Contacts of the helix formed by residues 476 - 491 (chain A) in PDB entry 1QU2
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 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ILE* 5.3 6.3 - - + -
475A MET* 1.3 81.2 - - - +
477A LYS* 1.3 65.5 + - - +
478A GLU* 3.7 9.7 + - - +
479A THR* 2.9 30.5 + - - +
480A VAL* 2.9 25.6 + - - +
508A PHE* 5.4 2.5 - - + -
510A HIS* 5.7 8.5 - - + -
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Residues in contact with LYS 477 (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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168A GLY* 5.8 4.0 - - - +
172A ASP* 3.3 31.6 - - + +
476A THR* 1.3 73.1 - - - +
478A GLU* 1.3 58.5 + - - +
480A VAL* 4.9 2.5 - - - -
481A ASN* 2.9 51.5 + - - +
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Residues in contact with GLU 478 (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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476A THR* 3.2 8.4 + - - +
477A LYS* 1.3 79.4 - - - +
479A THR* 1.3 62.0 + - - +
481A ASN* 4.0 2.4 - - - +
482A HIS* 3.1 24.1 + - + +
505A PRO* 3.9 26.5 - - + +
506A GLU* 4.8 12.3 - - - +
508A PHE* 3.8 23.6 - - - -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PRO 5.5 0.2 - - - -
466A PHE* 4.3 16.3 - - - -
474A ILE* 3.7 22.4 - - + -
475A MET* 3.8 6.9 - - - -
476A THR* 2.9 41.2 + - - +
478A GLU* 1.3 73.6 - - - +
480A VAL* 1.3 63.3 + - - +
482A HIS* 3.3 2.9 + - - +
483A VAL* 3.1 28.7 + - - +
503A LEU 5.1 0.3 - - - +
504A LEU* 3.7 18.6 - - + -
505A PRO* 4.5 9.4 - - + -
508A PHE* 4.1 15.5 - - + -
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 3.6 24.7 - - + +
165A ARG* 4.9 0.9 - - - -
167A PHE* 4.7 0.7 - - + -
168A GLY* 3.5 33.0 - - - +
171A ALA* 5.7 0.2 - - + -
464A PRO* 3.9 28.0 - - + +
475A MET* 4.4 17.3 - - + -
476A THR 2.9 21.4 + - - +
477A LYS* 4.1 2.7 - - - +
479A THR* 1.3 77.7 + - - +
481A ASN* 1.3 65.8 + - - +
483A VAL* 3.1 8.4 + - - +
484A ALA* 2.9 24.8 + - - +
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Residues in contact with ASN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 4.3 25.9 + - - +
168A GLY* 6.1 0.5 - - - -
477A LYS* 2.9 43.9 + - - +
478A GLU* 4.3 2.0 - - - +
480A VAL* 1.3 80.5 - - - +
482A HIS* 1.3 57.4 + - - +
484A ALA* 3.4 6.5 + - + +
485A ASP* 2.9 31.5 + - - +
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Residues in contact with HIS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLU* 3.1 19.9 + - + +
479A THR 3.8 3.8 - - - +
480A VAL 3.2 0.2 - - - -
481A ASN* 1.3 74.6 - - - +
483A VAL* 1.3 65.3 + - - +
485A ASP* 3.2 13.4 + - + +
486A LEU* 3.0 50.0 + - + +
502A ASP 4.7 2.0 - - - -
503A LEU 3.3 14.9 + - - -
504A LEU 3.5 23.4 - - - -
505A PRO* 3.9 26.5 - - + +
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Residues in contact with VAL 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 4.5 2.7 - - + -
464A PRO* 3.9 23.3 - - + -
466A PHE* 3.5 33.7 - - + -
479A THR 3.1 16.1 + - - +
480A VAL 3.4 7.4 - - - +
482A HIS* 1.3 75.3 - - - +
484A ALA* 1.3 58.7 + - - +
486A LEU* 3.3 8.2 + - + +
