Contacts of the helix formed by residues 478 - 489 (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 TRP 478 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.9 39.5 - - + +
26A HIS* 5.6 2.0 - - + -
46A ASP* 4.9 3.6 + - - +
47A THR 4.0 11.3 + - - -
48A ARG* 4.0 19.3 - - - -
421B MSE 4.8 11.2 - - + -
449B GLY* 3.4 38.4 - - - -
450B SER* 3.9 3.8 - - - -
453B TYR* 3.7 26.7 - + - -
477B SER* 1.3 68.2 - - - +
479B GLY* 1.3 58.0 + - - +
480B ALA 3.8 0.7 - - - -
481B THR* 2.9 38.6 - - + +
482B LEU* 2.9 13.0 + - - +
496B GLY 3.9 19.6 + - - -
497B THR* 2.9 18.5 + - - +
499B LEU* 3.6 26.4 - - + +
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Residues in contact with GLY 479 (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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394B ALA* 6.0 0.8 - - - +
395B LEU* 3.6 18.4 - - - -
475B ASN* 4.1 5.1 + - - +
477B SER* 3.0 22.3 + - - -
478B TRP* 1.3 66.5 - - - +
480B ALA* 1.3 66.7 + - - +
481B THR 3.0 2.0 - - - -
482B LEU* 3.0 3.5 + - - +
483B HIS* 2.9 27.2 + - - -
546B LEU* 3.9 5.2 - - - -
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ALA* 3.6 30.3 - - + +
395B LEU* 3.4 21.5 - - + +
398B LEU* 5.5 4.9 - - + -
479B GLY* 1.3 72.6 - - - +
481B THR* 1.3 57.0 + - - +
483B HIS* 3.2 3.5 + - - +
484B PHE* 2.9 28.8 + - - +
553B GLU* 4.0 13.7 - - - +
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Residues in contact with THR 481 (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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26A HIS* 2.9 29.5 + - + +
27A GLY* 3.8 10.0 - - - -
28A ALA* 3.9 5.7 + - - +
478B TRP* 2.9 37.7 - - + +
479B GLY 3.0 0.2 - - - -
480B ALA* 1.3 81.1 - - - +
482B LEU* 1.3 59.9 + - - +
484B PHE* 3.5 9.0 + - - +
485B GLN* 3.3 24.4 + - - +
497B THR* 3.3 22.7 - - + -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B SER* 3.9 20.0 - - - +
478B TRP 2.9 14.6 + - - +
479B GLY* 3.0 9.8 + - - +
481B THR* 1.3 75.6 - - - +
483B HIS* 1.3 64.4 + - + +
485B GLN* 3.2 5.8 + - - +
486B GLN* 3.2 49.2 + - + +
494B VAL* 3.8 20.0 - - + -
497B THR* 3.6 24.7 - - - +
498B ARG* 3.8 29.2 - - + +
546B LEU* 4.2 15.7 - - + -
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Residues in contact with HIS 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 3.6 14.7 - - + +
479B GLY 2.9 16.1 + - - -
480B ALA 3.2 9.4 + - - +
482B LEU* 1.3 76.4 - - + +
484B PHE* 1.3 55.1 + - - +
486B GLN* 3.3 19.8 + - - +
487B LEU* 2.8 46.0 + - + +
546B LEU* 2.8 33.1 + - + +
547B ASP* 3.9 9.0 + - - -
548B PRO 3.2 27.8 - - - -
549B ILE* 4.2 4.7 - - + +
553B GLU* 2.8 38.1 + - - +
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Residues in contact with PHE 484 (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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26A HIS* 5.1 0.7 - - - -
28A ALA* 3.8 38.1 - - + -
31A ASP* 3.8 31.9 - - + -
163A TRP* 4.1 21.5 - + - -
167A MSE 5.2 7.4 - - - -
480B ALA 2.9 12.8 + - - +
481B THR* 3.5 12.6 - - - +
483B HIS* 1.3 75.5 - - - +
485B GLN* 1.3 58.2 + - + +
487B LEU* 4.6 4.5 - - - -
488B ALA* 2.7 61.5 + - + +
489B VAL* 4.8 1.6 - - + -
553B GLU* 5.7 0.2 - - - -
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Residues in contact with GLN 485 (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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26A HIS* 3.2 13.4 + - + +
31A ASP* 2.9 32.0 + - - +
34A PHE* 4.6 2.2 - - - +
35A GLN* 4.1 2.7 - - - +
481B THR 3.3 8.5 + - - +
482B LEU* 3.2 8.1 + - - +
483B HIS 3.2 0.6 - - - -
484B PHE* 1.3 77.0 - - + +
486B GLN* 1.3 56.8 + - - +
489B VAL* 3.0 18.9 + - - +
490B GLY 2.9 26.0 + - - +
493B ARG 3.6 21.0 + - - +
494B VAL* 3.3 5.6 - - - +
495B THR* 3.0 33.1 + - - +
497B THR* 2.8 31.4 + - - +
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Residues in contact with GLN 486 (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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482B LEU* 3.2 41.0 + - + +
483B HIS* 3.9 19.7 + - - +
485B GLN* 1.3 77.7 - - + +
487B LEU* 1.3 73.7 - - + +
490B GLY* 3.1 31.3 + - - +
491B PRO* 3.9 22.5 - - + +
494B VAL* 5.1 6.7 - - + +
498B ARG* 5.8 1.4 + - - -
547B ASP* 5.5 6.2 + - - +
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Residues in contact with LEU 487 (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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483B HIS* 2.8 31.8 + - + +
484B PHE* 4.1 3.4 - - - +
486B GLN* 1.3 88.8 - - + +
488B ALA* 1.3 58.9 + - + +
490B GLY 5.1 0.2 + - - -
549B ILE* 4.6 22.9 - - + -
553B GLU* 3.6 29.8 - - + +
554B LEU* 5.3 7.4 - - + -
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B PHE* 2.7 52.8 + - + +
487B LEU* 1.3 73.4 - - + +
489B VAL* 1.3 59.3 + - + +
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.3 26.7 - - - +
35A GLN* 3.6 32.5 - - + +
484B PHE* 4.4 2.9 - - + +
485B GLN* 3.0 16.2 + - - +
487B LEU 5.2 0.4 - - - -
488B ALA* 1.3 86.8 - - + +
490B GLY* 1.3 57.4 + - - +
493B ARG* 3.7 19.0 - - + +
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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