Contacts of the helix formed by residues 505 - 523 (chain B) in PDB entry 5FLZ
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 505 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B THR* 6.1 0.5 - - - +
503B PRO* 3.8 9.0 - - - +
504B SER* 1.4 83.3 - - - +
506B SER* 1.3 65.5 + - - +
507B LEU* 3.4 2.9 - - + +
508B PRO* 3.4 30.1 - - + +
509B ASN* 4.1 4.3 + - - +
545B VAL* 5.5 4.7 - - - +
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Residues in contact with SER 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP* 1.3 76.2 - - - +
507B LEU* 1.3 66.7 + - - +
509B ASN* 3.3 21.9 + - - +
510B TYR* 4.2 2.3 + - - +
545B VAL* 6.4 0.2 - - - -
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP* 4.3 2.1 - - + +
506B SER* 1.3 79.1 - - - +
508B PRO* 1.3 73.8 - - + +
509B ASN 3.0 2.0 - - - -
510B TYR* 3.0 48.7 + - + -
511B LYS* 3.4 21.0 + - - +
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Residues in contact with PRO 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ILE* 4.1 21.5 - - + +
500B LEU* 6.4 0.2 - - + -
502B THR* 6.5 0.7 - - - -
503B PRO 4.9 4.0 - - - +
504B SER* 4.7 8.3 - - - -
505B ASP* 3.4 35.2 - - + +
507B LEU* 1.3 93.3 - - + +
509B ASN* 1.4 51.1 + - - +
511B LYS* 3.1 22.9 + - + +
512B LEU* 2.8 45.0 + - + +
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Residues in contact with ASN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ASP 4.1 2.2 + - - +
506B SER* 3.3 19.0 + - - +
507B LEU 3.0 0.4 - - - -
508B PRO* 1.4 73.0 - - - +
510B TYR* 1.3 55.7 + - - +
512B LEU* 3.5 11.0 + - - +
513B THR* 2.8 39.2 + - - -
542B ASP* 5.8 0.6 + - - -
543B ALA* 3.3 27.5 + - - +
544B ARG* 4.2 6.4 + - - +
545B VAL* 3.0 34.4 + - + +
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Residues in contact with TYR 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B SER 4.2 2.1 + - - +
507B LEU* 3.0 48.8 + - + -
509B ASN* 1.3 79.0 - - - +
511B LYS* 1.4 92.1 + - + +
513B THR* 3.1 9.3 + - - -
514B ARG* 3.0 27.1 + - + +
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Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ILE* 3.6 36.3 - - + -
507B LEU* 3.6 16.9 - - - +
508B PRO* 3.1 31.6 + - + +
510B TYR* 1.4 110.9 + - + +
512B LEU* 1.4 53.2 + - - +
514B ARG* 3.1 8.9 + - - +
515B VAL* 2.8 38.8 + - + +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B LEU* 5.6 2.6 - - + +
496B ALA* 4.0 28.3 - - + -
499B ILE* 4.6 12.3 - - + -
500B LEU* 4.1 28.0 - - + -
508B PRO* 2.8 35.3 + - + +
509B ASN* 3.6 9.6 - - - +
511B LYS* 1.4 70.9 - - - +
513B THR* 1.4 59.1 + - - +
515B VAL* 3.4 10.3 + - + +
516B LEU* 2.8 28.1 + - - +
543B ALA* 4.7 10.5 - - + -
545B VAL* 6.3 1.8 - - + -
558B PHE* 4.4 27.2 - - + -
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Residues in contact with THR 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B ASN* 2.8 20.5 + - - -
510B TYR* 3.1 9.8 + - - -
512B LEU* 1.4 76.5 - - - +
514B ARG* 1.3 54.5 + - - +
516B LEU* 3.2 13.7 + - + +
517B GLN* 3.0 45.4 + - + +
541B LEU 5.6 1.3 - - - +
542B ASP* 4.1 19.9 + - - +
543B ALA* 3.5 23.8 + - - +
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B TYR* 3.0 19.1 + - + +
511B LYS* 3.1 12.3 + - - +
513B THR* 1.3 72.1 - - - +
515B VAL* 1.4 52.5 + - + +
517B GLN* 3.2 31.3 + - - +
518B GLU* 2.9 51.0 + - + +
