Contacts of the helix formed by residues 520 - 539 (chain A) in PDB entry 1QFM
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 LEU 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ILE* 1.3 88.9 - - + +
521A ALA* 1.3 66.1 + - - +
522A ASN 3.1 0.9 + - - -
523A LYS* 3.2 16.7 + - - +
596A THR 3.8 4.3 - - - +
597A THR 3.7 21.5 - - - +
598A ASP 2.8 15.3 + - - +
599A TYR 4.4 3.9 - - - +
600A GLY* 3.7 26.5 - - - +
607A HIS* 5.1 3.8 - - + -
610A TRP* 3.6 39.9 - - + +
614A TYR* 5.2 0.3 - - - -
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE 3.2 0.2 + - - -
520A LEU* 1.3 80.2 - - - +
522A ASN* 1.3 66.9 + - - +
523A LYS 3.4 0.9 + - - -
524A GLN* 4.7 5.5 + - - +
606A GLN* 5.5 1.6 - - - +
610A TRP* 3.5 41.3 - - + +
790A GOL 5.1 1.2 + - - -
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Residues in contact with ASN 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LYS 3.8 12.9 + - - +
517A GLY* 3.6 14.5 - - - +
518A GLY* 3.7 1.4 - - - -
519A ILE 2.8 13.6 + - - +
521A ALA* 1.3 85.5 - - - +
523A LYS* 1.3 63.7 + - - +
524A GLN* 3.1 3.6 - - - +
525A ASN* 2.9 39.0 + - - +
790A GOL 3.0 23.8 + - - -
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Residues in contact with LYS 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR 5.0 1.2 + - - -
474A GLY 2.9 28.5 + - - -
475A GLY* 4.7 1.2 - - - -
518A GLY 3.4 18.6 + - - +
519A ILE* 3.5 7.4 + - - -
520A LEU 3.2 17.0 + - - +
521A ALA 3.4 1.2 - - - -
522A ASN* 1.3 76.2 - - - +
524A GLN* 1.3 63.0 + - - +
526A CYS* 2.9 32.1 + - - +
527A PHE* 3.7 25.4 - - + -
555A ASN* 3.3 22.9 + - - +
558A LEU* 4.1 11.0 - - - +
559A LEU* 6.1 1.8 - - - +
598A ASP* 5.0 3.2 + - - +
599A TYR* 4.2 10.6 - - + -
614A TYR* 3.5 37.9 - - + +
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Residues in contact with GLN 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ALA 4.7 4.8 + - - +
522A ASN* 3.1 2.1 + - - -
523A LYS* 1.3 77.6 - - - +
525A ASN* 1.3 62.5 + - - +
527A PHE* 3.2 22.1 + - - +
528A ASP* 2.9 53.3 + - - +
531A GLN* 5.0 0.2 + - - -
566A GLN* 3.0 42.2 + - - -
613A LYS* 5.7 1.7 - - - +
614A TYR* 4.3 9.3 - - + +
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Residues in contact with ASN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ASP* 5.1 0.2 - - - -
505A ARG* 3.6 27.8 + - - +
517A GLY* 2.8 30.1 + - - +
522A ASN* 2.9 24.5 + - - +
524A GLN* 1.3 80.3 - - - +
526A CYS* 1.3 56.0 + - - +
528A ASP* 3.7 10.2 - - - +
529A ASP* 2.8 38.0 + - - +
790A GOL 2.8 40.1 + - - -
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Residues in contact with CYS 526 (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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474A GLY 3.6 3.4 - - - +
504A ILE* 3.6 14.1 - - + +
505A ARG 3.3 25.6 - - - +
518A GLY* 3.2 31.4 - - - -
523A LYS* 2.9 38.5 + - - +
525A ASN* 1.3 79.0 - - - +
527A PHE* 1.3 62.1 + - + +
529A ASP* 3.5 5.7 - - - +
530A PHE* 3.0 29.3 + - - +
559A LEU* 4.3 3.6 - - + -
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LYS* 3.8 36.6 - - + -
