Contacts of the helix formed by residues 469 - 485 (chain A) in PDB entry 1Q9X
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 GLY 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ASN* 4.5 0.2 - - - -
426A SER* 4.1 0.7 - - - -
428A GLU* 3.1 13.6 + - - -
429A THR* 3.7 17.4 - - - +
467A ARG* 4.4 1.4 - - - +
468A ASP* 1.3 79.0 + - - +
470A VAL* 1.3 64.2 + - - -
471A VAL 3.2 2.7 - - - -
472A PRO* 3.6 8.1 - - - -
473A THR* 2.8 29.5 + - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.9 28.5 - - + +
369A ILE* 3.7 29.8 - - + -
373A LEU* 4.0 22.7 - - + -
378A LYS* 5.4 7.6 - - - +
426A SER* 3.4 5.9 + - - +
427A PRO* 6.0 0.4 - - + -
428A GLU* 2.7 26.9 + - + +
469A GLY* 1.3 71.9 - - - +
471A VAL* 1.3 68.8 + - + +
473A THR* 3.7 4.8 + - - -
474A GLU* 3.2 28.9 + - + +
577A TYR* 4.7 7.9 - - + -
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 5.2 10.3 - - + -
420A ILE* 3.9 16.2 - - + -
425A ILE 3.8 3.6 - - - +
426A SER* 3.0 17.9 + - - +
427A PRO* 4.2 13.5 - - + -
470A VAL* 1.3 81.7 - - + +
472A PRO* 1.3 71.6 - - + +
474A GLU* 2.9 18.4 + - + +
475A ILE* 3.1 15.1 + - + +
566A LEU* 3.9 26.9 - - + -
570A LEU* 4.1 24.0 - - + -
575A PHE* 5.9 0.2 - - + -
577A TYR* 4.7 11.9 - - + -
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Residues in contact with PRO 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE* 3.7 27.1 - - + +
421A ARG* 3.9 16.0 - - + +
424A ASN* 3.7 22.7 - - - +
425A ILE 3.1 25.8 - - - +
426A SER* 3.7 2.7 - - - +
468A ASP 3.5 10.5 - - - +
469A GLY* 3.4 9.9 - - - +
471A VAL* 1.3 88.0 - - + +
473A THR* 1.3 62.1 + - - +
475A ILE* 3.3 2.4 + - + -
476A THR* 2.9 28.5 + - - -
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Residues in contact with THR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ASP* 2.7 27.8 + - - +
469A GLY 2.8 23.0 + - - -
470A VAL* 3.7 5.2 - - - -
472A PRO* 1.3 75.8 - - - +
474A GLU* 1.3 66.8 + - - +
476A THR* 3.3 7.3 + - - -
477A LYS* 3.0 36.7 + - + +
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Residues in contact with GLU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 4.2 16.4 - - + -
368A ILE* 4.1 14.4 - - - +
369A ILE* 3.7 27.6 - - + -
372A SER* 2.9 38.4 + - - -
373A LEU* 5.3 3.8 - - - +
376A GLN* 5.1 1.6 - - - +
470A VAL* 3.2 15.4 + - + +
471A VAL* 2.9 10.6 + - + +
473A THR* 1.3 85.4 - - - +
475A ILE* 1.3 60.6 + - - +
477A LYS* 3.4 23.5 + - - +
478A VAL* 3.2 27.7 + - - +
566A LEU* 6.3 0.2 - - + -
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 4.7 4.9 - - + -
417A PRO* 3.8 28.9 - - + +
420A ILE* 3.6 40.4 - - + -
421A ARG* 4.3 7.0 - - + -
471A VAL 3.1 12.5 + - - +
472A PRO* 4.0 4.7 - - + +
474A GLU* 1.3 74.1 - - + +
476A THR* 1.3 55.8 + - - +
478A VAL* 2.9 7.7 + - - +
479A PHE* 2.8 45.2 + - + +
563A ILE* 4.3 14.8 - - + +
566A LEU* 3.5 32.3 - - + -
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 3.0 35.5 + - - +
472A PRO 2.9 18.5 + - - -
473A THR* 3.5 8.1 - - - -
475A ILE* 1.3 76.4 - - - +
477A LYS* 1.3 62.7 + - - +
479A PHE* 3.4 4.7 + - + +
480A ASN* 3.1 44.7 + - - +
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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
