Contacts of the helix formed by residues 591 - 600 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A ARG* 4.8 6.1 - - - +
549A GLU* 5.6 6.3 + - - -
551A ARG* 6.1 1.0 - - - +
590C ILE* 1.3 74.0 - - + +
592C LYS* 1.3 63.9 + - - +
594C LYS* 3.3 12.2 + - - +
595C ARG* 3.1 47.7 + - - +
630C ASP* 3.5 44.0 + - + +
632C VAL* 3.7 23.9 - - + +
1766C SO4 3.2 35.0 + - - +
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Residues in contact with LYS 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ASP* 4.8 2.2 + - - -
538A ASP* 5.1 2.4 + - - -
542A ARG* 5.1 2.8 - - - +
558A ARG* 3.3 31.1 - - - +
526C ILE* 4.0 16.4 - - + -
527C GLU* 3.8 25.9 + - - +
530C TYR* 3.7 37.8 - - + -
590C ILE* 3.3 9.4 - - + +
591C ARG* 1.3 78.1 - - - +
593C GLY* 1.3 57.7 + - - +
595C ARG* 3.3 24.6 + - - +
596C MET* 2.8 31.1 + - - +
1766C SO4 3.5 26.4 + - - +
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Residues in contact with GLY 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C ILE* 3.9 12.6 - - - +
587C ILE* 3.5 31.2 - - - -
590C ILE 3.1 5.3 + - - -
592C LYS* 1.3 78.7 - - - +
594C LYS* 1.3 56.0 + - - +
596C MET* 3.2 8.1 + - - +
597C VAL* 2.9 36.5 + - - +
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Residues in contact with LYS 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C ILE 4.1 0.6 + - - -
588C MET* 3.3 47.9 + - + +
589C CYS 4.1 4.0 + - - -
590C ILE 3.0 27.1 + - - +
591C ARG* 3.7 1.6 - - - +
593C GLY* 1.3 75.6 - - - +
595C ARG* 1.3 62.3 + - - +
597C VAL* 4.0 1.9 - - - +
598C ALA* 3.2 23.0 + - - +
623C LEU 5.1 0.6 + - - +
626C LYS 3.5 16.2 + - - -
627C ASP* 2.7 24.8 + - + +
630C ASP* 3.5 18.0 + - - +
632C VAL* 3.5 27.6 - - + +
633C LEU* 3.7 22.2 - - + -
635C CYS* 4.7 2.3 - - - -
636C LEU* 4.2 6.7 - - + +
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Residues in contact with ARG 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ARG* 3.3 39.2 - - - +
530C TYR* 3.6 14.3 + - - -
591C ARG* 3.1 35.4 + - - +
592C LYS* 3.3 40.4 - - - +
594C LYS* 1.3 76.2 - - - +
596C MET* 1.3 62.0 + - - +
598C ALA* 3.6 6.8 + - - +
599C ARG* 3.3 40.3 + - - +
632C VAL* 4.6 15.0 - - + -
635C CYS* 4.5 10.1 - - - -
1766C SO4 2.8 21.9 + - - -
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Residues in contact with MET 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C ILE* 3.6 28.3 - - + +
529C THR* 3.5 34.5 - - + -
530C TYR* 3.6 28.2 - - + -
533C LEU* 3.8 15.0 - - + -
569C LEU* 3.8 19.3 - - + -
587C ILE* 4.3 12.6 - - + -
592C LYS 2.8 18.6 + - - +
593C GLY* 3.2 11.0 + - - +
595C ARG* 1.3 74.7 - - - +
597C VAL* 1.3 67.3 + - + +
599C ARG* 2.8 15.2 + - - +
600C ILE* 3.0 26.4 + - + +
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Residues in contact with VAL 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C LEU* 4.1 28.7 - - + -
584C PHE* 4.3 7.6 - - + -
587C ILE* 4.4 4.5 - - + -
588C MET* 3.7 25.8 - - + -
593C GLY 2.9 23.8 + - - +
594C LYS 4.0 4.3 - - - +
596C MET* 1.3 73.2 - - + +
598C ALA* 1.3 62.9 + - - +
600C ILE* 3.1 18.5 + - + +
601C LEU* 3.1 25.6 + - + +
612C ILE* 4.2 17.0 - - + -
636C LEU* 3.7 16.8 - - + -
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Residues in contact with ALA 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C LYS 3.2 16.0 + - - +
595C ARG 3.6 6.7 - - - +
596C MET 3.1 0.4 - - - -
597C VAL* 1.3 79.0 - - - +
599C ARG* 1.3 63.1 + - + +
601C LEU* 4.5 2.0 - - - -
602C PRO* 3.5 15.1 - - - +
635C CYS* 3.5 36.1 - - + +
636C LEU* 3.6 17.9 - - + +
639C PRO* 4.0 11.8 - - - +
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Residues in contact with ARG 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 3.4 18.0 + - - -
542A ARG* 3.8 10.9 - - - +
530C TYR* 2.8 28.7 + - - -
533C LEU* 3.7 15.6 - - + +
534C LEU* 3.7 6.3 - - - +
537C GLU* 2.6 44.7 + - - +
595C ARG* 3.3 30.4 + - - +
596C MET 2.8 7.4 + - - +
598C ALA* 1.3 78.6 - - + +
600C ILE* 1.3 60.3 + - - +
602C PRO* 3.2 18.6 - - - +
603C PHE* 3.4 18.0 - - - -
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Residues in contact with ILE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C THR* 3.9 11.7 - - + -
533C LEU* 4.3 3.8 - - + -
565C MET* 3.3 40.6 - - + -
569C LEU* 3.8 25.1 - - + -
596C MET* 3.0 39.9 + - + +
597C VAL* 3.1 6.0 + - + +
599C ARG* 1.3 77.8 - - - +
601C LEU* 1.3 57.0 + - - +
602C PRO 3.2 2.7 - - - -
603C PHE* 2.7 37.3 + - + +
604C LEU* 3.4 28.2 + - + -
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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