Contacts of the helix formed by residues 589 - 601 (chain A) in PDB entry 2WXL
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 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A HIS* 4.1 8.1 + - + -
385A PRO* 5.8 1.2 - - - +
386A ARG* 4.8 8.8 + - - +
387A MET* 3.8 10.6 - - - +
555A TRP* 3.9 32.8 - - + -
561A VAL* 5.2 2.4 - - - +
565A LEU* 4.6 6.5 - - - +
587A PHE 3.3 3.6 - - - +
588A PRO* 1.3 83.9 - - + +
590A CYS* 1.3 65.9 + - - +
591A TYR* 2.7 43.5 + - - +
592A VAL* 3.2 17.7 + - + +
593A GLY* 3.0 23.7 + - - -
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Residues in contact with CYS 590 (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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386A ARG* 4.0 12.3 - - - -
387A MET* 3.2 37.1 - - + +
588A PRO 3.4 3.3 + - - -
589A ASP* 1.3 72.7 - - - +
591A TYR* 1.3 75.6 + - - +
593A GLY* 3.5 2.3 - - - +
594A SER* 2.8 34.8 + - - -
628A GLU* 5.8 0.2 - - - +
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Residues in contact with TYR 591 (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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386A ARG* 6.1 2.5 - - + -
485A PHE* 5.8 7.9 - + - -
486A PRO 5.1 3.3 + - - -
487A ALA 5.0 0.2 - - - -
488A LEU* 3.6 50.4 + - + +
491A ILE* 5.4 3.8 - - + -
565A LEU* 3.5 34.5 - - + -
568A LEU* 3.7 18.7 - - + +
569A CYS* 5.3 7.0 - - - -
589A ASP* 2.7 21.6 + - - +
590A CYS* 1.3 84.1 - - - +
592A VAL* 1.3 57.2 + - - +
594A SER* 3.4 8.9 + - - -
595A PHE* 3.0 28.2 + - - +
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Residues in contact with VAL 592 (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* 5.9 1.1 - - + -
550A LEU* 3.7 45.8 - - + -
555A TRP* 4.3 7.2 - - + -
565A LEU* 6.1 0.2 - - + -
568A LEU* 3.9 16.4 - - + -
582A LEU* 4.3 15.0 - - + +
587A PHE* 3.9 25.4 - - + +
589A ASP* 3.2 25.9 + - + +
590A CYS 3.3 0.2 - - - -
591A TYR* 1.3 75.1 - - - +
593A GLY* 1.3 65.0 + - - +
595A PHE* 3.2 6.7 + - + +
596A ALA* 2.9 22.0 + - - +
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Residues in contact with GLY 593 (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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582A LEU 5.3 2.9 - - - -
583A LEU* 4.8 4.2 - - - +
587A PHE 4.8 4.0 + - - -
589A ASP 3.0 15.3 + - - -
590A CYS* 3.2 5.6 + - - -
592A VAL* 1.3 76.3 - - - +
594A SER* 1.3 61.4 + - - +
596A ALA* 3.2 8.8 + - - +
597A ILE* 3.1 27.8 + - - +
628A GLU* 5.4 2.2 - - - -
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A CYS 2.8 20.0 + - - -
591A TYR* 3.7 11.2 - - - -
593A GLY* 1.3 72.7 - - - +
595A PHE* 1.3 57.1 + - - +
597A ILE* 3.4 3.6 + - - +
598A LYS* 2.9 29.0 + - - +
601A ARG* 4.7 2.3 + - - -
628A GLU* 4.1 32.9 + - - +
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Residues in contact with PHE 595 (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* 3.5 19.1 - - + -
568A LEU* 3.8 26.0 - - + -
571A TRP* 3.6 40.2 - + + -
572A PRO 3.3 19.7 - - - -
573A GLU* 4.7 2.7 - - - -
574A LEU* 3.9 13.0 - - + -
582A LEU* 3.9 21.5 - - + -
591A TYR 3.0 13.9 + - - +
592A VAL* 3.4 8.7 - - + +
594A SER* 1.3 74.7 - - - +
596A ALA* 1.3 58.7 + - - +
598A LYS* 3.1 21.8 + - - +
599A SER* 2.9 39.5 + - - -
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Residues in contact with ALA 596 (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* 3.7 7.5 - - - +
582A LEU* 3.8 28.9 - - + +
583A LEU* 3.8 20.4 - - + -
592A VAL 2.9 13.5 + - - +
593A GLY* 3.2 9.4 + - - +
595A PHE* 1.3 81.7 - - - +
597A ILE* 1.3 62.2 + - - +
599A SER* 3.3 7.4 + - - -
600A LEU* 3.1 28.0 + - - +
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Residues in contact with ILE 597 (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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583A LEU* 4.1 17.3 - - + -
593A GLY 3.1 17.1 + - - +
594A SER 3.8 6.3 - - - +
596A ALA* 1.3 72.4 - - - +
598A LYS* 1.3 65.3 + - - +
600A LEU* 2.9 23.7 + - + +
601A ARG* 3.1 37.3 + - - +
628A GLU* 4.1 12.6 - - + +
629A LEU* 3.6 48.5 - - + +
632A PHE* 3.7 27.8 - - + -
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Residues in contact with LYS 598 (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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571A TRP 5.4 4.2 + - - -
573A GLU* 2.6 48.7 + - - +
594A SER* 2.9 15.1 + - - +
595A PHE* 3.3 29.6 - - - +
597A ILE* 1.3 76.3 - - - +
599A SER* 1.3 62.0 + - - +
600A LEU 3.4 0.2 + - - -
601A ARG* 3.5 33.5 + - - +
602A LYS 4.9 0.5 + - - -
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Residues in contact with SER 599 (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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573A GLU* 3.5 11.4 - - - +
574A LEU* 2.8 39.8 + - - +
576A VAL* 4.5 3.3 - - - +
579A ALA* 3.8 14.2 - - - +
595A PHE* 2.9 22.4 + - - -
596A ALA* 3.7 9.4 - - - -
597A ILE 3.2 0.2 - - - -
598A LYS* 1.3 76.6 - - - +
600A LEU* 1.3 59.4 + - - +
601A ARG 3.4 0.4 - - - -
602A LYS* 2.9 33.0 + - - +
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Residues in contact with LEU 600 (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* 4.3 11.2 - - + +
579A ALA* 3.7 16.8 - - + -
580A LEU* 3.9 22.2 - - + -
583A LEU* 3.6 33.7 - - + -
596A ALA 3.1 16.4 + - - +
597A ILE* 2.9 23.9 + - + +
599A SER* 1.3 73.0 - - - +
601A ARG* 1.3 64.1 + - - +
602A LYS 3.1 2.5 - - - -
603A LEU* 3.0 50.3 + - + +
615A LEU* 4.9 6.5 - - + -
632A PHE* 3.7 14.5 - - + -
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Residues in contact with ARG 601 (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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594A SER* 4.7 1.2 + - - -
597A ILE* 3.1 32.9 + - - +
598A LYS* 3.6 37.6 - - - +
599A SER 3.4 1.0 - - - -
600A LEU* 1.3 78.4 - - - +
602A LYS* 1.3 57.4 + - - +
603A LEU 3.2 1.7 - - - +
628A GLU* 3.7 17.2 + - - -
632A PHE* 4.0 32.8 - - + +
636A ARG* 3.2 18.6 + - - +
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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