Contacts of the helix formed by residues 514 - 532 (chain A) in PDB entry 1F9O
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 ASP 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A ASN* 4.0 5.0 + - - -
508A TYR* 3.8 19.0 - - + +
509A ALA* 3.6 7.2 + - - +
512A SER* 3.2 17.2 + - - +
513A GLY* 1.3 74.4 - - - +
515A GLU* 1.3 66.3 + - - +
516A THR* 3.6 14.5 + - - -
517A SER* 2.8 44.3 + - - +
518A ARG* 3.1 8.5 + - - -
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Residues in contact with GLU 515 (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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513A GLY 2.7 11.0 + - - +
514A ASP* 1.3 71.8 - - - +
516A THR* 1.3 59.2 + - - +
518A ARG* 2.7 47.8 + - - +
519A GLN* 2.8 49.8 + - - +
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Residues in contact with THR 516 (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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446A ASN* 4.2 18.8 - - + +
514A ASP* 3.1 16.1 + - - -
515A GLU* 1.3 78.8 - - - +
517A SER* 1.3 63.2 + - - +
519A GLN* 3.6 14.9 + - + +
520A ASN* 3.1 37.8 + - - +
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Residues in contact with SER 517 (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 ALA* 4.4 0.2 - - - +
446A ASN* 3.5 17.0 + - - +
505A LEU* 3.5 25.2 - - - +
508A TYR* 3.3 22.3 - - - -
509A ALA* 3.8 14.1 - - - -
514A ASP* 2.8 30.5 + - - -
516A THR* 1.3 75.6 - - - +
518A ARG* 1.3 63.3 + - - +
520A ASN* 3.5 0.9 + - - +
521A ALA* 3.0 25.3 + - - +
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Residues in contact with ARG 518 (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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505A LEU 5.1 0.2 - - - -
506A THR* 5.9 0.4 - - - +
509A ALA* 3.7 14.3 - - + +
514A ASP 3.1 6.8 + - - +
515A GLU* 2.7 46.0 + - - +
517A SER* 1.3 78.0 - - - +
519A GLN* 1.3 77.0 + - - +
521A ALA* 3.3 6.3 + - - +
522A GLN* 3.1 38.6 + - - +
623A TYR* 2.7 36.7 + - + +
627A PHE* 3.5 43.1 - - + -
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Residues in contact with GLN 519 (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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515A GLU* 2.8 42.3 + - - +
516A THR* 3.6 15.7 + - + +
518A ARG* 1.3 95.4 - - - +
520A ASN* 1.3 64.6 + - - +
522A GLN* 3.8 3.9 - - - +
523A LYS* 2.9 49.4 + - + +
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Residues in contact with ASN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ASN* 3.0 41.7 + - - +
449A ILE* 4.0 18.5 - - + +
451A PHE* 4.0 15.9 - - + -
505A LEU* 4.3 7.2 - - + -
516A THR* 3.1 24.6 + - - +
517A SER 3.9 2.9 - - - +
519A GLN* 1.3 80.5 - - - +
521A ALA* 1.3 65.9 + - - +
523A LYS* 3.1 12.2 + - - +
524A LEU* 2.9 30.8 + - - +
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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
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502A ALA* 3.6 20.7 - - - +
505A LEU* 3.9 12.5 - - + +
506A THR* 3.5 27.4 - - - +
517A SER 3.0 17.7 + - - +
518A ARG* 3.7 5.2 - - - +
520A ASN* 1.3 76.9 - - - +
522A GLN* 1.3 58.3 + - - +
524A LEU* 3.6 4.3 + - - +
525A LEU* 3.2 32.8 + - - +
623A TYR* 5.0 3.4 - - + -
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Residues in contact with GLN 522 (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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9A TYR* 2.9 40.5 + - + +
518A ARG* 3.1 28.4 + - - +
519A GLN* 4.0 5.1 - - - +
521A ALA* 1.3 76.7 - - - +
523A LYS* 1.3 61.9 + - - +
525A LEU* 3.4 5.3 + - - +
526A ASP* 2.8 44.0 + - - +
623A TYR* 3.7 30.2 + - + +
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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
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451A PHE* 3.5 49.6 - - + +
519A GLN* 2.9 44.4 + - + +
520A ASN* 3.1 7.6 + - - +
522A GLN* 1.3 78.8 - - - +
524A LEU* 1.3 54.0 + - - +
526A ASP* 3.3 6.9 + - - +
527A ALA* 2.7 36.9 + - - +
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Residues in contact with LEU 524 (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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449A ILE* 4.4 14.4 - - + -