487A PHE* 2.9 58.4 + - + -
495A TRP* 3.9 10.8 - - + -
503A LEU* 3.8 8.3 - - + +
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Residues in contact with ALA 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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161A ALA* 3.4 8.6 - - - +
164A ILE* 3.9 15.0 - - + -
165A ARG* 3.8 38.1 - - + +
480A VAL 2.9 14.0 + - - +
481A ASN* 3.5 12.3 - - - +
483A VAL* 1.3 77.4 - - - +
485A ASP* 1.3 57.5 + - - +
487A PHE* 3.2 4.8 + - - +
488A ALA* 2.8 32.2 + - - +
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 4.9 8.6 + - - +
481A ASN* 2.9 21.0 + - - +
482A HIS* 3.3 19.6 - - + +
484A ALA* 1.3 78.5 - - - +
486A LEU* 1.3 63.1 + - + +
488A ALA* 3.3 13.3 + - - +
489A GLU* 3.3 14.4 + - - +
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Residues in contact with LEU 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 HIS* 3.0 45.4 + - + +
483A VAL* 3.3 8.9 + - - +
485A ASP* 1.3 76.9 - - + +
487A PHE* 1.3 54.5 + - - +
489A GLU* 3.0 5.7 + - + +
490A HIS* 2.6 47.6 + - + +
494A ILE* 4.5 12.8 - - + -
498A ARG* 3.7 23.1 - - - +
502A ASP 4.0 4.9 - - - +
503A LEU* 3.9 35.0 - - + +
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 3.4 9.3 - - - +
160A GLU* 4.5 9.9 - - + -
161A ALA* 4.2 11.0 - - - +
164A ILE* 3.5 33.9 - - + -
461A VAL* 4.0 3.1 - - + -
462A PRO* 3.7 37.5 - - + -
464A PRO* 6.0 0.2 - - + -
483A VAL* 2.9 34.9 + - + +
484A ALA* 3.6 4.5 - - - +
486A LEU* 1.3 76.6 - - + +
488A ALA* 1.3 60.9 + - - +
491A GLY* 2.6 35.6 + - - +
492A SER* 4.0 15.5 - - - +
494A ILE* 3.4 28.9 - - + -
495A TRP* 4.1 13.7 - + + -
503A LEU* 5.5 0.2 - - + -
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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
----------------------------------------------------------
157A PRO* 3.3 16.9 - - - +
158A GLU* 2.8 34.2 - - - +
161A ALA* 3.6 17.5 - - + -
165A ARG* 4.3 9.9 - - - +
484A ALA 2.8 17.5 + - - +
485A ASP* 3.5 7.6 - - - +
487A PHE* 1.3 77.9 - - - +
489A GLU* 1.3 58.4 + - - +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 4.9 4.3 - - - +
485A ASP 3.3 8.9 + - - +
486A LEU* 3.0 7.2 + - - +
488A ALA* 1.3 82.8 - - + +
490A HIS* 1.3 83.5 + - + +
491A GLY 3.7 0.4 - - - -
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Residues in contact with HIS 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 4.6 4.9 - - - +
486A LEU* 2.6 30.7 + - + +
489A GLU* 1.3 95.4 + - + +
491A GLY* 1.3 59.5 + - - +
493A ASN* 4.7 8.5 + - - +
494A ILE* 3.7 39.5 + - + +
498A ARG* 3.6 18.9 + - - -
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Residues in contact with GLY 491 (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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155A LEU 5.7 0.4 - - - -
157A PRO* 4.0 13.6 - - - +
160A GLU* 3.4 9.9 - - - -
487A PHE* 2.6 33.0 + - - -
489A GLU 3.7 0.6 - - - -
490A HIS* 1.3 76.5 - - - +
492A SER* 1.3 63.0 + - - -
493A ASN* 3.3 4.5 + - - -
494A ILE* 3.2 18.7 + - - +
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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