Contacts of the helix formed by residues 509 - 523 (chain I) in PDB entry 5IIO
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 509 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420I ARG* 3.7 27.2 - - - +
507I THR 3.6 0.6 + - - -
508I GLY* 1.3 75.3 + - - -
510I ALA* 1.3 54.9 + - - +
511I HIS* 3.1 16.6 + - - +
512I PHE* 3.0 7.0 + - - +
513I ASN* 2.7 33.7 + - - -
573I ARG 2.9 15.9 + - - -
574I ASP 2.7 29.1 + - - -
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Residues in contact with ALA 510 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508I GLY* 4.1 0.4 - - - -
509I SER* 1.3 74.3 - - - +
511I HIS* 1.3 63.7 + - + +
513I ASN* 3.5 11.4 + - - +
514I ARG* 3.0 34.5 + - - +
517I ARG* 4.9 1.9 + - - -
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Residues in contact with HIS 511 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I LEU* 5.9 0.2 - - + -
280I ALA* 4.1 22.0 - - + +
284I ASN* 3.6 19.8 + - - +
509I SER* 3.1 8.0 + - - +
510I ALA* 1.3 78.7 - - + +
512I PHE* 1.3 61.4 + - - +
514I ARG* 2.7 40.5 + - - +
515I SER* 3.0 31.8 + - - -
574I ASP 4.1 11.0 - - - -
575I TRP* 3.7 19.1 - + + -
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Residues in contact with PHE 512 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504I LEU* 4.4 11.7 - - + -
508I GLY 3.6 15.0 - - - -
509I SER* 3.0 11.8 + - - +
511I HIS* 1.3 74.2 - - - +
513I ASN* 1.3 65.1 + - - +
515I SER* 3.1 5.9 + - - -
516I MET* 2.9 60.2 + - + +
560I PHE* 3.7 29.6 - + - -
565I LEU* 6.0 0.2 - - + -
568I ARG* 3.6 41.7 - - + -
573I ARG* 3.3 47.1 - - + +
575I TRP* 3.9 15.6 - - - +
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Residues in contact with ASN 513 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504I LEU* 3.5 19.2 - - - +
505I TYR* 2.8 44.8 + - - -
508I GLY* 3.5 9.2 - - - -
509I SER 2.7 23.1 + - - +
510I ALA* 3.6 9.1 - - - +
512I PHE* 1.3 78.7 - - - +
514I ARG* 1.3 56.9 + - - +
516I MET* 3.2 7.4 + - - +
517I ARG* 2.9 51.2 + - - +
527I LEU* 5.6 0.2 - - - +
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Residues in contact with ARG 514 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I LEU* 3.4 40.6 - - - +
280I ALA* 5.1 1.0 - - - +
281I LYS* 4.0 21.9 - - - +
284I ASN* 5.0 0.8 - - - +
510I ALA* 3.0 24.4 + - - +
511I HIS* 2.7 45.2 + - - +
512I PHE 3.2 0.2 - - - -
513I ASN* 1.3 78.1 - - - +
515I SER* 1.3 61.9 + - - +
517I ARG* 3.6 17.6 + - - +
518I ALA* 3.1 23.9 + - + +
4J C 4.2 10.3 - - - +
5J 8OG 3.6 21.2 + - - +
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Residues in contact with SER 515 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511I HIS* 3.0 14.5 + - - +
512I PHE* 3.1 10.3 + - - -
514I ARG* 1.3 77.1 + - - +
516I MET* 1.3 61.0 + - - +
518I ALA* 3.3 7.0 + - - +
519I LEU* 3.0 28.6 + - - +
568I ARG* 6.3 1.3 - - - -
575I TRP 3.9 15.1 + - - -
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Residues in contact with MET 516 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504I LEU* 4.4 12.1 - - + -
512I PHE* 2.9 50.9 + - + +
513I ASN* 3.7 6.5 - - - +
515I SER* 1.3 74.0 - - - +
517I ARG* 1.3 60.7 + - - +
519I LEU* 3.3 5.3 + - - +
520I ALA* 2.9 29.8 + - - +
527I LEU* 3.9 21.6 - - + +
559I VAL* 4.7 1.8 - - + -
560I PHE* 3.9 25.1 - - + -
563I LEU* 3.6 27.8 - - + +
565I LEU* 3.6 25.1 - - + -
568I ARG* 6.1 0.2 - - - -
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Residues in contact with ARG 517 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505I TYR* 4.4 7.9 - - - -
510I ALA 4.9 1.8 + - - -
513I ASN* 2.9 39.2 + - - +
514I ARG* 3.7 19.7 - - - +
516I MET* 1.3 75.7 - - - +
518I ALA* 1.3 63.4 + - - +
520I ALA* 3.3 7.5 + - - +
521I LYS* 3.0 23.6 + - - +
525I MET 4.9 0.3 - - - +
526I SER* 6.0 0.2 - - - -
527I LEU* 3.5 28.5 - - + +
5J 8OG 2.9 109.5 + - - +
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Residues in contact with ALA 518 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514I ARG* 3.1 19.4 + - + +
515I SER* 3.6 7.2 - - - +
516I MET 3.2 0.4 - - - -
517I ARG* 1.3 77.6 - - - +
519I LEU* 1.3 61.7 + - - +
521I LYS* 3.2 18.8 + - - +
522I THR* 3.2 18.3 + - - +
4J C 6.4 3.6 - - - -
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Residues in contact with LEU 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515I SER 3.0 15.7 + - - +
516I MET* 3.6 8.5 - - - +
518I ALA* 1.3 76.3 - - - +
520I ALA* 1.3 62.4 + - - +
522I THR* 2.5 31.4 + - - +
523I LYS* 3.3 17.3 + - + +
563I LEU* 3.5 36.6 - - + +
565I LEU* 3.5 37.5 - - + -
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Residues in contact with ALA 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516I MET 2.9 18.3 + - - +
517I ARG 3.6 4.7 - - - +
519I LEU* 1.3 76.3 - - - +
521I LYS* 1.3 60.9 + - - +
523I LYS* 3.0 7.7 + - - +
525I MET* 2.8 44.5 + - + +
527I LEU* 4.2 22.0 - - + +
532I LEU* 4.4 0.2 - - + -
563I LEU* 3.7 25.7 - - + +
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Residues in contact with LYS 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517I ARG 3.0 13.7 + - - +
518I ALA* 3.3 14.8 - - - +
519I LEU 3.1 0.2 - - - -
520I ALA* 1.3 76.4 - - - +
522I THR* 1.3 62.7 + - + +
524I GLY* 3.2 13.0 + - - -
525I MET 3.4 9.8 + - - +
3J G 3.3 16.0 + - - -
4J C 2.8 33.7 + - - +
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Residues in contact with THR 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518I ALA 3.5 14.8 - - - +
519I LEU* 2.5 26.5 + - - +
521I LYS* 1.3 76.8 - - + +
523I LYS* 1.3 65.3 + - - +
524I GLY 3.2 4.0 + - - -
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Residues in contact with LYS 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN* 4.9 13.1 - - - +
519I LEU* 3.6 25.4 - - + +
520I ALA* 3.0 9.4 + - - +
522I THR* 1.3 79.6 - - - +
524I GLY* 1.3 62.5 + - - +
525I MET* 3.2 27.6 + - + +
562I LEU 5.3 2.7 - - - +
563I LEU* 3.5 32.7 + - + +
564I GLY* 4.9 4.9 - - - -
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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
------------------------------------------------------------
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