Contacts of the strand formed by residues 456 - 473 (chain A) in PDB entry 1QFG
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 VAL 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A ALA 5.2 0.7 - - - +
452A GLN* 3.0 8.6 - - - +
453A TRP* 2.9 54.3 + - + +
454A ASP 3.2 1.0 - - - -
455A LYS* 1.3 79.7 - - - +
457A LEU* 1.3 68.0 + - - +
458A VAL* 4.5 7.6 - - + +
493A VAL* 4.0 20.4 - - + -
494A ASN 4.0 1.8 - - - -
495A TYR* 3.6 29.6 - - + -
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Residues in contact with LEU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 3.3 60.1 - - + +
450A GLN* 4.2 11.4 - - + +
451A ALA 3.4 17.0 - - - +
452A GLN* 4.2 10.3 - - + +
455A LYS 5.5 0.2 - - - +
456A VAL* 1.3 77.4 - - - +
458A VAL* 1.3 93.0 + - - +
459A THR* 3.9 10.3 + - - +
493A VAL* 3.1 8.0 - - - +
494A ASN* 3.1 46.6 + - + +
496A LEU* 5.9 4.7 - - + -
1106A GOL 4.2 10.8 - - - +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ASP* 3.3 5.4 - - + +
450A GLN* 3.4 0.9 - - - -
451A ALA* 2.7 51.3 + - + +
456A VAL* 4.8 7.6 - - + -
457A LEU* 1.3 77.3 - - - +
459A THR* 1.3 68.3 + - - +
460A LEU* 5.2 6.5 - - + +
492A GLY 3.4 11.4 - - - +
493A VAL* 4.6 11.7 - - + -
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Residues in contact with THR 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 5.8 1.3 - - + -
45A LYS 4.4 1.7 + - - -
47A PRO* 3.7 31.6 - - + +
448A GLN* 4.0 17.5 - - + +
449A ASP 3.4 7.4 - - - +
450A GLN* 4.0 18.1 + - + +
457A LEU* 3.9 13.3 - - - +
458A VAL* 1.3 77.8 - - - +
460A LEU* 1.3 69.5 + - - +
490A ARG* 4.2 16.4 - - - +
491A GLY* 3.0 2.4 - - - -
492A GLY 2.6 41.9 + - - +
494A ASN* 4.8 1.2 + - - -
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLN* 3.4 4.2 - - - -
449A ASP* 2.9 37.1 + - + +
458A VAL* 3.9 8.9 + - + -
459A THR* 1.3 81.6 - - - +
461A GLY* 1.3 66.6 + - - +
489A TRP* 3.8 24.7 - - + -
490A ARG* 3.4 14.8 - - - +
491A GLY* 4.1 4.5 - - - -
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Residues in contact with GLY 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.9 6.3 - - - +
447A VAL* 3.0 15.9 - - - -
448A GLN* 3.8 7.5 - - - +
460A LEU* 1.3 82.0 - - - +
462A GLY* 1.3 58.5 + - - -
489A TRP* 3.0 21.4 - - - +
490A ARG* 2.9 15.9 + - - +
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Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.7 8.9 - - - +
446A TYR* 3.2 3.9 - - - +
447A VAL* 2.9 31.2 + - - +
461A GLY* 1.3 76.1 - - - -
463A ARG* 1.3 61.2 + - - -
487A PHE* 3.9 12.6 - - - -
488A THR 3.3 11.2 - - - -
489A TRP* 3.7 5.4 - - - -
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Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 3.6 16.6 - - - +
138A VAL 3.3 16.2 - - - +
139A LEU 3.1 20.7 + - - -
140A TYR* 3.6 2.2 + - - +
141A GLY* 3.3 18.4 - - - +
379A ASP* 2.9 48.2 + - - +
442A GLN* 3.9 7.7 - - - +
444A GLY* 3.9 8.9 - - - +
445A VAL 3.3 14.4 - - - +
446A TYR* 3.4 19.8 - - + -
462A GLY* 1.3 74.1 - - - -
464A TYR* 1.3 66.1 + - - +
465A ASP* 2.7 39.0 + - - +
487A PHE* 3.2 9.4 - - - -
488A THR* 2.7 36.1 + - - +
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Residues in contact with TYR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A THR 4.1 0.3 - - - +
444A GLY* 3.1 4.3 - - - -
445A VAL* 2.9 40.6 + - + +
463A ARG* 1.3 74.4 - - - +
465A ASP* 1.3 68.1 - - - +
466A TRP* 3.1 55.7 - + - -
485A LYS* 3.2 34.7 - - + +
486A GLN* 3.0 23.3 - - - -
487A PHE* 4.1 20.4 - + + -
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Residues in contact with ASP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 4.6 0.9 - - - +
