Contacts of the helix formed by residues 499 - 516 (chain B) in PDB entry 1F89
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 THR 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B ARG* 3.2 31.7 + - - +
495B PHE* 3.4 20.6 - - + -
496B ASN* 2.9 44.4 + - - +
498B VAL* 1.3 77.4 - - - +
500B GLY* 1.3 67.8 + - - +
502B LEU* 3.3 7.6 + - - +
503B HIS* 3.1 20.9 + - - +
532B TYR* 5.0 0.2 - - - +
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Residues in contact with GLY 500 (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 PHE* 3.9 13.9 - - - -
496B ASN 2.7 20.7 + - - -
499B THR* 1.3 75.0 - - - +
501B PRO* 1.3 65.1 - - - +
504B TRP* 3.0 27.3 + - - +
505B HIS* 4.6 1.7 + - - -
535B TYR* 3.4 25.3 + - - -
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Residues in contact with PRO 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B THR 3.3 26.5 - - - +
498B VAL 3.5 8.7 - - - +
500B GLY* 1.3 89.4 - - - +
502B LEU* 1.3 65.3 + - + +
505B HIS* 5.6 3.1 + - - +
526B ARG* 5.7 0.2 - - - +
535B TYR* 3.3 31.2 - - + +
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Residues in contact with LEU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 3.9 19.2 + - - -
244A ARG* 3.9 48.0 - - + +
498B VAL* 4.2 14.1 - - + +
499B THR* 3.3 10.2 + - - +
500B GLY 3.1 0.4 - - - -
501B PRO* 1.3 89.5 - - + +
503B HIS* 1.3 88.8 + - + +
506B LEU* 4.6 2.3 + - - +
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Residues in contact with HIS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.7 26.6 - - + +
244A ARG* 2.7 39.2 + - + +
274A VAL* 5.0 10.5 - - + -
473B ARG* 2.7 31.5 + - - +
495B PHE* 4.6 1.1 - - + -
499B THR* 3.1 6.7 + - - +
502B LEU* 1.3 101.6 - - + +
504B TRP* 1.3 58.9 + - - +
505B HIS 3.6 1.8 - - - -
506B LEU* 3.3 9.7 + - + +
507B LEU* 2.8 51.5 + - + +
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Residues in contact with TRP 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B MET* 4.8 2.0 - - - -
493B SER* 3.7 20.4 - - - -
495B PHE* 3.5 52.7 - + + -
499B THR 4.2 1.2 + - - -
500B GLY* 3.0 25.1 + - - +
503B HIS* 1.3 75.7 - - - +
505B HIS* 1.3 75.0 + + - +
507B LEU* 4.1 3.1 - - - +
508B ALA* 3.2 23.2 + - - +
521B LEU* 3.5 42.5 - - + +
523B SER* 3.7 24.7 - - - -
535B TYR* 3.8 21.3 - + + -
536B GLY 3.5 15.3 - - - -
537B HIS* 2.8 26.5 + - + +
538B SER* 4.3 1.1 - - - -
539B ILE* 4.3 6.6 - - + +
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLY 4.6 1.8 + - - -
501B PRO 5.6 2.8 + - - -
502B LEU 5.8 0.2 - - - -
503B HIS 3.6 0.4 - - - -
504B TRP* 1.3 85.9 - + - +
506B LEU* 1.3 62.5 + - - +
508B ALA* 3.7 3.6 - - - +
509B ARG* 3.0 38.3 + - - +
535B TYR* 3.4 34.7 + + - -
537B HIS* 4.2 5.2 - + - -
539B ILE* 4.7 6.7 - - + +
547B ILE* 3.7 24.5 - - + -
550B GLU* 2.6 30.7 + - - -
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Residues in contact with LEU 506 (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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206A LEU* 3.3 42.2 - - + +
209A ARG* 3.6 65.7 - - + +
210A SER* 4.2 8.3 - - - +
213A VAL* 4.0 19.5 - - + -
245A GLY* 4.8 0.2 - - - -
502B LEU 4.6 4.2 + - - +
503B HIS* 3.3 15.4 + - + +
505B HIS* 1.3 79.6 - - - +
507B LEU* 1.3 54.3 + - + +
509B ARG* 3.6 2.2 - - - +
510B SER* 2.7 38.2 + - - -
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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
----------------------------------------------------------
213A VAL* 4.7 13.7 - - + -
214A ASP* 4.0 20.2 - - - +
472B MET* 3.3 44.9 - - + +
473B ARG* 4.2 22.2 - - + -
495B PHE* 4.1 16.2 - - + -
503B HIS* 2.8 42.0 + - + +
506B LEU* 1.3 74.2 - - + +
508B ALA* 1.3 64.7 - - - +
510B SER* 4.1 4.7 - - - -
511B ARG* 2.9 34.2 + - + +
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Residues in contact with ALA 508 (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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472B MET* 3.9 2.6 - - - +
504B TRP 3.2 13.5 + - - +
505B HIS 3.7 1.3 - - - +
507B LEU* 1.3 81.7 - - - +
509B ARG* 1.3 61.2 + - - +
511B ARG* 3.6 0.4 + - - -
512B ALA* 3.4 19.9 + - - +
519B VAL* 3.7 17.9 - - + +
521B LEU* 3.5 17.5 - - + -
539B ILE* 3.2 36.3 - - + -
541B VAL* 3.7 7.4 - - + +