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Residues in contact with VAL 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 4.0 23.6 - - + +
495B LYS* 3.4 40.8 - - + +
496B ALA* 4.2 9.6 - - + +
499B ILE* 5.1 7.6 - - + -
511B LYS* 2.8 30.0 + - + +
512B LEU* 3.5 11.4 - - + +
514B ARG* 1.4 70.7 - - - +
516B LEU* 1.4 49.7 + - - +
518B GLU* 3.3 18.0 - - - +
519B ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PHE* 3.8 17.8 - - + -
492B LEU* 3.6 25.1 - - + -
512B LEU 2.8 14.7 + - - +
513B THR* 3.2 15.7 + - + +
515B VAL* 1.4 70.8 - - - +
517B GLN* 1.3 65.9 + - + +
519B ALA* 3.3 7.0 + - - +
520B VAL* 3.2 29.1 + - + +
541B LEU* 4.1 40.2 - - + +
542B ASP* 4.4 12.8 - - - +
543B ALA* 4.4 6.3 - - + +
558B PHE* 5.6 1.3 - - + -
560B LEU* 4.1 25.1 - - + -
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Residues in contact with GLN 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B THR* 3.0 37.7 + - + +
514B ARG* 3.2 34.4 + - - +
516B LEU* 1.3 75.4 - - + +
518B GLU* 1.4 62.9 + - + +
520B VAL* 3.2 20.1 + - - +
521B GLN* 3.3 19.8 + - - +
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Residues in contact with GLU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495B LYS* 3.7 31.1 - - - +
514B ARG* 2.9 43.0 + - + +
515B VAL* 3.1 18.6 + - - +
517B GLN* 1.4 78.1 - - + +
519B ALA* 1.4 54.1 + - - +
521B GLN* 3.3 18.9 + - - +
522B LEU* 2.9 30.1 + - - +
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B PHE* 3.5 44.2 - - + +
491B ALA* 4.7 3.8 - - + -
492B LEU* 4.3 15.0 - - + +
495B LYS* 5.1 1.3 - - - +
515B VAL 2.8 17.5 + - - +
516B LEU* 3.5 9.0 - - - +
518B GLU* 1.4 73.2 - - - +
520B VAL* 1.3 62.6 + - - +
522B LEU* 3.6 7.7 - - - +
523B SER* 3.0 20.1 + - - -
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B PHE* 3.8 10.9 - - + -
516B LEU* 3.2 21.8 + - + +
517B GLN* 3.2 10.7 + - - +
519B ALA* 1.3 75.6 - - - +
521B GLN* 1.4 62.9 + - + +
523B SER* 3.5 10.3 + - - -
524B SER 3.6 6.8 + - - -
525B LEU* 3.8 29.2 + - + +
526B ARG* 5.9 3.4 - - - +
532B PRO* 5.6 0.4 - - + -
537B VAL* 3.9 35.4 - - + +
538B ILE* 4.6 19.1 - - + -
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Residues in contact with GLN 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B GLN* 3.5 12.3 - - - +
518B GLU* 3.3 22.5 + - - +
519B ALA 3.3 0.2 - - - -
520B VAL* 1.4 75.8 - - + +
522B LEU* 1.4 58.6 + - - +
524B SER* 3.1 12.1 + - - -
525B LEU 5.5 3.1 - - - +
526B ARG* 5.6 8.7 - - - +
1D MET* 2.9 24.5 - - + +
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B ASP* 3.2 24.8 - - - +
491B ALA* 3.7 29.2 - - + -
495B LYS* 3.9 14.6 - - - +
518B GLU 2.9 17.3 + - - +
519B ALA* 3.3 6.0 + - - +
521B GLN* 1.4 75.0 - - - +
523B SER* 1.3 55.5 + - - +
524B SER* 3.2 4.2 + - - -
1D MET* 3.3 44.7 - - + +
2D GLY 5.0 2.0 - - - +
131D ASP* 6.5 0.9 - - + -
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Residues in contact with SER 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LYS* 3.7 14.7 - - - +
487B ASP* 3.6 17.4 - - - +
488B PHE* 3.5 30.6 + - - +
519B ALA 3.0 17.3 + - - -
520B VAL 3.7 6.7 - - - -
521B GLN 3.3 0.2 - - - -
522B LEU* 1.3 71.9 - - - +
524B SER* 1.3 74.8 + - - +
525B LEU* 4.0 17.9 - - - +
48D ASP* 3.6 6.2 - - - +
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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