----------------------------------------------------------
350A TYR* 5.2 9.2 - - - +
368A ILE* 6.0 1.1 - - - -
372A SER* 3.5 17.4 + - - +
473A THR* 3.0 21.2 + - + +
474A GLU* 3.4 41.3 - - - +
475A ILE 3.2 0.2 - - - -
476A THR* 1.3 75.7 - - - +
478A VAL* 1.3 64.2 + - + +
480A ASN* 3.7 4.8 + - - +
481A GLN* 3.3 32.8 + - - +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TYR* 4.2 20.2 - - + +
365A TRP* 3.8 21.8 - - + -
368A ILE* 5.3 2.9 - - + -
474A GLU* 3.2 16.4 - - - +
475A ILE* 2.9 7.2 + - - +
477A LYS* 1.3 78.3 - - + +
479A PHE* 1.3 53.7 + - - +
481A GLN* 3.1 7.8 + - - +
482A ARG* 2.7 32.9 + - - +
559A ARG* 3.8 28.3 - - + +
562A LEU* 4.4 9.9 - - + -
563A ILE* 3.7 24.2 - - + -
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Residues in contact with PHE 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A THR* 5.3 8.5 - - + -
414A SER* 3.3 33.9 - - - -
417A PRO* 4.4 13.0 - - + -
418A SER* 4.8 5.2 - - - -
421A ARG* 3.7 30.7 - - - +
475A ILE* 2.8 31.8 + - + +
476A THR* 3.7 7.9 - - + +
478A VAL* 1.3 71.7 - - - +
480A ASN* 1.3 59.5 + - - +
482A ARG* 3.1 21.7 + - + +
483A LYS* 3.0 36.2 + - + +
563A ILE* 4.0 19.4 - - + +
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Residues in contact with ASN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A THR* 3.1 34.5 + - - +
477A LYS* 4.0 5.8 - - - +
479A PHE* 1.3 77.6 - - - +
481A GLN* 1.3 60.2 + - - +
483A LYS* 3.5 24.4 + - - +
484A GLU* 2.9 27.8 + - - +
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Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TYR* 3.1 34.1 + - - -
477A LYS* 3.3 25.3 + - - +
478A VAL* 3.1 10.8 + - - +
480A ASN* 1.3 71.9 - - - +
482A ARG* 1.3 55.8 + - - +
483A LYS 3.0 4.3 - - - -
484A GLU* 2.8 32.3 + - - +
485A HIS* 2.9 34.5 + - + +
559A ARG* 3.0 40.1 - - - +
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Residues in contact with ARG 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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478A VAL 2.7 16.6 + - - +
479A PHE* 3.1 24.2 + - + +
481A GLN* 1.3 71.7 - - - +
483A LYS* 1.3 58.9 + - + +
486A LYS* 3.4 36.5 + - - +
556A GLN* 3.8 35.5 + - + +
559A ARG* 3.8 20.6 - - + +
560A LYS* 3.4 49.3 - - - +
563A ILE* 4.2 13.2 - - + -
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PHE* 3.0 21.7 + - + +
480A ASN* 3.9 23.8 - - - +
481A GLN 3.0 0.4 - - - -
482A ARG* 1.3 79.9 - - + +
484A GLU* 1.3 66.7 + - - +
486A LYS* 3.9 20.7 - - + +
487A GLY* 3.7 10.7 + - - -
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ASN 2.9 14.5 + - - +
481A GLN* 2.8 23.7 + - - +
483A LYS* 1.3 76.9 - - - +
485A HIS* 1.3 65.4 + - + +
487A GLY* 2.9 21.7 + - - -
488A TYR* 2.7 52.7 + - + +
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Residues in contact with HIS 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLN* 2.9 41.7 + - - +
484A GLU* 1.3 82.8 + - + +
486A LYS* 1.3 58.9 + - - +
487A GLY 3.1 2.0 - - - -
488A TYR* 3.0 20.8 + + + +
489A MET* 2.9 31.6 + - - +
552A GLY* 4.2 12.0 - - - +
555A ALA* 4.1 14.4 - - + +
556A GLN* 4.3 17.9 - - + +
559A ARG* 3.1 30.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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