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Residues in contact with ARG 509 (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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202A LEU 3.9 15.8 + - - -
206A LEU* 3.6 40.7 - - + +
209A ARG* 6.0 1.8 - - - +
505B HIS* 3.0 24.0 + - - +
506B LEU* 4.0 2.8 - - - +
508B ALA* 1.3 73.7 - - + +
510B SER* 1.3 64.4 + - - +
512B ALA* 3.9 0.8 - - - +
513B VAL* 3.2 29.1 + - - +
541B VAL* 3.8 23.3 - - + -
544B ARG 5.4 0.2 + - - -
545B GLY* 2.8 32.4 + - - +
547B ILE* 4.3 18.3 - - + +
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Residues in contact with SER 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.5 8.1 - - - -
210A SER* 2.5 36.7 + - - -
211A ARG* 4.7 0.2 + - - -
214A ASP* 5.0 0.4 + - - -
506B LEU* 2.7 25.6 + - - -
507B LEU* 3.0 6.5 + - - -
509B ARG* 1.3 74.7 - - - +
511B ARG* 1.3 76.6 + - - +
513B VAL* 4.1 0.7 - - - +
514B ASP* 3.1 35.7 + - - +
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Residues in contact with ARG 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP* 2.8 43.2 + - - -
472B MET* 3.1 29.2 + - + +
473B ARG 3.8 4.4 - - - -
474B PHE 4.2 0.8 + - - -
475B PRO* 3.4 32.1 - - - +
478B ALA* 3.6 27.7 - - + +
489B MET* 5.8 0.7 - - + -
491B TYR* 4.0 18.1 + - + +
507B LEU* 2.9 23.9 + - + +
508B ALA* 4.0 4.3 - - - +
510B SER* 1.3 100.7 + - - +
512B ALA* 1.3 60.5 + - - +
514B ASP* 4.2 4.4 + - - +
515B ASN* 2.7 32.3 + - - +
517B VAL* 4.1 4.2 - - - +
519B VAL* 4.0 11.9 - - + -
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Residues in contact with ALA 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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508B ALA 3.4 4.2 + - - +
509B ARG* 4.0 3.8 - - - +
510B SER 3.2 0.6 - - - -
511B ARG* 1.3 79.7 - - - +
513B VAL* 1.3 56.2 + - + +
516B GLN* 2.7 32.4 + - - -
517B VAL 3.1 22.8 + - - +
519B VAL* 3.5 17.5 - - + +
541B VAL* 3.6 24.9 - - + -
542B ASP 3.7 9.0 - - - +
543B PRO 3.2 5.0 - - - +
545B GLY 5.1 0.4 - - - +
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Residues in contact with VAL 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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173A ARG* 5.4 4.0 - - + +
203A HIS* 3.6 31.4 - - + +
206A LEU* 3.8 9.2 - - + -
207A LEU* 4.8 16.4 - - + -
509B ARG 3.2 14.1 + - - +
510B SER* 4.3 1.6 - - - +
512B ALA* 1.3 74.0 - - - +
514B ASP* 1.3 66.6 + - - +
516B GLN* 3.6 15.8 - - - +
543B PRO 3.7 6.5 - - - +
544B ARG 3.2 34.3 - - - +
545B GLY* 3.3 11.7 - - - +
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Residues in contact with ASP 514 (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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173A ARG 4.2 7.8 - - - +
175A PRO* 3.6 21.5 - - + +
207A LEU* 4.0 13.3 - - - +
210A SER* 5.1 0.2 + - - -
211A ARG* 2.6 46.0 + - - -
214A ASP* 5.4 1.2 - - - +
475B PRO* 5.8 2.1 - - - +
479B MET* 6.3 0.9 - - + -
483B ARG* 5.7 0.9 + - - -
510B SER* 3.1 24.1 + - - +
511B ARG* 4.8 5.3 + - - +
513B VAL* 1.3 81.7 - - - +
515B ASN* 1.3 69.2 + - - +
516B GLN* 4.5 4.7 + - - +
578B LYS* 4.3 16.5 + - - -
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Residues in contact with ASN 515 (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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475B PRO* 6.1 0.3 - - - +
478B ALA* 3.5 13.9 + - - +
479B MET* 3.0 48.3 - - - +
482B ALA* 3.6 21.1 - - + +
483B ARG* 5.1 5.3 - - - +
511B ARG* 2.7 32.1 + - - +
514B ASP* 1.3 83.3 + - - +
516B GLN* 1.3 74.8 + - - +
517B VAL* 3.3 14.4 + - + +
571B ARG* 3.8 8.0 + - - -
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Residues in contact with GLN 516 (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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512B ALA 2.7 20.1 + - - -
513B VAL 3.6 15.5 - - - +
514B ASP 3.4 4.6 + - - +
515B ASN* 1.3 78.4 + - - +
517B VAL* 1.3 56.0 + - - +
543B PRO* 3.7 20.2 - - + +
567B ILE* 3.9 10.0 - - - +
570B PHE* 3.1 20.7 - - + +
571B ARG* 3.5 34.5 + - + +
574B VAL* 2.7 37.2 + - - +
575B PRO 4.4 0.2 + - - -
576B LEU* 3.7 32.3 - - - +
578B LYS* 5.9 1.0 - - - +
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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