Contacts of the helix formed by residues 536 - 552 (chain D) in PDB entry 2P5G
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 LYS 536 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534D SER* 4.6 0.4 - - - -
535D ALA* 1.3 76.3 - - + +
537D SER* 1.3 54.0 + - - +
538D LEU 3.2 2.2 - - - -
539D ASN* 3.1 8.8 + - - +
540D GLU* 2.7 36.7 + - + +
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Residues in contact with SER 537 (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 PRO* 3.2 37.4 - - - +
533D LEU* 5.3 4.0 - - - -
534D SER* 3.5 22.3 - - - -
535D ALA 3.6 0.4 - - - -
536D LYS* 1.3 74.5 - - - +
538D LEU* 1.3 60.9 + - - +
540D GLU* 4.1 8.2 - - - +
541D MSE 2.9 31.0 + - - +
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Residues in contact with LEU 538 (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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499D ILE* 4.7 8.7 - - - +
502D ALA* 4.9 16.4 - - + -
530D ILE 4.8 7.0 - - - +
531D LYS 5.9 0.4 - - - +
533D LEU* 4.5 11.9 - - + +
534D SER* 3.4 29.1 + - - +
535D ALA 4.2 4.3 - - - +
536D LYS 3.2 0.6 - - - -
537D SER* 1.3 77.4 - - - +
539D ASN* 1.3 57.1 + - - +
541D MSE 3.9 5.0 - - - +
542D LEU* 3.2 23.0 + - - +
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Residues in contact with ASN 539 (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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535D ALA 4.2 6.4 + - - +
536D LYS* 3.1 10.7 + - - +
538D LEU* 1.3 78.5 - - - +
540D GLU* 1.3 58.6 + - - +
541D MSE 3.3 0.7 - - - -
542D LEU* 3.3 8.5 + - - +
543D PHE* 3.1 26.7 + - - +
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Residues in contact with GLU 540 (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 PRO* 6.1 2.7 - - + -
536D LYS* 2.7 21.7 + - + +
537D SER* 4.0 9.0 - - - +
539D ASN* 1.3 69.8 - - - +
541D MSE 1.3 64.5 + - - +
543D PHE* 3.8 5.6 + - - +
544D ARG* 3.3 22.2 + - - +
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Residues in contact with MSE 541 (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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499D ILE* 5.7 1.3 - - + -
513D PRO* 4.8 2.8 - - + +
514D LEU* 4.3 29.8 - - + +
537D SER 2.9 20.0 + - - +
538D LEU* 3.9 6.1 - - - +
540D GLU* 1.3 76.1 - - - +
542D LEU* 1.3 57.8 + - - +
543D PHE 3.5 0.2 - - - -
544D ARG* 3.7 6.4 - - - +
545D ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 542 (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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496D GLY* 5.5 3.8 - - - +
499D ILE* 4.2 28.5 - - + +
500D LYS* 5.5 1.6 - - - +
538D LEU 3.2 17.4 + - - +
539D ASN* 3.4 11.7 - - - +
540D GLU 3.3 0.2 - - - -
541D MSE 1.3 76.2 - - - +
543D PHE* 1.3 60.1 + - - +
545D ALA* 3.4 3.7 + - - +
546D GLN* 2.9 27.9 + - - +
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Residues in contact with PHE 543 (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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539D ASN 3.1 16.0 + - - +
540D GLU* 3.8 6.5 + - - +
542D LEU* 1.3 72.5 - - - +
544D ARG* 1.3 60.2 + - - +
546D GLN* 3.1 8.9 + - - +
547D ARG* 3.0 28.9 + - - +
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Residues in contact with ARG 544 (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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518D TYR* 5.2 2.0 - - - +
540D GLU 3.3 17.2 + - - +
541D MSE 3.7 8.3 - - - +
542D LEU 3.3 0.2 - - - -
543D PHE* 1.3 80.0 - - - +
545D ALA* 1.3 57.9 - - - +
546D GLN 3.5 0.3 + - - -
547D ARG* 3.5 14.2 + - - +
548D THR* 3.6 11.3 + - - -
