Contacts of the helix formed by residues 505 - 518 (chain D) in PDB entry 1HQR
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 ASP 505 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503D LYS 3.5 1.9 - - - +
504D LYS* 1.3 75.3 - - - +
506D ILE* 1.3 73.7 + - - +
507D SER* 2.8 34.1 + - - +
508D ASN* 2.6 21.6 + - + +
509D VAL 3.4 3.1 + - - -
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Residues in contact with ILE 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LYS 3.1 5.5 + - - +
505D ASP* 1.3 76.1 + - - +
507D SER* 1.3 70.3 + - - +
509D VAL* 2.8 43.0 + - + +
510D LYS* 2.9 16.7 + - + +
653D TYR 5.4 1.8 - - - +
654D VAL* 3.2 45.5 - - + +
655D SER* 5.6 0.4 - - - -
673D PHE* 3.9 19.7 - - + +
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Residues in contact with SER 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D ASP* 2.7 24.5 + - - -
506D ILE* 1.3 83.4 - - - +
508D ASN* 1.3 65.2 + - - -
510D LYS* 4.1 6.1 - - - +
511D SER* 3.7 17.2 + - - -
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Residues in contact with ASN 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LYS* 4.2 22.8 - - + +
505D ASP* 2.6 19.3 + - + +
507D SER* 1.3 80.2 + - - +
509D VAL* 1.3 69.9 + - - +
511D SER* 3.1 21.7 + - - -
512D ASP* 3.1 16.1 + - - +
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Residues in contact with VAL 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LYS* 3.9 31.1 - - + +
505D ASP 3.4 1.2 + - - -
506D ILE* 2.8 22.8 + - + +
508D ASN* 1.3 83.1 - - - +
510D LYS* 1.3 66.6 + - - +
512D ASP* 2.9 12.0 + - - +
513D LEU* 3.1 15.2 + - + +
673D PHE* 3.5 44.4 - - + +
674D ASP* 3.9 2.2 - - - +
675D SER* 3.9 24.2 - - - +
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Residues in contact with LYS 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D ILE* 2.9 19.8 + - + +
507D SER* 4.1 6.5 - - - +
509D VAL* 1.3 76.1 - - - +
511D SER* 1.3 64.7 + - - +
513D LEU* 2.9 8.0 + - - +
514D LEU* 2.8 23.0 + - - +
646D ILE 5.2 0.2 - - - +
647D TYR* 3.9 27.2 - - - +
648D ASP 5.3 2.9 - - - +
649D ALA* 6.1 2.0 - - - -
651D SER* 5.6 1.6 - - - +
673D PHE* 4.8 11.9 - - + -
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Residues in contact with SER 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D SER 3.7 9.9 + - - -
508D ASN* 3.1 19.7 + - - -
510D LYS* 1.3 77.5 - - - +
512D ASP* 1.3 69.2 + - - +
514D LEU* 4.1 10.3 - - - -
515D TYR* 2.9 49.5 + - - -
647D TYR 4.3 2.6 + - - -
649D ALA* 6.5 1.1 - - - -
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Residues in contact with ASP 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LYS* 3.7 16.5 + - - -
508D ASN* 3.1 16.3 + - - +
509D VAL 2.9 9.1 + - - +
511D SER* 1.3 84.1 + - - +
513D LEU* 1.3 53.4 - - - +
515D TYR* 4.0 4.2 - - - +
516D ALA* 2.7 38.5 + - - +
675D SER* 3.0 26.7 + - - +
678D GLU 4.1 5.2 - - - +
679D GLY* 3.5 23.5 - - - +
684D ILE* 3.8 2.5 - - + +
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Residues in contact with LEU 513 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509D VAL* 3.1 13.9 + - + +
510D LYS 2.9 7.2 + - - +
512D ASP* 1.3 72.6 - - - +
514D LEU* 1.3 68.0 + - - +
516D ALA* 3.0 0.9 + - - -
517D TYR* 2.7 47.4 + - + +
637D ARG* 4.4 2.7 - - - +
647D TYR* 3.4 25.4 - - + +
672D LEU 2.9 29.4 - - - +
673D PHE* 3.4 6.1 - - - -
674D ASP 3.4 33.7 - - - +
675D SER* 4.8 0.7 - - - -
684D ILE* 3.6 25.4 - - + -
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Residues in contact with LEU 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D LYS 2.8 9.4 + - - +
511D SER* 3.6 10.5 - - - +
513D LEU* 1.3 75.3 - - - +
515D TYR* 1.3 88.9 + - + +
517D TYR* 3.7 1.0 - - - +
518D THR* 2.7 42.7 + - - +
641D MET* 4.8 5.6 - - - +
647D TYR* 3.5 46.9 - - + +
648D ASP* 4.2 16.6 - - - +
649D ALA* 4.6 4.5 - - + +
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Residues in contact with TYR 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D SER* 2.9 40.1 + - - +
512D ASP* 4.0 4.7 - - - +
514D LEU* 1.3 101.0 - - + +
516D ALA* 1.3 68.4 + - - +
518D THR* 3.3 12.0 + - - +
681D ARG* 3.2 18.2 + - - -
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Residues in contact with ALA 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ASP 2.7 24.5 + - - +
513D LEU* 3.6 3.1 - - - +
515D TYR* 1.3 72.4 - - - +
517D TYR* 1.3 62.5 + - + +
518D THR 3.4 0.7 + - - -
519D ILE* 3.6 6.2 - - - +
679D GLY 5.4 0.7 - - - +
681D ARG* 3.0 42.6 + - + +
684D ILE* 3.5 24.0 - - + -
685D PHE* 3.5 20.0 - - + -
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Residues in contact with TYR 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D LEU* 2.7 34.3 + - + +
514D LEU 3.7 1.1 - - - -
516D ALA* 1.3 72.2 - - + +
518D THR* 1.3 58.1 + - - -
519D ILE* 3.0 14.7 + - - +
574D LEU* 3.8 8.1 - - + -
633D ASP* 4.3 0.7 - - - -
634D PHE* 4.1 26.2 - + - -
637D ARG* 3.5 47.0 - - - -
641D MET* 3.4 33.6 - - + +
647D TYR* 4.2 2.9 - + - -
684D ILE* 3.7 18.2 - - + -
685D PHE* 3.3 22.7 - + - -
687D LYS* 2.9 29.5 + - - -
688D TYR* 3.0 16.5 + - - -
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Residues in contact with THR 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D LEU* 2.7 37.3 + - - +
515D TYR* 3.3 8.5 + - - -
517D TYR* 1.3 73.4 - - - +
519D ILE* 1.3 58.2 + - - +
641D MET* 5.2 4.4 - - - -
681D ARG* 3.0 20.2 + - - -
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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