Contacts of the helix formed by residues 502 - 515 (chain B) in PDB entry 4F1P
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 SER 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442B GLN* 5.2 0.2 - - - +
500B SER 3.9 0.4 + - - -
501B CYS* 1.3 78.9 - - - +
503B ARG* 1.3 64.3 + - - +
504B GLN* 3.3 19.7 + - - +
505B GLU* 3.3 22.0 + - - +
506B LYS* 3.1 20.9 + - - +
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Residues in contact with ARG 503 (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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442B GLN* 3.7 31.5 + - + +
445B GLY* 3.6 32.1 + - - -
446B ILE* 3.7 24.2 - - + +
449B SER* 4.5 7.5 + - - -
502B SER* 1.3 72.8 - - - +
504B GLN* 1.3 67.0 + - - +
506B LYS* 3.3 5.0 + - - +
507B GLU* 2.7 60.2 + - - +
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Residues in contact with GLN 504 (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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502B SER* 3.1 20.2 - - - +
503B ARG* 1.3 93.8 + - - +
505B GLU* 1.3 57.1 + - - +
507B GLU* 3.3 22.6 + - - +
508B ALA* 3.0 28.9 + - - +
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Residues in contact with GLU 505 (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* 4.7 6.5 - - - +
496B LYS 5.1 0.3 - - - +
497B PRO* 3.9 16.9 - - + +
501B CYS* 3.4 35.3 - - + +
502B SER* 3.3 19.0 + - - +
504B GLN* 1.3 78.8 - - - +
506B LYS* 1.3 59.0 + - - +
508B ALA* 3.5 6.9 + - + +
509B TRP* 3.0 28.1 + - - +
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Residues in contact with LYS 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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423B CYS* 3.1 24.5 - - + -
425B GLU* 4.5 3.0 + - - -
440B CYS* 4.5 0.6 - - - -
442B GLN* 3.0 30.2 + - + +
443B CYS* 3.8 22.0 - - - -
446B ILE* 3.8 11.9 - - + -
497B PRO* 4.2 19.7 - - + -
498B GLY 3.5 17.5 - - - -
499B PRO 2.9 20.6 + - - -
501B CYS* 3.4 20.2 - - + +
502B SER 3.1 12.0 + - - +
503B ARG* 3.7 3.8 - - - +
505B GLU* 1.3 74.5 - - - +
507B GLU* 1.3 59.1 + - - +
509B TRP* 3.3 0.9 + - - +
510B ILE* 2.9 38.3 + - + +
801B ZN 4.3 0.8 - - - -
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Residues in contact with GLU 507 (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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446B ILE* 3.9 30.8 - - + +
450B LEU* 6.0 0.2 - - - +
503B ARG* 2.7 56.0 + - - +
504B GLN* 3.4 19.6 + - - +
506B LYS* 1.3 71.2 - - - +
508B ALA* 1.3 58.7 + - - +
510B ILE* 3.3 1.9 + - - +
511B HIS* 2.8 31.8 + - - +
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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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504B GLN 3.0 16.1 + - - +
505B GLU* 3.8 7.2 - - + +
507B GLU* 1.3 73.9 - - - +
509B TRP* 1.3 65.1 + - - +
511B HIS* 3.5 5.8 + - - +
512B ALA* 3.0 25.6 + - - +
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Residues in contact with TRP 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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422B ASP* 3.8 17.2 + - + -
486B GLU* 3.2 28.7 + - + -
489B VAL* 3.6 30.7 - - + -
494B VAL* 3.9 17.7 - - + -
495B LYS 3.6 25.6 - - - -
496B LYS* 3.8 20.6 - - + +
497B PRO* 3.4 29.2 - - + +
505B GLU 3.0 19.0 + - - +
506B LYS 3.3 2.9 + - - +
508B ALA* 1.3 75.3 - - - +
510B ILE* 1.3 60.7 + - + +
512B ALA* 3.4 4.8 + - + +
513B LYS* 2.9 44.2 + - + +
519B PHE* 3.5 30.1 - + - -
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Residues in contact with ILE 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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422B ASP* 3.4 31.4 - - + +
443B CYS* 4.0 22.4 - - + +
446B ILE* 3.7 40.2 - - + -
447B HIS* 3.9 6.1 - - + +
450B LEU* 3.9 21.3 - - + -
506B LYS* 2.9 21.1 + - + +
507B GLU 3.8 2.9 - - - +
509B TRP* 1.3 75.0 - - + +
511B HIS* 1.3 64.7 + - - +
513B LYS* 4.2 5.2 - - - -
514B TYR* 3.0 40.8 + - + +
515B VAL* 4.8 0.9 - - - +
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Residues in contact with HIS 511 (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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450B LEU* 5.0 8.5 - - + +
507B GLU 2.8 18.3 + - - +
508B ALA* 3.9 6.9 + - - +
510B ILE* 1.3 77.1 - - - +
512B ALA* 1.3 58.5 + - - +
515B VAL* 3.0 51.3 + - + +
516B GLU* 2.9 35.9 + - + +
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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 3.0 18.8 + - - +
509B TRP* 3.7 4.5 - - + +
511B HIS* 1.3 76.4 + - - +
513B LYS* 1.3 55.2 + - - +
516B GLU* 3.5 23.5 - - - +
517B LYS 2.9 8.7 + - - -
518B LYS* 2.8 50.5 + - + +
519B PHE* 4.1 10.5 - - + -
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Residues in contact with LYS 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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421B CYS* 3.3 8.7 + - - -
422B ASP* 2.8 22.6 + - - +
481B ILE* 6.0 0.2 - - - -
482B ASN* 2.8 28.6 + - - -
485B TYR* 3.4 44.2 - - + +
486B GLU* 2.9 25.8 + - + +
509B TRP* 2.9 29.2 + - + +
510B ILE 3.7 3.8 - - - +
512B ALA* 1.3 76.8 - - - +
514B TYR* 1.3 87.9 + - + +
517B LYS* 3.4 18.7 - - - -
519B PHE* 3.9 15.7 - - + -
520B LEU* 4.9 0.3 - - - +
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Residues in contact with TYR 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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421B CYS* 3.7 12.8 - - - +
422B ASP* 2.5 30.8 + - - -
435B LEU* 3.6 31.1 - - + +
437B VAL* 4.6 1.9 - - - +
447B HIS* 3.4 27.2 + + - -
450B LEU* 4.5 13.2 - - + -
454B PHE* 3.8 14.4 - - + +
481B ILE* 5.0 3.8 - - + -
485B TYR* 3.8 30.5 - + - -
510B ILE* 3.0 32.5 + - + +
513B LYS* 1.3 101.8 + - + +
515B VAL* 1.3 62.4 + - + +
517B LYS* 3.1 28.2 + - - -
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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
----------------------------------------------------------
450B LEU* 4.1 24.5 - - + -
454B PHE* 3.8 41.7 - - + -
511B HIS* 3.0 43.9 + - + +
514B TYR* 1.3 79.0 - - + +
516B GLU* 1.3 64.9 + - - +
517B LYS* 3.2 9.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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