Contacts of the helix formed by residues 516 - 525 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A PRO 3.8 4.9 - - - +
489A ASP* 3.6 16.6 - - - +
512A THR 5.0 0.2 + - - -
513A ALA 2.9 28.9 + - - -
514A GLN 3.1 1.7 + - - +
515A ASP* 1.3 79.6 - - - +
517A PRO* 1.3 75.7 - - + +
518A LYS* 3.0 12.2 + - - +
519A SER* 2.7 36.4 + - - -
520A ALA* 3.1 15.9 + - - +
580A ASN* 4.3 0.2 - - - -
582A PHE* 3.3 13.4 - - - -
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Residues in contact with PRO 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TRP* 3.8 15.3 - - + +
485A ASP* 3.6 12.8 - - - +
487A GLY 4.0 1.8 - - - +
488A PRO 3.2 16.8 - - - +
489A ASP 3.5 0.2 - - - -
490A VAL 3.4 40.4 - - - +
491A GLY* 3.5 7.6 - - - +
516A ASN* 1.3 84.6 - - + +
518A LYS* 1.3 53.4 + - - +
520A ALA* 3.4 2.8 + - + +
521A THR* 2.6 38.6 + - - -
529A ARG* 3.5 17.7 + - - +
582A PHE* 3.7 10.3 - - + -
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A TRP* 3.6 30.5 - - + +
197A ASN 5.9 0.4 - - - -
488A PRO* 3.0 30.3 + - + +
489A ASP* 5.6 1.8 - - - +
516A ASN* 3.0 9.0 + - - +
517A PRO* 1.3 75.4 - - - +
519A SER* 1.3 59.8 + - - +
521A THR* 3.1 4.5 + - - -
522A GLU* 3.1 50.6 + - - +
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Residues in contact with SER 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ALA 3.4 6.4 + - - -
514A GLN* 3.5 49.9 + - - +
516A ASN* 2.7 28.6 + - - -
518A LYS* 1.3 73.7 - - - +
520A ALA* 1.3 59.8 + - - +
522A GLU* 3.8 21.1 + - - +
523A GLN* 3.6 17.0 + - - +
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Residues in contact with ALA 520 (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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514A GLN 4.3 3.0 + - - +
516A ASN 3.1 8.5 + - - +
517A PRO* 3.6 8.1 - - + +
519A SER* 1.3 75.0 - - - +
521A THR* 1.3 64.8 + - - +
522A GLU 3.1 0.2 - - - -
523A GLN* 3.0 27.2 + - - +
524A SER* 3.7 5.7 + - - -
529A ARG* 5.6 3.6 - - - +
582A PHE* 3.6 41.7 - - + -
583A ASN* 4.6 9.4 + - - +
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Residues in contact with THR 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLN* 3.9 6.5 - - + -
196A TRP* 3.5 16.7 - - - +
197A ASN* 2.7 58.5 + - - +
517A PRO 2.6 29.0 + - - -
518A LYS 3.1 5.8 + - - -
520A ALA* 1.3 73.5 - - - +
522A GLU* 1.3 52.7 + - - +
523A GLN 3.2 0.2 - - - -
524A SER* 5.3 0.4 - - - -
525A GLY* 2.9 16.9 - - - -
526A THR 3.6 29.4 - - - +
527A GLY* 3.7 4.9 - - - +
529A ARG* 3.7 9.6 + - - -
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Residues in contact with GLU 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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197A ASN* 3.5 26.4 - - + +
514A GLN* 5.5 1.7 + - - -
518A LYS* 3.1 46.0 + - - +
519A SER* 3.8 20.4 + - - +
520A ALA 3.1 0.8 - - - -
521A THR* 1.3 76.0 - - - +
523A GLN* 1.3 61.0 + - + +
525A GLY* 4.7 2.0 - - - -
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Residues in contact with GLN 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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514A GLN* 4.8 13.9 + - - +
519A SER 3.6 14.5 + - - +
520A ALA* 3.0 11.8 + - - +
522A GLU* 1.3 81.5 - - - +
524A SER* 1.3 67.1 + - - +
525A GLY 3.7 0.8 + - - -
583A ASN* 2.8 31.6 + - - +
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Residues in contact with SER 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ALA 3.7 6.2 + - - -
521A THR 4.5 0.9 - - - -
523A GLN* 1.3 82.7 - - - +
525A GLY* 1.3 51.6 + - - -
526A THR* 3.2 39.2 - - - +
583A ASN* 4.7 9.7 + - - -
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Residues in contact with GLY 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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195A GLN* 3.0 13.5 + - - +
197A ASN* 3.4 14.9 + - - -
199A LYS* 3.9 15.2 + - - +
521A THR 2.9 20.0 - - - -
522A GLU 4.7 1.1 - - - -
523A GLN 3.7 2.6 + - - -
524A SER* 1.3 67.8 + - - +
526A THR* 1.3 59.9 + - - -
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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