Contacts of the helix formed by residues 546 - 560 (chain D) in PDB entry 1WSU
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 546 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536D PHE* 5.1 0.2 - - - -
540D ALA* 5.0 1.8 - - - +
545D LEU* 1.3 80.5 - - - +
547D PRO* 1.3 83.7 - - + +
549D GLU* 3.0 34.3 + - + +
550D LEU* 3.4 12.8 + - - +
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Residues in contact with PRO 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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536D PHE* 3.1 26.9 - - + -
540D ALA* 5.8 3.4 - - + -
546D ASP* 1.3 94.9 - - + +
548D SER* 1.3 58.4 + - - +
549D GLU 2.6 14.6 + - - -
550D LEU* 3.0 8.0 + - - +
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Residues in contact with SER 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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536D PHE* 4.3 1.9 - - - -
547D PRO* 1.3 76.4 - - - +
549D GLU* 1.3 56.8 + - - +
550D LEU 3.5 0.4 - - - -
551D GLU* 3.2 35.6 - - - +
552D GLU* 4.2 7.4 + - - +
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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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545D LEU* 3.0 24.9 - - - +
546D ASP* 3.0 51.1 + - + +
547D PRO 2.6 6.7 + - - -
548D SER* 1.3 73.2 - - - +
550D LEU* 1.3 58.9 + - - +
551D GLU 3.0 5.5 + - - -
552D GLU* 3.3 32.3 + - - +
553D LEU* 4.3 14.0 + - - +
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Residues in contact with LEU 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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522D LEU* 3.8 22.2 - - + -
536D PHE* 3.4 30.3 - - + +
539D VAL* 4.4 12.1 - - + +
540D ALA* 4.3 24.0 - - - +
543D PHE* 5.9 0.7 - - + -
545D LEU* 4.1 15.3 - - + +
546D ASP 3.4 7.8 + - - +
547D PRO 3.0 11.7 + - - +
549D GLU* 1.3 85.3 - - - +
551D GLU* 1.3 58.7 + - - +
552D GLU 3.2 0.2 - - - -
553D LEU* 2.9 27.8 + - + +
554D LEU* 2.9 35.3 + - + +
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Residues in contact with GLU 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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536D PHE* 4.4 13.0 - - + -
548D SER* 3.2 37.4 - - - +
550D LEU* 1.3 73.6 - - - +
552D GLU* 1.3 59.6 + - + +
553D LEU 2.9 5.4 - - - -
554D LEU* 3.9 12.7 - - - +
555D HIS* 2.8 66.0 + - - +
571D TYR* 3.6 17.9 + - - -
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Residues in contact with GLU 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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519D LEU* 5.6 0.2 - - - +
548D SER 4.4 7.7 - - - +
549D GLU* 3.6 29.9 - - - +
550D LEU 3.2 0.4 - - - -
551D GLU* 1.3 76.1 - - + +
553D LEU* 1.3 62.6 + - + +
555D HIS* 5.4 0.9 - - - -
556D TYR* 3.4 21.7 + - - +
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Residues in contact with LEU 553 (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 GLN* 3.7 27.1 - - - +
518D LEU* 3.7 28.3 - - + -
519D LEU* 3.9 20.2 - - + +
522D LEU* 3.8 17.0 - - + -
545D LEU* 3.8 8.5 - - + -
549D GLU* 4.3 13.5 - - - +
550D LEU* 2.9 30.4 + - + +
551D GLU 2.9 0.2 - - - -
552D GLU* 1.3 81.8 - - + +
554D LEU* 1.3 66.5 + - - +
555D HIS 3.4 0.2 - - - -
556D TYR* 3.3 4.0 + - - +
557D LEU* 3.1 28.5 + - - +
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Residues in contact with LEU 554 (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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522D LEU* 4.8 7.4 - - + +
526D TYR* 3.5 26.0 - - + +
536D PHE* 3.6 33.0 - - + -
539D VAL* 6.2 0.2 - - + -
550D LEU* 2.9 27.6 + - + +
551D GLU* 3.9 13.9 - - - +
553D LEU* 1.3 76.4 - - - +
555D HIS* 1.3 58.0 + - - +
557D LEU* 3.2 7.0 + - - +
558D VAL* 2.7 31.4 + - - +
563D LEU* 3.3 30.6 - - + +
571D TYR* 3.7 28.5 - - + -
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Residues in contact with HIS 555 (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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551D GLU* 2.8 47.1 + - - +
552D GLU* 5.4 1.1 - - - -
554D LEU* 1.3 71.3 - - - +
556D TYR* 1.3 55.1 + - - +
558D VAL* 2.7 21.2 + - + +
559D ARG* 2.7 35.8 + - - +
565D LYS* 4.0 19.3 + - + -
571D TYR* 3.5 25.5 + + - -
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Residues in contact with TYR 556 (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* 3.7 37.7 - - + -
552D GLU 3.4 21.6 + - - +
553D LEU* 3.3 5.5 + - - +
555D HIS* 1.3 75.8 - - - +
557D LEU* 1.3 71.7 + - + +
559D ARG* 2.8 54.2 - - - +
560D GLU* 3.0 38.9 + - + +
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Residues in contact with LEU 557 (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* 3.8 46.7 - - + +
522D LEU* 4.3 14.4 - - + -
523D GLU* 4.5 9.2 - - + +
553D LEU 3.1 16.5 + - - +
554D LEU 3.4 6.7 - - - +
556D TYR* 1.3 89.8 - - + +
558D VAL* 1.3 61.7 + - - +
560D GLU* 3.4 4.6 + - + +
561D GLY 3.0 4.0 + - - -
562D VAL* 3.0 50.3 + - + -
563D LEU* 3.4 30.5 + - + -
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Residues in contact with VAL 558 (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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554D LEU 2.7 22.9 + - - +
555D HIS* 2.7 24.8 + - + +
557D LEU* 1.3 75.0 - - - +
559D ARG* 1.3 57.0 + - - +
561D GLY* 2.8 25.3 + - - -
563D LEU* 3.6 20.8 - - + +
564D VAL* 5.6 0.4 - - - -
565D LYS* 5.2 11.9 - - + +
571D TYR* 3.6 35.7 - - + -
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Residues in contact with ARG 559 (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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555D HIS 2.7 13.1 + - - +
556D TYR* 2.8 54.4 - - - +
558D VAL* 1.3 74.6 - - - +
560D GLU* 1.3 79.1 + - - +
561D GLY* 3.2 1.4 + - - -
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Residues in contact with GLU 560 (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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556D TYR* 3.0 48.9 + - + +
557D LEU* 3.7 8.5 - - + +
558D VAL 3.2 0.2 - - - -
559D ARG* 1.3 102.7 + - + +
561D GLY* 1.3 56.9 + - - +
562D VAL* 3.4 10.8 - - + -
574D ARG* 3.0 15.4 + - - -
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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