Contacts of the helix formed by residues 509 - 521 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420P ARG* 3.8 25.7 - - - +
507P THR 3.9 0.2 + - - -
508P GLY* 1.3 73.1 + - - -
510P ALA* 1.3 59.8 + - - +
511P ALA* 3.5 4.6 + - - +
512P PHE* 2.8 16.9 + - - +
513P ASN* 2.8 29.6 + - - -
573P ARG 3.3 20.6 + - - -
574P ASP* 3.4 19.6 + - - -
704P D3T 4.4 2.9 - - - -
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Residues in contact with ALA 510 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509P SER* 1.3 74.1 - - - +
511P ALA* 1.3 61.1 + - - +
513P ASN* 3.6 4.8 + - - +
514P ALA* 3.1 23.0 + - - +
517P ARG* 4.9 2.3 + - - -
704P D3T 3.6 43.6 - - + +
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Residues in contact with ALA 511 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284P ASN* 5.4 5.2 - - - +
509P SER* 3.0 4.5 + - - +
510P ALA* 1.3 77.6 - - - +
512P PHE* 1.3 62.1 + - - +
514P ALA* 3.3 8.1 + - - +
515P SER* 2.8 28.9 + - - +
574P ASP 3.6 20.0 - - - +
575P TRP* 4.8 8.7 - - + +
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Residues in contact with PHE 512 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504P LEU* 3.8 23.6 - - + -
508P GLY 3.5 11.4 - - - -
509P SER* 2.8 23.2 + - - +
511P ALA* 1.3 79.1 - - - +
513P ASN* 1.3 61.1 + - - +
515P SER* 3.0 8.3 + - - -
516P MET* 2.6 66.9 + - + +
560P PHE* 3.8 14.4 - + - -
568P ARG* 4.0 22.7 - - - -
573P ARG* 3.3 47.6 - - + +
574P ASP 4.3 1.7 + - - +
575P TRP 4.1 16.4 - - - -
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Residues in contact with ASN 513 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504P LEU* 3.5 20.6 - - - +
505P TYR* 2.9 38.3 + - + +
508P GLY* 3.3 8.2 - - - -
509P SER 2.8 23.3 + - - +
510P ALA* 3.9 4.3 - - - +
512P PHE* 1.3 81.3 - - - +
514P ALA* 1.3 53.4 + - - +
516P MET* 3.4 8.4 - - - +
517P ARG* 2.7 55.1 + - - +
527P LEU* 6.1 0.7 - - - +
704P D3T 3.6 15.0 - - - +
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Residues in contact with ALA 514 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510P ALA 3.1 16.6 + - - +
511P ALA* 3.5 7.9 - - - +
512P PHE 3.2 0.2 - - - -
513P ASN* 1.3 79.4 - - - +
515P SER* 1.3 62.4 + - - +
517P ARG* 3.4 18.3 + - - +
518P ALA* 3.1 23.6 + - - +
4Q C 5.3 1.8 - - - +
5Q A 4.0 15.1 + - - +
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Residues in contact with SER 515 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P LYS* 6.0 2.3 - - - -
511P ALA 2.8 18.6 + - - -
512P PHE* 3.0 10.6 + - - -
514P ALA* 1.3 73.1 - - - +
516P MET* 1.3 66.3 + - - +
517P ARG 3.0 2.8 + - - -
518P ALA* 3.2 8.1 + - - +
519P LEU* 3.2 22.1 + - - +
568P ARG* 6.2 0.9 - - - -
575P TRP* 4.0 20.5 + - - -
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Residues in contact with MET 516 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504P LEU* 4.9 6.1 - - + -
512P PHE* 2.6 52.6 + - + +
513P ASN* 3.4 11.0 - - - +
515P SER* 1.3 72.3 - - - +
517P ARG* 1.3 62.9 + - - +
519P LEU* 3.7 7.0 + - + +
520P ALA* 3.5 15.9 + - - +
527P LEU* 4.0 24.9 - - + +
559P VAL* 5.6 0.2 - - - -
560P PHE* 4.1 18.2 - - + -
563P LEU* 3.4 27.7 - - + +
565P LEU* 3.3 37.0 - - + -
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Residues in contact with ARG 517 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505P TYR* 4.3 6.7 - - - -
510P ALA 4.9 1.8 + - - -
513P ASN* 2.7 34.4 + - - +
514P ALA* 3.4 21.0 - - - +
516P MET* 1.3 70.8 - - - +
518P ALA* 1.3 55.5 + - - +
519P LEU 2.9 4.3 - - - -
520P ALA* 2.6 31.6 + - - +
521P LYS* 3.0 10.7 + - - +
526P SER* 5.6 1.4 - - - +
527P LEU* 3.5 37.1 + - + +
5Q A 2.9 97.3 + - - +
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Residues in contact with ALA 518 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514P ALA 3.1 13.1 + - - +
515P SER* 3.2 7.4 + - - +
517P ARG* 1.3 78.6 - - - +
519P LEU* 1.3 58.4 + - - +
521P LYS* 3.5 14.7 + - + +
522P THR* 3.1 27.9 + - - +
4Q C 5.9 9.0 - - - +
5Q A 6.3 0.2 - - - -
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Residues in contact with LEU 519 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515P SER 3.2 10.5 + - - +
516P MET* 3.8 11.7 - - + +
517P ARG 2.8 1.2 + - - -
518P ALA* 1.3 74.7 - - - +
520P ALA* 1.3 64.4 + - - +
521P LYS 3.2 0.2 - - - -
522P THR* 2.5 27.8 + - - +
523P LYS* 3.5 17.0 + - - +
563P LEU* 3.5 19.1 - - + +
565P LEU* 3.2 53.4 - - + -
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Residues in contact with ALA 520 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516P MET 3.5 6.9 + - - +
517P ARG* 2.6 15.9 + - - +
519P LEU* 1.3 75.5 - - - +
521P LYS* 1.3 51.9 + - - +
523P LYS* 3.0 11.3 + - - -
525P MET* 2.8 37.3 + - + +
526P SER* 3.9 27.4 - - - +
527P LEU* 4.4 4.0 - - + +
532P LEU* 4.5 5.4 - - + -
563P LEU* 3.6 23.6 - - + -
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Residues in contact with LYS 521 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517P ARG 3.0 8.7 + - - +
518P ALA* 3.5 17.7 - - - +
520P ALA* 1.3 78.8 - - - +
522P THR* 1.3 59.1 + - + +
523P LYS 3.2 1.3 + - - -
524P GLY* 3.8 8.2 + - - -
525P MET 3.5 13.0 + - - +
526P SER* 5.2 0.4 - - - +
538P ARG* 6.2 2.2 - - - +
3Q G 3.0 19.0 + - - -
4Q C 2.7 36.7 + - - +
5Q A 6.2 1.1 - - - -
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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