Contacts of the helix formed by residues 509 - 522 (chain K) in PDB entry 3HX0
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420K ARG* 3.4 31.2 - - - +
508K GLY* 1.3 76.7 + - - -
510K ALA* 1.3 66.0 + - - +
511K ALA* 3.5 3.4 + - - +
512K PHE* 3.0 9.8 + - - +
513K ASN* 2.9 19.8 + - - -
573K ARG 2.8 19.2 + - - -
574K ASP 2.7 31.4 + - - -
703K D3T 4.7 2.5 - - - -
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Residues in contact with ALA 510 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508K GLY* 4.0 0.8 - - - -
509K SER* 1.3 73.7 - - - +
511K ALA* 1.3 62.5 + - - +
513K ASN* 3.1 14.5 + - - +
514K ALA* 3.0 21.7 + - - +
517K ARG* 4.6 2.8 + - - -
703K D3T 4.0 29.6 + - + +
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Residues in contact with ALA 511 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284K ASN* 4.5 7.0 - - - +
509K SER* 3.1 7.0 + - - +
510K ALA* 1.3 79.5 - - - +
512K PHE* 1.3 61.7 + - - +
514K ALA* 3.1 18.1 + - - +
515K SER* 3.1 13.9 + - - -
574K ASP 3.9 2.5 - - - +
575K TRP* 3.8 25.6 - - + +
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Residues in contact with PHE 512 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K LEU* 4.2 11.2 - - + -
508K GLY 3.7 13.9 - - - -
509K SER* 3.0 9.4 + - - +
511K ALA* 1.3 79.7 - - - +
513K ASN* 1.3 67.1 + - - +
515K SER* 2.5 24.9 + - - -
516K MET* 3.1 39.3 + - + +
560K PHE* 3.7 29.4 - + - -
565K LEU* 6.3 1.1 - - + -
568K ARG* 3.3 43.1 - - - -
573K ARG* 3.3 47.1 - - + +
575K TRP* 3.7 11.4 - - - +
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Residues in contact with ASN 513 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K LEU* 3.7 20.1 - - - +
505K TYR* 3.0 35.0 + - + +
508K GLY* 3.6 4.0 - - - -
509K SER 2.9 19.6 + - - +
510K ALA* 3.4 6.9 - - - +
512K PHE* 1.3 80.9 - - - +
514K ALA* 1.3 65.6 + - - +
516K MET* 3.1 11.3 + - - +
517K ARG* 2.9 42.5 + - - +
703K D3T 3.5 22.4 - - + -
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Residues in contact with ALA 514 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510K ALA 3.0 12.3 + - - +
511K ALA* 3.1 13.9 + - - +
513K ASN* 1.3 76.1 - - - +
515K SER* 1.3 64.5 + - - +
517K ARG* 3.2 25.8 + - - +
518K ALA* 2.9 22.0 + - - +
4L C 5.6 1.1 - - - +
5L A 4.4 6.8 + - - +
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Residues in contact with SER 515 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511K ALA 3.1 6.9 + - - -
512K PHE* 2.5 32.6 + - - -
514K ALA* 1.3 79.5 - - - +
516K MET* 1.3 68.0 + - - +
518K ALA* 2.9 11.3 + - - +
519K LEU* 2.7 25.4 + - - +
568K ARG* 5.5 1.2 + - - -
575K TRP 3.9 10.5 + - - -
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Residues in contact with MET 516 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504K LEU* 4.4 18.8 - - + -
512K PHE* 3.2 42.0 - - + +
513K ASN* 3.1 12.2 + - - +
515K SER* 1.3 82.5 + - - +
517K ARG* 1.3 58.4 + - - +
519K LEU* 3.1 5.4 + - - +
520K ALA* 2.8 31.6 + - - +
527K LEU* 4.0 16.2 - - + -
559K VAL* 4.4 2.5 - - + -
560K PHE* 4.2 29.2 - - + -
563K LEU* 3.6 27.4 - - + +
565K LEU* 4.3 22.0 - - + -
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Residues in contact with ARG 517 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505K TYR* 4.3 7.5 - - - -
510K ALA 4.6 2.8 + - - -
513K ASN* 2.9 30.2 + - - +
514K ALA* 3.3 28.4 - - - +
516K MET* 1.3 75.5 - - + +
518K ALA* 1.3 64.9 + - - +
520K ALA* 3.0 9.3 + - - +
521K LYS* 2.9 23.5 + - - +
526K SER* 5.8 0.7 - - - -
527K LEU* 3.7 30.4 + - + +
5L A 2.9 103.3 + - - +
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Residues in contact with ALA 518 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514K ALA 2.9 11.7 + - - +
515K SER* 2.9 14.0 + - - +
517K ARG* 1.3 75.8 - - - +
519K LEU* 1.3 61.2 + - - +
521K LYS* 3.3 23.3 + - - +
522K THR* 3.4 14.5 + - - +
4L C 6.2 2.9 - - - +
5L A 6.0 1.1 - - - -
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Residues in contact with LEU 519 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515K SER 2.7 15.6 + - - +
516K MET* 3.6 9.0 - - - +
518K ALA* 1.3 70.4 - - - +
520K ALA* 1.3 66.3 + - - +
522K THR* 2.7 27.2 + - - +
523K LYS* 3.2 23.3 - - - +
563K LEU* 3.6 24.0 - - + +
565K LEU* 3.3 51.4 - - + -
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Residues in contact with ALA 520 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516K MET 2.8 21.0 + - - +
517K ARG* 3.4 8.1 - - - +
519K LEU* 1.3 73.4 - - - +
521K LYS* 1.3 60.7 + - - +
523K LYS* 3.1 7.3 + - - +
525K MET* 2.9 43.8 + - + +
526K SER 4.3 2.7 - - - +
527K LEU* 4.4 14.1 - - + +
532K LEU* 4.7 0.4 - - + -
563K LEU* 3.5 27.4 - - + -
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Residues in contact with LYS 521 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517K ARG 2.9 12.1 + - - +
518K ALA* 3.3 15.9 - - - +
520K ALA* 1.3 72.6 - - - +
522K THR* 1.3 60.2 + - + +
523K LYS 2.8 11.4 + - - -
524K GLY* 3.1 12.6 + - - -
525K MET 3.5 10.3 + - - +
3L G 3.3 16.6 + - - -
4L C 3.0 35.3 + - - +
5L A 6.2 1.1 - - - -
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Residues in contact with THR 522 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518K ALA 3.6 12.1 - - - +
519K LEU* 2.7 24.2 + - - +
521K LYS* 1.3 77.7 - - + +
523K LYS* 1.3 72.1 + - - +
524K GLY 3.7 0.2 - - - -
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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