451A PHE* 3.9 18.8 - - + -
457A PHE* 3.8 36.3 - - + -
459A ILE* 4.7 3.4 - - + -
498A ALA* 3.8 17.7 - - + +
501A LEU* 3.7 32.3 - - + -
502A ALA* 4.2 12.3 - - + +
505A LEU* 5.0 1.1 - - + -
520A ASN 2.9 20.2 + - - +
521A ALA* 3.6 5.6 - - - +
523A LYS* 1.3 77.5 - - - +
525A LEU* 1.3 63.0 + - - +
527A ALA* 3.3 3.0 + - - +
528A MET* 3.0 33.9 + - + +
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Residues in contact with LEU 525 (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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9A TYR* 4.6 10.5 - - + -
12A ARG* 4.4 1.1 + - - -
502A ALA* 3.9 14.6 - - + -
506A THR* 5.2 1.6 - - - +
521A ALA 3.2 17.5 + - - +
522A GLN* 3.8 5.2 - - - +
524A LEU* 1.3 78.3 - - - +
526A ASP* 1.3 59.2 + - - +
528A MET* 3.5 8.5 + - + +
529A TRP* 3.0 29.7 + - - +
616A PHE* 4.1 17.7 - - + -
619A ALA* 3.8 31.4 - - + +
620A ASN* 3.7 25.4 - - - +
623A TYR* 3.8 36.8 - - + -
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Residues in contact with ASP 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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9A TYR* 2.8 28.5 + - - -
12A ARG* 2.9 23.3 + - - +
522A GLN* 2.8 33.7 + - - +
523A LYS* 3.7 6.4 - - - +
525A LEU* 1.3 72.6 - - - +
527A ALA* 1.3 67.0 + - - +
529A TRP* 3.2 0.9 + - - -
530A ASN* 2.9 40.5 + - - +
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Residues in contact with ALA 527 (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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451A PHE* 4.6 7.2 - - + -
455A GLY 3.7 16.4 - - - +
457A PHE* 3.7 24.9 - - + -
523A LYS 2.7 22.2 + - - +
524A LEU* 3.5 5.6 - - - +
526A ASP* 1.3 72.9 - - - +
528A MET* 1.3 56.2 + - - +
530A ASN* 5.1 0.7 - - - -
531A ASN* 2.9 33.6 + - - +
532A TYR* 3.6 8.5 - - - -
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Residues in contact with MET 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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457A PHE* 3.7 17.3 - - + -
495A LEU* 3.7 23.8 - - + +
498A ALA* 3.7 23.6 - - + +
499A SER* 3.1 44.0 - - - +
524A LEU* 3.0 25.5 + - + +
525A LEU* 4.4 5.8 - - + -
527A ALA* 1.3 76.1 - - - +
529A TRP* 1.3 62.5 + - - +
532A TYR* 3.0 34.0 + - + +
533A SER* 3.6 3.1 + - - -
538A ILE* 4.1 7.5 - - + +
616A PHE* 3.7 27.6 - - + -
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Residues in contact with TRP 529 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP 5.5 0.2 - - - -
12A ARG* 3.6 74.8 - - + +
15A SER* 3.7 28.0 - - - -
16A MET* 4.8 9.0 - - + -
19A LYS* 5.7 5.6 - - - -
525A LEU 3.0 19.5 + - - +
526A ASP 3.8 2.7 - - - +
528A MET* 1.3 78.0 - - - +
530A ASN* 1.3 77.4 + - - +
533A SER* 2.7 36.6 + - - -
616A PHE* 3.9 21.0 - + + -
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Residues in contact with ASN 530 (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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12A ARG* 4.8 5.9 + - - +
526A ASP* 2.9 35.8 + - - +
527A ALA* 5.1 0.2 - - - -
529A TRP* 1.3 96.2 + - - +
531A ASN* 1.3 71.6 + - - +
532A TYR 3.7 0.2 - - - -
533A SER* 5.0 1.6 + - - -
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Residues in contact with ASN 531 (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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454A ASP 3.8 5.8 + - - +
455A GLY* 2.8 47.3 + - - -
456A THR* 3.7 4.5 - - + +
527A ALA* 2.9 19.7 + - - +
530A ASN* 1.3 87.7 - - - +
532A TYR* 1.3 76.8 + - + +
533A SER 3.8 1.1 - - - -
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Residues in contact with TYR 532 (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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456A THR* 3.3 36.8 - - + +
457A PHE* 3.6 23.7 + + - -
493A THR* 3.6 25.0 + - + +
495A LEU* 4.2 16.6 - - + -
527A ALA 3.6 16.6 - - - -
528A MET* 3.0 20.0 + - - +
531A ASN* 1.3 92.6 - - + +
533A SER* 1.3 66.5 + - - +
534A ASP* 4.8 0.2 - - - +
538A ILE* 3.1 6.0 - - + -
539A SER* 2.9 45.7 + - - +
540A THR* 3.8 21.8 - - - -
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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
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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