Contacts of the helix formed by residues 575 - 583 (chain A) in PDB entry 2WXF
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 PRO 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A GLU* 3.6 32.3 - - + +
573A GLU 4.7 1.1 - - - +
574A LEU* 1.3 93.9 - - + +
576A VAL* 1.3 66.4 + - - +
577A LEU* 4.3 7.9 - - + +
578A SER* 3.1 16.3 + - - +
579A ALA* 3.1 17.8 + - - +
602A LYS* 4.1 8.3 - - - -
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Residues in contact with VAL 576 (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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574A LEU 3.9 0.2 + - - -
575A PRO* 1.3 71.7 - - - +
577A LEU* 1.3 66.2 + - - +
579A ALA* 3.1 9.6 + - - +
580A LEU* 3.0 28.3 + - + +
599A SER 4.3 6.3 - - - +
600A LEU* 4.1 4.6 - - + +
602A LYS* 4.2 26.4 - - + +
603A LEU* 3.6 42.4 - - + +
607A GLU* 4.6 12.6 - - - +
611A TYR* 4.2 16.2 - - + +
973A LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 577 (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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575A PRO* 3.3 6.1 - - + +
576A VAL* 1.3 83.2 - - - +
578A SER* 1.3 63.0 + - - +
580A LEU* 3.3 13.2 + - + +
581A GLU 3.5 0.2 + - - -
972A LEU* 4.3 22.7 - - + -
973A LEU* 3.6 47.3 - - + +
976A HIS* 3.3 38.0 - - + +
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Residues in contact with SER 578 (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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544A GLU* 4.3 20.1 + - - +
547A ALA* 6.0 0.2 - - - +
574A LEU* 3.8 25.8 - - - -
575A PRO* 3.1 22.7 + - - +
577A LEU* 1.3 79.3 - - - +
579A ALA* 1.3 62.3 + - - +
581A GLU* 3.2 23.1 + - - +
582A LEU* 3.3 16.5 + - - +
976A HIS* 5.3 1.1 - - - -
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Residues in contact with ALA 579 (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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574A LEU* 4.9 0.8 - - - +
575A PRO 3.1 11.7 + - - +
576A VAL 3.1 8.5 + - - +
578A SER* 1.3 77.1 - - - +
580A LEU* 1.3 63.1 + - - +
582A LEU* 3.1 24.0 + - - +
583A LEU* 3.4 15.6 + - - +
596A ALA* 3.7 15.5 - - - +
599A SER* 3.9 16.4 - - - -
600A LEU* 3.7 26.5 - - + +
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Residues in contact with LEU 580 (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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576A VAL* 3.0 22.8 + - + +
577A LEU* 3.5 12.1 - - + +
578A SER 3.2 0.2 - - - -
579A ALA* 1.3 73.6 - - - +
581A GLU* 1.3 65.2 + - - +
583A LEU* 3.4 25.3 + - + +
600A LEU* 4.2 15.9 - - + -
603A LEU* 5.8 0.2 - - + -
611A TYR* 4.2 32.3 - - + -
615A LEU* 4.9 6.3 - - + -
973A LEU* 3.9 27.1 - - + -
976A HIS* 4.4 12.5 - - + +
977A LEU* 4.3 12.3 - - + -
980A LEU* 3.7 31.8 - - + +
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Residues in contact with GLU 581 (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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544A GLU 5.8 0.5 - - - +
547A ALA* 3.6 26.8 - - + +
551A LEU* 5.8 2.3 - - - +
577A LEU 3.5 2.6 + - - -
578A SER* 3.2 15.2 + - - +
580A LEU* 1.3 79.8 - - - +
582A LEU* 1.3 56.6 + - + +
583A LEU 3.1 0.2 - - - -
584A ASP* 3.0 31.6 + - + +
587A PHE* 3.3 16.1 - - + -
976A HIS* 3.7 42.8 + - + +
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Residues in contact with LEU 582 (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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546A LEU* 4.2 7.9 - - + -
547A ALA* 4.0 25.4 - - + +
550A LEU* 3.9 28.7 - - + -
574A LEU* 4.3 9.6 - - + -
578A SER* 3.5 15.3 - - - +
579A ALA* 3.1 17.3 + - + +
581A GLU* 1.3 73.8 - - - +
583A LEU* 1.3 59.2 + - - +
584A ASP 3.2 2.1 - - - +
587A PHE* 3.4 30.5 - - + +
592A VAL* 4.4 8.9 - - + +
593A GLY* 5.4 2.4 - - - -
595A PHE* 4.0 31.6 - - + -
596A ALA* 3.8 17.3 - - + +
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Residues in contact with LEU 583 (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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579A ALA 3.4 10.9 + - - +
580A LEU* 3.7 11.9 - - + +
581A GLU 3.1 1.0 - - - -
582A LEU* 1.3 73.9 - - - +
584A ASP* 1.3 66.6 + - - +
585A PHE 3.6 0.7 + - - -
587A PHE 5.7 0.2 - - - -
593A GLY* 5.0 4.5 - - - +
596A ALA* 3.8 20.6 - - + -
597A ILE* 4.5 13.9 - - + -
600A LEU* 3.4 20.0 - - + -
615A LEU* 3.4 33.2 - - + -
618A VAL* 3.9 30.0 - - + +
621A TYR* 4.3 3.6 - - - -
629A LEU* 5.3 4.0 - - + -
980A LEU* 3.7 22.8 - - + +
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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