Contacts of the helix formed by residues 477 - 493 (chain X) in PDB entry 6AH0
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 477 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475X ALA 4.4 5.4 - - - +
476X PRO* 1.3 77.9 - - - +
478X ARG* 1.3 61.2 + - - +
479X GLU* 3.2 3.4 - - - +
480X LEU* 3.2 7.4 + - - +
481X ALA* 2.9 24.6 + - - -
525X THR* 5.7 3.7 - - - -
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Residues in contact with ARG 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477X THR* 1.3 71.6 - - - +
479X GLU* 1.3 56.9 + - - +
481X ALA* 3.2 3.1 + - - +
482X GLN* 2.9 25.8 + - - -
503X ILE* 5.6 4.3 - - - +
504X GLY 5.0 17.7 - - - +
525X THR* 6.0 2.7 - - - +
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Residues in contact with GLU 479 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477X THR* 3.2 1.2 - - - +
478X ARG* 1.3 75.0 - - - +
480X LEU* 1.3 63.5 + - - +
482X GLN* 3.3 3.4 + - - +
483X GLN* 3.2 16.8 + - - -
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Residues in contact with LEU 480 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475X ALA* 5.9 2.7 - - - +
477X THR* 3.2 11.6 + - - +
479X GLU* 1.3 77.6 - - - +
481X ALA* 1.3 61.3 + - - +
483X GLN* 3.3 3.7 + - - +
484X ILE* 3.2 16.6 + - - -
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Residues in contact with ALA 481 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475X ALA* 5.4 8.6 - - - +
477X THR 2.9 13.8 + - - -
478X ARG* 3.2 5.3 + - - +
480X LEU* 1.3 77.8 - - - +
482X GLN* 1.3 55.4 + - - +
484X ILE* 3.1 4.0 + - - +
485X GLU* 2.8 26.7 + - - -
523X ILE* 6.0 3.2 - - - +
524X ALA 5.6 9.0 - - - +
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Residues in contact with GLN 482 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478X ARG 2.9 13.6 + - - -
479X GLU* 3.3 4.5 + - - +
480X LEU 3.3 0.2 - - - -
481X ALA* 1.3 73.7 - - - +
483X GLN* 1.3 65.1 + - - +
485X GLU* 3.2 2.4 + - - +
486X GLU* 2.9 21.1 + - - -
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Residues in contact with GLN 483 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479X GLU 3.2 12.8 + - - -
480X LEU* 3.3 4.9 + - - +
481X ALA 3.3 0.2 - - - -
482X GLN* 1.3 76.4 - - - +
484X ILE* 1.3 63.9 + - - +
486X GLU* 3.2 1.4 + - - +
487X GLU* 3.2 16.6 + - - -
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Residues in contact with ILE 484 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480X LEU 3.2 9.3 + - - -
481X ALA* 3.1 8.2 + - - +
483X GLN* 1.3 76.4 - - - +
485X GLU* 1.3 51.2 + - - +
487X GLU* 3.2 2.3 + - - +
488X THR* 2.7 32.9 + - - -
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Residues in contact with GLU 485 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481X ALA 2.8 17.6 + - - -
482X GLN* 3.2 4.4 + - - +
484X ILE* 1.3 74.4 - - - +
486X GLU* 1.3 53.0 + - - +
488X THR* 3.1 1.3 + - - +
489X ILE* 2.7 33.4 + - - -
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Residues in contact with GLU 486 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482X GLN 2.9 15.1 + - - -
483X GLN 3.9 1.6 - - - -
485X GLU* 1.3 75.5 - - - +
487X GLU* 1.3 62.4 + - - +
489X ILE* 3.5 1.3 + - - +
490X LYS* 3.1 18.5 + - - -
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Residues in contact with GLU 487 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483X GLN 3.2 12.0 + - - -
484X ILE 3.7 2.7 - - - -
485X GLU 3.1 0.4 - - - -
486X GLU* 1.3 75.0 - - - +
488X THR* 1.3 62.1 + - - +
490X LYS* 3.4 1.7 + - - +
491X PHE* 3.1 18.4 + - - -
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Residues in contact with THR 488 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484X ILE 2.7 18.9 + - - -
485X GLU* 3.6 3.1 - - - +
487X GLU* 1.3 73.2 - - - +
489X ILE* 1.3 56.4 + - - +
491X PHE* 3.2 2.1 + - - +
492X GLY* 2.7 29.1 + - - -
499X THR* 6.6 0.2 - - - -
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Residues in contact with ILE 489 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485X GLU 2.7 19.3 + - - -
486X GLU* 3.9 1.8 - - - +
488X THR* 1.3 72.2 - - - +
490X LYS* 1.3 61.6 + - - +
492X GLY* 3.1 0.6 + - - -
493X LYS* 2.9 27.9 + - - +
499X THR* 6.4 2.0 - - - +
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Residues in contact with LYS 490 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409X CYS* 6.2 0.2 - - - -
486X GLU 3.1 14.3 + - - -
487X GLU* 3.4 3.3 + - - +
488X THR 3.3 0.4 - - - -
489X ILE* 1.3 75.9 - - - +
491X PHE* 1.3 59.7 + - - +
493X LYS 4.7 1.0 + - - -
494X PRO* 4.7 5.2 - - - +
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Residues in contact with PHE 491 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487X GLU 3.1 13.6 + - - -
488X THR* 3.7 2.5 - - - +
490X LYS* 1.3 80.4 - - - +
492X GLY* 1.3 61.1 + - - +
494X PRO* 4.2 1.7 - - - +
495X LEU* 4.2 9.2 + - - -
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Residues in contact with GLY 492 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488X THR 2.7 19.8 + - - -
489X ILE* 3.1 0.6 + - - -
491X PHE* 1.3 73.1 - - - +
493X LYS* 1.3 64.8 + - - +
495X LEU* 2.9 10.5 + - - -
497X ILE* 2.8 38.8 + - - -
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Residues in contact with LYS 493 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489X ILE* 2.9 16.2 + - - +
492X GLY* 1.3 75.1 - - - +
494X PRO* 1.3 62.0 - - - +
496X GLY* 2.8 16.4 + - - +
497X ILE 3.8 7.0 + - - +
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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