Contacts of the helix formed by residues 560 - 574 (chain A) in PDB entry 1WBP
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A SER* 3.7 5.2 - - - -
558A GLU 5.5 1.3 - - - +
559A TYR* 1.3 96.4 - - - +
561A ARG* 1.3 61.9 + - - +
562A ASP* 2.9 23.2 + - - +
563A GLU* 2.9 20.5 + - - +
564A ASP 3.4 6.2 + - - -
589A GLU 6.0 0.9 - - - +
590A PHE* 4.1 11.3 - - + -
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ARG* 3.4 39.0 - - - +
553A PRO* 2.7 37.4 + - + +
554A HIS* 3.0 29.0 - - - +
555A SER* 3.5 37.9 + - - +
560A THR* 1.3 73.4 - - - +
562A ASP* 1.3 66.5 + - - +
564A ASP 3.5 0.3 + - - -
565A HIS* 3.0 21.3 + - - +
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Residues in contact with ASP 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A ARG* 2.9 31.4 + - - +
518A ARG* 4.9 1.7 + - - -
523A LEU* 3.7 19.0 - - + +
560A THR* 2.9 10.3 + - - +
561A ARG* 1.3 78.0 - - - +
563A GLU* 1.3 64.3 + - - +
565A HIS* 3.3 3.2 + - - +
566A ILE* 3.1 28.9 + - + +
590A PHE* 3.8 23.7 - - + -
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Residues in contact with GLU 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A TYR* 3.2 21.1 - - + +
560A THR* 2.9 24.2 + - - +
562A ASP* 1.3 74.2 - - - +
564A ASP* 1.3 61.1 + - - +
566A ILE* 2.8 10.0 + - - +
567A ALA* 2.8 26.2 + - - +
589A GLU 5.1 1.0 - - - +
590A PHE* 4.2 21.6 - - + +
597A LEU* 4.0 18.2 - - + +
598A LYS* 3.9 9.7 + - - +
599A HIS* 3.0 47.9 + - - +
600A ILE* 3.6 13.5 + - + -
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Residues in contact with ASP 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A GLU 5.2 0.2 - - - +
553A PRO* 4.0 5.8 - - - +
554A HIS* 3.0 45.4 + - - +
559A TYR* 3.7 13.1 + - + -
560A THR 3.4 3.4 + - - +
561A ARG 4.0 4.9 - - - +
562A ASP 3.5 0.2 - - - -
563A GLU* 1.3 79.6 - - - +
565A HIS* 1.3 60.7 + - - +
567A ALA* 3.7 0.7 - - - -
568A LEU* 3.0 28.8 + - - +
600A ILE* 3.5 10.0 - - - +
3B ARG* 3.2 37.7 + - - +
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Residues in contact with HIS 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ARG* 3.6 31.5 + - - +
516A GLN 4.7 2.0 - - - -
518A ARG 3.3 23.1 + - - -
523A LEU* 3.2 31.6 - - + +
551A PHE* 3.5 36.4 - + + +
553A PRO* 3.6 23.4 - - + +
561A ARG 3.0 17.5 + - - +
562A ASP* 3.5 8.5 - - - +
563A GLU 3.0 1.0 - - - -
564A ASP* 1.3 76.8 - - - +
566A ILE* 1.3 60.8 + - - +
568A LEU* 3.5 3.3 + - - +
569A ILE* 2.8 33.7 + - + +
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Residues in contact with ILE 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A LEU* 4.1 14.4 - - + -
523A LEU* 4.0 18.4 - - + -
524A ILE* 3.6 30.1 - - + -
562A ASP 3.1 16.2 - - - +
563A GLU 2.8 6.1 + - - +
565A HIS* 1.3 76.5 - - - +
567A ALA* 1.3 60.6 + - - +
569A ILE* 2.8 24.7 + - + +
570A ILE* 2.9 30.5 + - + +
576A VAL* 4.6 2.2 - - + -
590A PHE* 3.9 24.5 - - + -
591A PHE* 3.8 25.6 - - + -
597A LEU* 4.7 3.8 - - + -
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Residues in contact with ALA 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A GLU 2.8 16.1 + - - +
564A ASP 3.8 1.8 - - - +