141A GLY* 3.4 15.9 - - - -
442A GLN* 3.6 14.2 - - + +
443A THR 3.6 0.7 - - - -
444A GLY* 3.3 7.3 - - - -
463A ARG* 2.7 56.6 + - - +
464A TYR* 1.3 77.1 + - - +
466A TRP* 1.3 64.2 + - - +
467A ALA* 3.7 1.0 + - - +
484A ASP 3.8 0.7 - - - +
485A LYS* 3.3 7.3 - - - -
486A GLN* 2.5 39.9 + - - +
488A THR* 5.1 2.1 + - - +
511A PHE* 3.7 29.4 - - + -
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Residues in contact with TRP 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LYS* 3.7 1.4 - - - +
442A GLN* 2.9 24.6 + - - -
443A THR* 2.8 35.8 + - - +
445A VAL* 4.2 18.8 - - + -
464A TYR* 3.1 44.9 - + - -
465A ASP* 1.3 69.5 - - - +
467A ALA* 1.3 60.7 + - - +
468A ASP* 3.7 11.9 + - - +
484A ASP 3.6 3.4 - - - -
485A LYS* 3.6 39.2 - - + +
1103A GOL 3.3 49.7 + - - +
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 5.2 4.5 - - + -
441A LYS 3.4 7.2 - - - +
442A GLN* 4.2 15.0 - - + +
465A ASP 3.7 1.3 - - - +
466A TRP* 1.3 71.7 - - - +
468A ASP* 1.3 62.6 - - - +
469A GLN* 4.0 1.9 + - - +
482A ARG 4.2 0.2 - - - +
483A ASP* 3.6 0.5 - - - -
484A ASP* 2.8 38.8 + - + +
511A PHE* 4.3 15.7 - - + -
513A PRO* 4.2 23.4 - - + +
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Residues in contact with ASP 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS 4.8 0.2 - - - -
440A GLN* 3.5 2.0 - - - -
441A LYS* 2.9 53.8 + - + +
466A TRP* 3.7 11.5 + - - +
467A ALA* 1.3 86.9 + - - +
469A GLN* 1.3 59.4 + - - +
482A ARG 3.6 2.2 - - - -
483A ASP* 3.1 41.9 - - - +
484A ASP 3.8 3.1 - - - +
485A LYS* 4.5 4.1 + - - -
1100A DDQ 5.8 3.8 - - - -
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Residues in contact with GLN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS 3.5 12.6 - - - +
440A GLN* 4.7 10.5 + - + +
467A ALA 5.3 2.0 - - - +
468A ASP* 1.3 76.2 - - - +
470A GLU* 1.3 66.9 + - - +
471A SER* 5.7 3.1 - - - -
481A LYS* 3.4 2.8 - - - +
482A ARG* 2.8 43.4 + - + +
483A ASP* 4.6 2.3 - - - +
484A ASP* 4.7 4.0 + - - +
513A PRO* 3.9 17.4 - - - +
514A SER 2.6 29.8 + - - +
515A SER* 3.9 15.8 - - - +
523A ILE* 4.1 25.3 - - + +
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU 4.1 1.4 - - - +
438A ASN* 3.9 1.0 - - - -
439A LYS* 3.0 59.3 + - + +
469A GLN* 1.3 82.1 - - - +
471A SER* 1.3 63.7 + - - +
472A LEU* 5.4 2.0 - - + +
479A THR* 4.0 11.6 - - + +
480A ASP 3.2 5.8 - - - -
481A LYS* 3.3 35.2 + - + +
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ILE* 3.6 12.3 - - - +
437A LEU 3.8 2.7 - - - -
438A ASN* 2.9 23.5 + - - -
469A GLN* 5.7 4.0 - - - -
470A GLU* 1.3 75.3 - - - +
472A LEU* 1.3 61.6 + - - +
473A ASN* 5.4 0.7 - - - +
478A THR 3.6 0.5 - - - +
479A THR* 3.3 7.6 - - - -
480A ASP* 2.5 51.7 + - - +
515A SER 6.2 0.2 - - - -
523A ILE* 5.7 2.2 - - - -
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ILE* 3.3 5.5 - - - +
437A LEU* 2.9 53.6 + - + +
470A GLU* 4.3 2.4 - - + +
471A SER* 1.3 74.2 - - - +
473A ASN* 1.3 78.7 + - - +
474A ARG* 3.2 41.4 + - + +
477A GLY* 4.5 7.4 - - - -
478A THR 3.4 11.9 - - - +
479A THR* 3.9 14.8 - - + +
2004A DPO 5.6 1.1 - - - +
4B GMH 3.9 11.2 - - - +
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Residues in contact with ASN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TYR* 5.8 1.0 - - - -
435A ARG 3.5 6.3 + - - +
436A ILE* 3.8 23.0 - - + +
471A SER* 3.9 1.3 + - - +
472A LEU* 1.3 71.6 - - - +
474A ARG* 1.3 53.4 + - - +
475A VAL* 3.0 12.9 + - - +
476A ALA* 2.9 30.5 + - - +
477A GLY* 2.6 38.3 + - - -
478A THR* 2.7 26.8 + - - +
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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