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Residues in contact with ALA 545 (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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492D ALA* 3.7 16.4 - - + +
495D ASN 5.8 0.9 - - - +
496D GLY* 5.1 12.6 - - - -
499D ILE* 5.7 3.6 - - + -
518D TYR* 4.1 25.4 - - + +
541D MSE 2.9 19.7 + - - +
542D LEU* 3.7 5.6 - - - +
543D PHE 3.3 0.2 - - - -
544D ARG* 1.3 73.1 - - - +
546D GLN* 1.3 61.7 + - - +
548D THR* 3.6 10.5 + - - -
549D GLU 3.7 7.6 + - - -
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Residues in contact with GLN 546 (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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492D ALA 5.3 1.1 - - - -
496D GLY* 6.0 2.0 - - - -
542D LEU 2.9 17.8 + - - +
543D PHE* 3.1 12.1 + - - +
545D ALA* 1.3 79.1 - - - +
547D ARG* 1.3 57.4 + - - +
548D THR 3.2 0.4 - - - -
549D GLU* 3.1 25.5 + - - +
550D VAL* 3.7 6.8 + - - +
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Residues in contact with ARG 547 (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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543D PHE 3.0 13.9 + - - +
544D ARG* 3.9 7.9 - - - +
545D ALA 3.4 0.4 - - - -
546D GLN* 1.3 75.8 - - - +
548D THR* 1.3 57.7 + - - +
550D VAL* 4.3 4.9 - - - +
551D ALA* 3.4 22.0 + - - +
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Residues in contact with THR 548 (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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488D TYR 5.2 2.4 - - - +
492D ALA* 4.0 4.9 - - - +
518D TYR* 4.3 25.6 - - - -
519D ARG* 5.8 1.6 - - - -
544D ARG 3.6 9.8 + - - -
545D ALA 3.8 10.1 - - - -
546D GLN 3.2 0.8 - - - -
547D ARG* 1.3 78.5 - - - +
549D GLU* 1.3 62.9 + - - +
550D VAL 3.5 0.2 - - - -
551D ALA* 3.5 8.1 - - - +
552D GLY* 3.4 17.5 + - - -
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Residues in contact with GLU 549 (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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488D TYR 5.5 0.2 - - - +
489D MSE 3.7 22.4 - - - +
492D ALA* 3.7 34.3 - - - +
493D GLN* 3.9 14.4 - - + +
545D ALA 3.7 3.6 + - - +
546D GLN* 3.1 14.4 + - - +
548D THR* 1.3 79.5 - - - +
550D VAL* 1.3 59.9 + - - +
552D GLY* 3.9 1.0 + - - -
553D MSE 3.7 14.2 + - - +
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Residues in contact with VAL 550 (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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339D GLN* 4.3 14.7 + - - +
546D GLN 3.7 7.7 + - - +
547D ARG* 4.1 4.9 + - - +
549D GLU* 1.3 76.4 - - - +
551D ALA* 1.3 55.8 + - - +
553D MSE 3.4 18.1 - - + +
554D THR* 2.7 38.7 + - - +
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Residues in contact with ALA 551 (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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346D ASP* 5.0 1.0 - - - +
485D HIS* 5.5 0.6 - - - -
547D ARG 3.4 20.0 + - - +
548D THR* 3.5 11.9 - - - +
549D GLU 3.3 0.2 - - - -
550D VAL* 1.3 77.9 - - - +
552D GLY* 1.3 57.5 + - - +
553D MSE 3.3 1.7 + - - -
554D THR* 3.2 25.4 + - - +
555D ALA* 3.6 11.4 + - - +
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Residues in contact with GLY 552 (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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485D HIS* 3.1 41.1 - - - +
488D TYR* 4.9 9.4 - - - -
489D MSE 3.8 8.4 - - - +
548D THR 3.4 10.3 + - - -
549D GLU 3.9 2.6 + - - -
550D VAL 3.4 0.2 - - - -
551D ALA* 1.3 76.7 - - - +
553D MSE 1.3 56.5 + - - +
555D ALA 4.2 2.7 - - - -
556D GLN* 3.3 14.8 + - - +
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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