Contacts of the helix formed by residues 591 - 600 (chain A) in PDB entry 2XER
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 ARG 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A ARG* 5.2 2.4 - - - +
589A CYS 3.7 3.2 + - - -
590A ILE* 1.3 75.8 - - + +
592A LYS* 1.3 64.9 + - - +
594A LYS* 3.3 6.8 + - - +
595A ARG* 3.2 47.5 + - - +
630A ASP* 3.2 41.0 + - - +
632A VAL* 3.2 37.7 - - + +
550C GLU 4.8 2.6 + - - -
551C ARG* 3.5 34.7 - - - +
552C PRO* 3.3 40.3 - - - +
1767C SO4 3.7 11.9 + - - -
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Residues in contact with LYS 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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523A LEU* 5.8 5.4 - - + -
526A ILE* 3.6 21.3 - - + -
527A GLU* 3.2 30.2 + - - +
530A TYR* 4.0 35.9 - - + -
590A ILE* 3.2 10.0 - - + +
591A ARG* 1.3 82.2 - - - +
593A GLY* 1.3 58.1 + - - +
595A ARG* 3.3 7.1 + - + +
596A MET* 2.8 28.4 + - - +
542C ARG* 4.4 6.9 - - - +
551C ARG* 6.1 0.2 - - - +
1765C SO4 2.9 45.6 + - - +
1767C SO4 5.2 4.5 - - - -
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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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526A ILE* 3.8 17.2 - - - +
587A ILE* 3.3 28.0 - - - -
588A MET* 4.9 0.2 - - - -
590A ILE 2.8 7.1 + - - -
592A LYS* 1.3 78.3 - - - +
594A LYS* 1.3 54.7 + - - -
596A MET* 3.2 8.2 + - - +
597A VAL* 2.9 35.8 + - - +
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Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ILE 4.1 0.2 + - - -
588A MET* 2.9 52.7 - - + +
589A CYS 3.7 17.3 + - - -
590A ILE 3.8 6.7 - - - +
591A ARG 3.8 2.7 - - - +
592A LYS 3.3 0.6 - - - -
593A GLY* 1.3 70.8 - - - +
595A ARG* 1.3 68.6 + - - +
596A MET 3.0 0.2 + - - -
597A VAL* 3.1 3.3 + - - +
598A ALA* 2.9 23.7 + - - +
623A LEU 4.6 1.3 + - - -
626A LYS 3.7 8.3 + - - -
627A ASP* 2.6 44.4 + - - +
630A ASP* 4.6 5.1 + - - +
632A VAL* 3.4 30.5 - - + +
633A LEU* 4.1 13.5 - - + -
635A CYS* 4.5 2.9 - - - -
636A LEU* 3.9 8.7 - - + +
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Residues in contact with ARG 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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530A TYR* 6.1 0.9 - - + -
591A ARG* 3.2 33.9 + - - +
592A LYS* 3.3 10.9 + - - +
594A LYS* 1.3 79.0 - - - +
596A MET* 1.3 63.0 - - - +
598A ALA* 3.5 12.5 + - - +
599A ARG* 3.5 21.1 + - - +
632A VAL* 4.3 18.3 - - + +
635A CYS* 3.2 33.1 - - - +
545C LEU* 4.4 21.6 - - - +
1767C SO4 3.0 55.2 + - - +
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Residues in contact with MET 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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526A ILE* 3.5 46.7 - - + +
529A THR* 4.0 9.9 - - - -
530A TYR* 3.8 33.6 - - + -
533A LEU* 4.1 10.8 - - + -
569A LEU* 4.3 17.3 - - + -
587A ILE* 4.1 20.6 - - + -
592A LYS* 2.8 17.3 + - + +
593A GLY* 3.3 10.1 - - - +
595A ARG* 1.3 74.7 - - - +
597A VAL* 1.3 61.1 + - - +
599A ARG* 2.8 23.8 + - - +
600A ILE* 3.0 28.0 + - + +
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Residues in contact with VAL 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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569A LEU* 4.3 29.6 - - + -
584A PHE* 4.5 4.5 - - + -
587A ILE* 4.6 4.7 - - + -
588A MET* 3.6 25.6 - - + -
593A GLY 2.9 21.3 + - - +
594A LYS 3.7 3.8 - - - +
596A MET* 1.3 75.7 - - + +
598A ALA* 1.3 62.7 + - - +
600A ILE* 3.7 8.4 - - + -
601A LEU* 3.1 30.1 + - + +
604A LEU* 6.5 0.4 - - + -
612A ILE* 4.1 26.0 - - + -
636A LEU* 4.2 11.7 - - + -
640A PHE* 5.7 0.4 - - + -
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Residues in contact with ALA 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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594A LYS 2.9 8.6 + - - +
595A ARG* 3.5 11.4 - - - +
596A MET 3.1 0.2 - - - -
597A VAL* 1.3 76.8 - - - +
599A ARG* 1.3 60.8 + - + +
601A LEU* 4.2 4.0 - - - -
602A PRO* 3.9 7.1 - - - +
635A CYS* 3.4 35.2 - - + +
636A LEU* 3.5 19.9 - - + +
639A PRO* 3.4 21.7 - - + +
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Residues in contact with ARG 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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530A TYR* 2.8 29.4 + - - -
533A LEU* 3.6 13.0 - - + +
534A LEU* 3.5 6.7 - - - +
537A GLU* 2.9 44.1 + - - +
595A ARG* 3.6 20.2 - - - +
596A MET 2.8 7.6 + - - +
598A ALA* 1.3 79.2 - - + +
600A ILE* 1.3 63.9 + - - +
601A LEU 3.4 0.7 - - - -
602A PRO* 3.4 9.9 - - - +
603A PHE* 3.3 22.0 - - - -
538C ASP* 3.4 20.6 + - - -
541C ARG* 5.9 3.4 - - - +
542C ARG* 4.4 10.0 - - - +
1767C SO4 4.5 12.1 + - - -
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Residues in contact with ILE 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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529A THR* 3.9 13.0 - - + -
533A LEU* 4.2 3.6 - - + -
565A MET* 3.4 44.0 - - + -
569A LEU* 4.1 20.6 - - + -
596A MET* 3.0 39.0 + - + +
597A VAL* 3.1 13.2 + - + +
599A ARG* 1.3 79.6 - - - +
601A LEU* 1.3 66.8 + - - +
602A PRO 3.4 0.2 - - - -
603A PHE* 3.0 24.5 + - + +
604A LEU* 3.5 25.2 + - + +
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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