Contacts of the helix formed by residues 516 - 525 (chain B) in PDB entry 5FS9
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 ASN 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B PRO 3.5 4.7 - - - +
489B ASP* 3.7 15.5 - - - +
512B THR 4.9 0.6 + - - -
513B ALA 2.9 28.3 + - - -
514B GLN 3.0 6.5 + - - +
515B ASP* 1.3 76.5 - - - +
517B PRO* 1.3 76.7 - - + +
518B LYS* 3.0 14.2 + - - +
519B SER* 2.8 33.6 + - - -
520B ALA* 3.1 17.8 + - - +
580B ASN* 4.1 0.9 - - - -
582B PHE* 3.2 12.9 - - - -
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Residues in contact with PRO 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TRP* 3.6 21.5 - - + +
485B ASP* 3.5 12.8 - - - +
487B GLY 3.8 5.2 - - - +
488B PRO 3.2 15.3 - - - +
489B ASP 3.6 0.2 - - - -
490B VAL 3.5 33.0 - - - +
491B GLY* 3.6 9.4 - - - +
516B ASN* 1.3 84.5 - - + +
518B LYS* 1.3 50.5 + - - +
520B ALA* 3.4 4.6 + - + +
521B THR* 2.7 40.1 + - - +
529B ARG* 3.7 12.8 - - - +
582B PHE* 3.5 11.9 - - + -
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Residues in contact with LYS 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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196B TRP* 3.5 35.9 + - + +
197B ASN* 4.7 1.0 - - - +
488B PRO* 3.1 31.3 + - + +
516B ASN* 3.0 9.9 + - - +
517B PRO* 1.3 75.6 - - - +
519B SER* 1.3 59.0 + - - +
521B THR* 3.1 2.3 + - - -
522B GLU* 2.9 61.9 + - - +
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Residues in contact with SER 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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513B ALA 3.4 7.6 + - - -
514B GLN* 3.5 33.7 - - - +
516B ASN* 2.8 25.3 + - - -
518B LYS* 1.3 76.2 - - - +
520B ALA* 1.3 58.2 + - - +
522B GLU* 3.7 16.6 + - - +
523B GLN* 2.8 36.3 + - - +
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLN 4.5 2.1 + - - +
516B ASN 3.1 7.7 + - - +
517B PRO* 3.6 7.4 - - + +
519B SER* 1.3 75.8 - - - +
521B THR* 1.3 60.4 + - - +
522B GLU 3.2 0.2 - - - -
523B GLN* 3.2 10.0 + - - +
524B SER* 2.9 33.2 + - - -
529B ARG* 5.2 6.3 - - + -
582B PHE* 3.6 41.7 - - + -
583B ASN* 4.6 6.6 + - - +
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Residues in contact with THR 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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195B GLN* 3.7 17.0 - - + -
196B TRP* 3.5 17.7 - - - +
197B ASN* 2.6 57.6 + - - +
517B PRO* 2.7 26.6 + - - +
518B LYS 3.7 3.4 - - - -
520B ALA* 1.3 73.1 - - - +
522B GLU* 1.3 55.0 + - - +
525B GLY 3.0 15.9 + - - -
526B THR 3.5 25.8 + - - +
527B GLY* 3.8 5.2 - - - +
529B ARG* 5.6 3.8 + - - +
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Residues in contact with GLU 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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197B ASN* 3.6 25.1 + - + +
199B LYS* 5.5 1.9 - - - -
518B LYS* 2.9 53.1 + - - +
519B SER* 3.8 16.5 + - - +
521B THR* 1.3 78.5 - - - +
523B GLN* 1.3 60.8 + - + +
525B GLY* 4.2 3.6 + - - -
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Residues in contact with GLN 523 (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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514B GLN* 3.4 45.5 + - - +
519B SER* 2.8 26.5 + - - +
520B ALA* 3.2 7.6 + - - +
522B GLU* 1.3 81.1 - - + +
524B SER* 1.3 60.2 + - - +
525B GLY 3.4 0.4 + - - -
583B ASN* 3.7 18.9 + - - +
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Residues in contact with SER 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ALA 2.9 16.4 + - - -
523B GLN* 1.3 76.7 - - - +
525B GLY* 1.3 60.4 + - - +
526B THR* 3.0 40.8 + - - +
583B ASN* 4.9 12.1 - - - -
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Residues in contact with GLY 525 (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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195B GLN* 2.9 18.2 + - - +
197B ASN* 3.7 1.8 - - - -
199B LYS* 3.3 32.9 - - - +
521B THR 3.0 13.1 + - - -
522B GLU 4.2 2.1 + - - -
523B GLN 3.4 2.8 + - - -
524B SER* 1.3 77.7 - - - +
526B THR* 1.3 58.4 + - - +
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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