Contacts of the helix formed by residues 515 - 523 (chain D) in PDB entry 6PUO
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 THR 515 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512D GLU 4.6 3.1 - - - +
513D PHE 3.0 15.5 + - - +
514D VAL* 1.3 79.0 - - - +
516D TRP* 1.3 65.4 + - - +
517D ASP* 3.2 6.6 + - - +
518D THR* 3.0 30.4 + - - +
519D LEU* 3.5 18.4 + - - +
615D VAL* 4.9 19.1 - - + -
616D THR 3.9 10.1 - - - -
617D PHE* 4.2 18.6 - - + -
618D THR* 5.5 3.8 - - - +
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Residues in contact with TRP 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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515D THR* 1.3 76.7 - - - +
517D ASP* 1.3 75.4 + - - +
519D LEU* 3.2 12.4 + - + +
520D LEU* 3.0 38.2 + - + +
558D MET* 3.9 37.1 - - + +
577D TYR* 4.5 18.6 - + + -
578D PRO* 5.3 10.5 - - + -
616D THR* 3.1 36.4 + - + +
617D PHE* 4.8 0.9 - - - +
618D THR* 4.2 32.3 - - + +
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Residues in contact with ASP 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D THR* 3.2 5.6 + - - +
516D TRP* 1.3 93.3 - - - +
518D THR* 1.3 61.4 + - - +
520D LEU* 3.3 10.6 + - + +
521D TYR* 2.9 29.1 + - - +
614D HIS 5.4 3.6 - - - +
615D VAL* 5.7 3.5 - - - -
616D THR* 5.6 3.0 - - - +
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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
----------------------------------------------------------
489D THR* 4.4 11.7 - - + +
513D PHE* 4.2 33.2 + - + +
514D VAL* 4.9 2.5 - - + -
515D THR* 3.0 30.7 + - - +
517D ASP* 1.3 76.8 - - - +
519D LEU* 1.3 58.3 + - - +
521D TYR* 3.3 8.0 + - + +
522D LEU* 2.9 39.5 + - + +
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Residues in contact with LEU 519 (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 VAL* 4.4 14.3 - - + +
515D THR 3.5 13.8 + - - +
516D TRP* 3.2 17.4 + - + +
517D ASP 3.2 0.4 - - - -
518D THR* 1.3 79.6 - - - +
520D LEU* 1.3 56.2 + - - +
522D LEU* 3.1 11.9 + - + +
523D TYR* 3.0 45.4 + - + -
558D MET* 3.8 26.2 - - + -
577D TYR* 4.4 12.3 - - + +
618D THR* 5.6 4.0 - - + -
624D ASP* 3.9 39.7 - - + +
625D LEU* 4.8 5.4 - - + +
628D TRP* 5.2 3.1 - - + -
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Residues in contact with LEU 520 (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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516D TRP* 3.0 27.7 + - + +
517D ASP* 3.7 13.0 - - - +
519D LEU* 1.3 75.6 - - - +
521D TYR* 1.3 62.7 + - - +
523D TYR* 3.4 8.8 + - + -
524D GLU* 3.5 21.5 + - - +
555D ARG* 5.0 9.4 - - - +
556D LEU* 3.7 38.8 - - + +
557D GLN* 4.6 10.3 - - - +
558D MET* 3.7 29.8 - - + +
561D VAL* 6.3 0.2 - - + -
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Residues in contact with TYR 521 (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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317D GLY 3.2 25.8 + - - -
318D GLY* 4.0 8.1 - - - -
489D THR* 4.0 27.8 - - + -
493D ILE* 4.3 3.6 - - + -
517D ASP 2.9 17.0 + - - +
518D THR* 3.6 10.5 - - + +
519D LEU 3.2 0.2 - - - -
520D LEU* 1.3 75.7 - - - +
522D LEU* 1.3 65.0 + - + +
524D GLU* 3.2 28.9 + - - +
525D ASN* 3.3 34.1 + - - -
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Residues in contact with LEU 522 (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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489D THR* 4.4 12.8 - - + -
492D LEU* 4.2 16.4 - - + -
493D ILE* 3.8 32.1 - - + -
513D PHE* 5.3 4.7 - - + -
514D VAL* 5.9 2.0 - - + -
518D THR* 2.9 32.9 + - + +
519D LEU* 3.1 11.9 + - + +
521D TYR* 1.3 78.1 - - + +
523D TYR* 1.3 60.6 + - - +
524D GLU 3.1 1.3 + - - -
525D ASN* 3.3 15.1 + - - -
526D LEU* 4.1 0.5 - - - +
625D LEU* 4.1 26.0 - - + -
628D TRP* 3.0 44.0 + - + +
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Residues in contact with TYR 523 (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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519D LEU* 3.0 46.3 + - + +
520D LEU* 3.4 7.2 + - - +
521D TYR 3.2 0.6 - - - -
522D LEU* 1.3 76.4 - - - +
524D GLU* 1.3 58.3 + - - +
525D ASN 3.4 0.4 - - - -
526D LEU* 3.3 31.0 - - + +
532D PHE* 4.3 16.8 - + - -
536D LEU* 4.5 6.8 - - + +
556D LEU* 3.4 21.8 - - + +
558D MET* 4.4 14.6 - - + -
561D VAL* 4.0 32.5 - - + +
565D LEU* 5.3 0.2 - - - +
577D TYR* 5.1 6.4 + - - -
624D ASP 4.1 2.3 + - - -
627D ILE* 3.7 15.2 - - - +
628D TRP* 3.4 44.7 + + + +
631D VAL* 5.1 3.5 - - + +
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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