - -
499A LEU* 3.6 24.5 - - + +
25B LEU* 3.9 37.3 - - + +
26B HIS* 5.5 1.8 - - + -
46B ASP* 5.1 4.0 + - - +
47B THR 4.0 9.8 + - - -
48B ARG* 4.1 18.8 - - - -
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Residues in contact with GLY 479 (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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394A ALA* 5.9 0.8 - - - +
395A LEU* 3.6 20.2 - - - -
475A ASN* 4.0 4.7 - - - +
477A SER* 2.9 22.1 + - - -
478A TRP* 1.3 65.8 - - - +
480A ALA* 1.3 67.4 + - - +
481A THR 3.0 1.1 - - - -
482A LEU* 3.0 4.4 + - - +
483A HIS* 2.9 26.2 + - - -
546A LEU* 3.9 5.2 - - - -
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Residues in contact with ALA 480 (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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394A ALA* 3.5 30.1 - - + +
395A LEU* 3.4 21.6 - - + +
398A LEU* 5.5 4.9 - - + -
479A GLY* 1.3 72.7 - - - +
481A THR* 1.3 56.4 + - - +
483A HIS* 3.4 3.4 + - - +
484A PHE* 2.9 28.1 + - - +
553A GLU* 4.0 13.3 - - - +
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Residues in contact with THR 481 (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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478A TRP* 2.9 36.1 - - + +
479A GLY 3.0 0.6 - - - -
480A ALA* 1.3 81.6 - - - +
482A LEU* 1.3 59.6 + - - +
484A PHE* 3.5 8.4 + - - +
485A GLN* 3.4 24.3 + - - +
497A THR* 3.2 23.7 - - + +
26B HIS* 2.9 28.9 + - + +
27B GLY* 3.8 4.0 - - - -
28B ALA* 3.7 13.1 + - - +
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Residues in contact with LEU 482 (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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477A SER* 3.9 19.7 - - - +
478A TRP 2.9 13.6 + - - +
479A GLY* 3.0 9.4 + - - +
481A THR* 1.3 73.9 - - - +
483A HIS* 1.3 65.6 + - + +
485A GLN* 3.2 5.6 + - - +
486A GLN* 3.2 56.0 + - + +
494A VAL* 3.8 19.7 - - + -
497A THR* 3.6 26.5 - - - +
498A ARG* 3.8 28.5 - - + +
546A LEU* 4.2 15.7 - - + -
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Residues in contact with HIS 483 (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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395A LEU* 3.6 14.9 - - + +
479A GLY 2.9 15.2 + - - +
480A ALA 3.4 8.7 - - - +
481A THR 3.3 0.2 - - - -
482A LEU* 1.3 74.8 - - + +
484A PHE* 1.3 56.1 + - - +
486A GLN* 3.3 21.3 + - - +
487A LEU* 2.8 45.9 + - + +
546A LEU* 2.7 32.1 + - + +
547A ASP* 3.8 10.0 + - - -
548A PRO 3.2 28.9 - - - -
549A ILE* 4.1 4.9 - - + +
553A GLU* 2.8 38.9 + - - +
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Residues in contact with PHE 484 (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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480A ALA 2.9 13.1 + - - +
481A THR* 3.5 10.8 - - - +
482A LEU 3.3 0.2 - - - -
483A HIS* 1.3 74.6 - - - +
485A GLN* 1.3 62.4 + - + +
487A LEU* 4.6 4.9 - - - +
488A ALA* 2.7 58.7 + - + +
489A VAL* 4.8 2.2 - - + -
553A GLU* 5.7 0.2 - - - -
26B HIS* 5.3 0.7 - - - -
28B ALA* 3.8 37.7 - - + -
31B ASP* 4.1 20.2 - - + -
163B TRP* 3.9 32.5 - + - -
167B MSE 5.2 7.2 - - + -
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Residues in contact with GLN 485 (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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481A THR 3.4 9.4 + - - +
482A LEU* 3.2 8.0 + - - +
483A HIS 3.2 0.6 - - - -
484A PHE* 1.3 78.7 - - + +
486A GLN* 1.3 57.3 + - - +
489A VAL* 2.9 20.6 + - - +
490A GLY 2.9 24.6 + - - +
493A ARG 3.6 20.5 + - - +
494A VAL* 3.2 6.1 - - + +
495A THR* 3.1 34.5 + - - +
497A THR* 2.9 32.1 + - - +
26B HIS* 3.3 12.1 + - + +
31B ASP* 2.8 32.1 + - - +
34B PHE* 4.7 2.0 - - - +
35B GLN* 3.9 2.5 - - - +
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Residues in contact with GLN 486 (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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482A LEU* 3.2 38.2 + - + +
483A HIS* 3.8 21.2 + - - +
485A GLN* 1.3 78.0 - - + +
487A LEU* 1.3 74.3 + - + +
490A GLY* 3.2 30.2 + - - +
491A PRO* 4.0 24.2 - - + +
494A VAL* 5.1 7.1 - - + +
498A ARG* 5.7 1.6 + - - -
547A ASP* 5.5 6.6 + - - +
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Residues in contact with LEU 487 (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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483A HIS* 2.8 31.0 + - + +
484A PHE* 4.2 4.0 - - - +
486A GLN* 1.3 89.7 - - + +
488A ALA* 1.3 59.9 + - + +
489A VAL 5.2 0.2 - - - -
549A ILE* 4.4 22.4 - - + -
553A GLU* 3.5 30.1 - - + +
554A LEU* 5.3 7.4 - - + -
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Residues in contact with ALA 488 (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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484A PHE* 2.7 51.6 + - + +
487A LEU* 1.3 74.8 - - + +
489A VAL* 1.3 60.4 + - + +
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Residues in contact with VAL 489 (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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484A PHE* 4.4 4.7 - - + +
485A GLN* 2.9 17.1 + - - +
486A GLN 4.2 0.2 - - - -
487A LEU 5.2 0.2 - - - -
488A ALA* 1.3 87.3 - - + +
490A GLY* 1.3 59.9 + - - +
493A ARG* 3.8 26.1 - - + +
31B ASP* 3.3 25.1 - - - +
35B GLN* 3.8 23.1 - - + +
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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