524A GLN* 3.2 37.8 + - - +
526A CYS* 1.3 71.9 - - + +
528A ASP* 1.3 61.9 + - - +
530A PHE* 3.3 1.6 + - - +
531A GLN* 2.9 48.3 + - - +
558A LEU* 4.2 4.5 - - + -
559A LEU* 3.8 32.5 - - + -
562A THR* 3.6 30.1 - - + -
563A CYS* 4.0 5.1 - - - -
566A GLN* 3.8 1.3 - - - +
614A TYR* 3.5 43.5 - + + -
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Residues in contact with ASP 528 (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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444A SER* 3.9 10.3 - - - +
445A LYS* 3.9 36.5 + - + +
505A ARG* 5.7 0.7 - - - +
524A GLN* 2.9 49.6 + - - +
525A ASN* 3.7 11.9 - - - +
527A PHE* 1.3 74.1 - - - +
529A ASP* 1.3 65.8 + - - +
531A GLN* 3.3 12.3 + - - +
532A CYS* 2.9 29.7 + - - -
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Residues in contact with ASP 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 2.7 26.4 + - - +
444A SER* 2.6 33.7 + - - -
450A ILE* 3.6 11.7 - - + +
504A ILE* 3.6 14.8 - - + -
505A ARG* 2.8 56.1 + - - +
525A ASN 2.8 21.2 + - - +
526A CYS 3.5 4.9 - - - +
528A ASP* 1.3 76.1 - - - +
530A PHE* 1.3 55.8 + - - +
532A CYS 3.2 1.4 + - - -
533A ALA 3.0 15.6 + - - -
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Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A LEU* 3.5 39.2 - - + +
471A TYR 3.6 21.8 - - - -
472A GLY* 3.6 13.7 - - - -
502A ALA* 4.2 6.1 - - + -
504A ILE* 3.8 16.5 - - + +
526A CYS 3.0 16.9 + - - +
527A PHE 3.8 3.6 - - - +
529A ASP* 1.3 75.1 - - - +
531A GLN* 1.3 64.2 + - - +
533A ALA* 3.0 14.5 + - - +
534A ALA* 3.2 11.8 + - - +
550A ILE* 3.7 28.3 - - + -
559A LEU* 3.8 24.2 - - + -
560A VAL* 3.9 13.2 - - + -
563A CYS* 3.8 19.5 - - + -
571A PHE* 5.3 1.8 - + - -
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Residues in contact with GLN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A GLN* 5.0 0.2 + - - -
527A PHE* 2.9 25.2 + - - +
528A ASP* 3.7 13.5 - - - +
530A PHE* 1.3 74.1 - - - +
532A CYS* 1.3 60.9 + - - +
534A ALA* 3.2 7.5 + - - +
535A GLU* 3.0 31.0 + - - +
563A CYS* 3.6 26.4 - - + +
566A GLN* 2.9 36.8 + - - +
567A ARG* 3.4 33.3 + - + +
570A LEU* 3.6 16.1 - - + +
571A PHE* 4.5 2.9 - - + -
784A SGM 4.9 0.2 - - - -
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Residues in contact with CYS 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 3.6 15.9 - - + -
443A PRO 4.0 3.8 - - - +
444A SER* 4.1 2.9 - - - -
445A LYS* 3.7 24.0 - - - -
528A ASP* 2.9 24.0 + - - +
529A ASP 3.5 4.5 - - - +
530A PHE 3.1 0.2 - - - -
531A GLN* 1.3 77.8 - - - +
533A ALA* 1.3 58.1 + - - +
535A GLU* 3.7 1.8 - - - +
536A TYR* 2.9 29.1 + - - +
784A SGM 2.0 54.4 - - + +
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Residues in contact with ALA 533 (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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442A TYR* 3.4 31.4 - - + +
452A MET* 3.8 12.1 - - - +
470A LEU* 4.0 9.2 - - + -
502A ALA* 3.8 20.0 - - + -
529A ASP 3.0 6.0 + - - +
530A PHE* 3.0 10.5 + - - +
532A CYS* 1.3 77.7 - - - +
534A ALA* 1.3 63.3 + - - +