566A ILE* 1.3 72.7 - - - +
568A LEU* 1.3 55.9 + - - +
570A ILE* 3.9 2.1 - - - +
571A GLU* 2.8 35.6 + - - +
597A LEU* 3.6 27.2 - - + +
600A ILE* 3.6 11.0 - - + -
603A LEU* 3.7 11.0 - - + +
3B ARG* 3.0 25.4 - - - +
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A PHE* 3.8 15.9 - - + -
552A GLU 4.0 15.0 - - - +
553A PRO* 3.9 30.3 - - + -
564A ASP* 3.0 37.2 + - - +
565A HIS* 3.8 4.7 - - - +
567A ALA* 1.3 74.6 - - - +
569A ILE* 1.3 65.6 + - - +
570A ILE 3.1 0.4 - - - -
571A GLU* 3.8 19.8 - - - +
572A LEU* 3.1 25.1 + - - +
3B ARG* 4.2 4.3 - - - +
4B GLU* 4.1 22.0 - - - +
5B ARG* 4.2 12.8 + - + +
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Residues in contact with ILE 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A LEU* 4.0 21.1 - - + +
523A LEU* 3.3 33.7 - - + -
535A TRP* 3.8 39.5 - - + -
551A PHE* 3.9 14.8 - - + -
565A HIS* 2.8 27.4 + - + +
566A ILE* 2.8 10.0 + - + +
568A LEU* 1.3 78.9 - - - +
570A ILE* 1.3 58.4 + - + +
572A LEU* 3.9 0.3 - - - +
573A LEU* 2.9 29.4 + - + +
574A GLY 4.7 0.3 - - - +
636A LEU* 3.8 17.9 - - + -
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Residues in contact with ILE 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A ILE* 2.9 31.3 + - + +
567A ALA* 3.9 4.0 - - - +
569A ILE* 1.3 76.3 - - + +
571A GLU* 1.3 63.0 + - - +
572A LEU 2.8 4.7 - - - -
574A GLY* 2.4 35.9 + - - +
575A LYS* 3.2 30.3 - - + +
576A VAL* 3.8 33.4 - - + +
591A PHE* 4.5 7.9 - - + -
597A LEU* 4.5 15.5 - - + -
603A LEU* 4.1 16.2 - - + -
605A PRO* 5.4 1.0 - - - +
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ALA 2.8 27.6 + - - +
568A LEU* 3.8 18.7 - - + +
570A ILE* 1.3 76.8 - - - +
572A LEU* 1.3 49.6 + - - +
603A LEU* 3.6 24.5 - - + +
604A LYS* 3.5 30.7 + - - +
605A PRO* 3.3 13.0 - - - +
606A TRP* 2.7 38.4 + - + +
3B ARG* 2.7 37.5 + - - -
4B GLU* 4.1 1.8 - - - +
5B ARG* 4.0 14.9 + - - +
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Residues in contact with LEU 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A LEU* 4.0 20.6 - - + -
551A PHE* 3.4 33.2 - - + -
568A LEU 3.1 15.9 + - - +
569A ILE 4.0 2.2 - - - +
570A ILE 2.8 1.8 + - - -
571A GLU* 1.3 80.9 - - + +
573A LEU* 1.3 74.8 + - + +
574A GLY 3.6 0.7 - - - -
606A TRP* 3.3 15.1 - - + +
607A GLY* 4.2 3.1 - - - -
608A LEU* 3.8 39.3 + - + +
611A VAL* 4.3 10.5 - - + -
631A LEU* 5.8 0.2 - - - +
634A LEU* 5.5 1.6 - - + -
5B ARG* 4.1 18.6 - - - +
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A TRP* 3.9 19.7 - - + -
551A PHE* 4.9 2.9 - - + -
569A ILE* 2.9 17.9 + - + +
572A LEU* 1.3 97.4 - - + +
574A GLY* 1.3 65.5 + - - +
575A LYS 4.7 0.3 - - - +
631A LEU* 3.8 28.7 - - + -
634A LEU* 3.1 45.5 - - + +
636A LEU* 4.2 16.8 - - + +
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Residues in contact with GLY 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ILE* 2.4 39.0 + - - +
571A GLU 4.6 0.2 - - - -
572A LEU 3.6 1.0 - - - -
573A LEU* 1.3 73.2 - - - +
575A LYS* 1.3 71.3 + - - +
636A LEU* 3.5 9.7 - - - +
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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