536A TYR* 3.2 3.6 + - - +
537A LEU* 3.0 26.9 + - - +
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Residues in contact with ALA 534 (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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470A LEU* 3.7 11.3 - - + +
530A PHE 3.2 6.8 + - - +
531A GLN 3.4 9.9 - - - +
533A ALA* 1.3 79.9 - - - +
535A GLU* 1.3 62.3 + - - +
537A LEU* 3.2 6.1 + - - +
538A ILE* 3.1 28.8 + - - +
548A LEU* 3.6 25.3 - - + +
570A LEU* 3.9 8.3 - - + -
571A PHE* 3.8 20.6 - - + -
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Residues in contact with GLU 535 (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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531A GLN* 3.0 17.7 + - - +
532A CYS* 3.7 9.2 - - - +
533A ALA 3.3 0.2 - - - -
534A ALA* 1.3 74.6 - - - +
536A TYR* 1.3 56.8 + - - +
538A ILE* 3.3 8.5 + - - +
539A LYS* 2.8 36.5 + - + +
567A ARG* 2.9 27.8 + - - -
570A LEU* 4.1 16.4 - - + -
784A SGM 3.5 31.6 + - + +
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Residues in contact with TYR 536 (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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440A ILE* 3.6 42.7 - - + +
441A PHE 5.1 2.7 - - - -
442A TYR* 3.6 27.6 - - + -
443A PRO* 5.4 1.1 - - + -
452A MET* 3.6 16.2 - - + -
454A ILE* 4.1 13.0 - - + -
532A CYS 2.9 14.2 + - - +
533A ALA 3.4 8.1 - - - +
534A ALA 3.2 0.4 - - - -
535A GLU* 1.3 77.0 - - - +
537A LEU* 1.3 61.7 + - + +
539A LYS* 3.7 30.5 - - - +
540A GLU* 2.9 63.0 + - + +
542A TYR* 4.2 9.1 + + - -
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Residues in contact with LEU 537 (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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452A MET* 3.9 10.5 - - + -
454A ILE* 3.9 30.5 - - + -
468A ALA* 4.8 8.5 - - + -
470A LEU* 4.2 24.5 - - + -
498A VAL* 5.3 2.2 - - + -
500A ALA* 3.8 26.0 - - + -
533A ALA 3.0 17.7 + - - +
534A ALA* 3.6 6.5 - - - +
536A TYR* 1.3 77.6 - - + +
538A ILE* 1.3 59.6 + - - +
541A GLY 3.5 1.7 + - - -
542A TYR* 2.9 46.1 + - + -
543A THR* 3.3 16.0 + - + -
548A LEU* 4.5 11.7 - - + -
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Residues in contact with ILE 538 (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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464A GLY* 5.7 0.2 - - - -
534A ALA 3.1 19.5 + - - +
535A GLU* 3.7 4.9 - - - +
537A LEU* 1.3 74.1 - - - +
539A LYS* 1.3 66.8 + - - +
541A GLY* 3.1 13.2 + - - -
543A THR* 3.5 25.7 - - + +
544A SER* 4.1 1.3 - - - +
545A PRO* 3.8 44.2 - - + -
548A LEU* 4.4 4.0 - - + -
570A LEU* 3.6 34.3 - - + +
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Residues in contact with LYS 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A PRO* 5.5 10.1 - - - +
535A GLU* 2.8 20.5 + - + +
536A TYR* 3.3 39.4 - - - +
538A ILE* 1.3 76.3 - - - +
540A GLU* 1.3 88.6 + - - +
541A GLY 3.3 1.2 + - - -
784A SGM 5.7 7.9 - - - +
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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