Contacts of the helix formed by residues 591 - 606 (chain x) in PDB entry 5Z58
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 TYR 591 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588x GLU* 4.8 10.8 - - + +
589x ALA 3.7 3.7 + - - +
590x ASP* 1.3 73.8 - - - +
592x LEU* 1.3 66.3 + - - +
593x GLU 3.5 0.2 - - - -
594x ALA* 3.1 8.5 + - - +
595x CYS* 2.9 22.9 + - - +
692x PRO* 4.6 23.8 - - + +
694x PHE* 6.1 4.0 - - + -
737x LEU* 5.6 3.7 - - + +
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Residues in contact with LEU 592 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590x ASP 3.5 1.0 - - - -
591x TYR* 1.3 77.3 - - - +
593x GLU* 1.3 59.1 + - - +
595x CYS* 2.9 23.1 + - - +
596x VAL* 3.2 11.1 + - - +
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Residues in contact with GLU 593 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590x ASP* 4.5 7.6 + - + +
592x LEU* 1.3 78.4 - - - +
594x ALA* 1.3 57.3 + - - +
595x CYS 3.2 0.2 - - - -
596x VAL* 3.8 9.3 - - + +
597x VAL* 3.1 28.9 + - - +
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Residues in contact with ALA 594 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588x GLU* 4.4 15.9 - - + -
590x ASP 3.4 18.1 + - - +
591x TYR* 3.1 16.4 + - - +
592x LEU 3.1 0.8 - - - -
593x GLU* 1.3 77.9 - - - +
595x CYS* 1.3 58.8 + - - +
597x VAL* 4.0 6.9 + - - +
598x SER* 4.0 16.3 + - - -
737x LEU* 4.9 13.6 - - + +
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Residues in contact with CYS 595 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591x TYR 2.9 10.1 + - - +
592x LEU* 2.9 12.7 + - - +
594x ALA* 1.3 76.5 - - - +
596x VAL* 1.3 63.3 + - - +
597x VAL 3.2 0.4 + - - -
598x SER* 3.5 4.3 + - - -
599x VAL* 3.5 22.3 + - - +
614x PHE 5.8 3.1 - - - +
690x LEU* 5.8 5.2 - - + -
692x PRO* 4.9 14.4 - - + -
737x LEU* 5.9 2.5 - - - -
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Residues in contact with VAL 596 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592x LEU 3.2 8.8 + - - +
593x GLU* 3.5 10.3 + - - +
595x CYS* 1.3 78.9 - - - +
597x VAL* 1.3 63.3 + - - +
598x SER 3.5 0.3 + - - -
599x VAL* 3.7 4.2 + - - +
600x LEU* 3.6 22.2 + - - +
624x ALA* 6.0 6.1 - - + +
627x MET* 5.5 11.4 - - + -
628x LEU* 5.6 11.5 - - + +
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Residues in contact with VAL 597 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593x GLU 3.1 18.8 + - - +
594x ALA* 4.2 7.4 - - - +
595x CYS 3.2 0.6 - - - -
596x VAL* 1.3 79.0 - - - +
598x SER* 1.3 60.6 + - - +
600x LEU* 4.4 1.7 - - - +
601x GLN* 3.6 18.9 + - - +
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Residues in contact with SER 598 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594x ALA 4.0 9.3 + - - -
595x CYS* 3.5 6.7 + - - -
596x VAL 3.3 0.4 - - - -
597x VAL* 1.3 78.9 - - - +
599x VAL* 1.3 66.1 + - - +
601x GLN* 3.2 7.4 + - - +
602x ILE* 2.9 23.1 + - - +
735x PHE* 5.4 12.3 - - - -
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Residues in contact with VAL 599 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595x CYS 3.5 14.2 + - - +
596x VAL* 4.4 4.7 - - - +
597x VAL 3.5 0.4 - - - -
598x SER* 1.3 78.8 - - - +
600x LEU* 1.3 57.3 + - + +
602x ILE* 3.3 10.5 + - - +
603x HIS* 3.2 22.3 + - - +
611x ILE* 5.4 9.2 - - + -
628x LEU* 6.2 3.8 - - + -
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Residues in contact with LEU 600 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596x VAL 3.6 13.6 + - - +
597x VAL 4.6 1.8 - - - +
598x SER 3.3 0.4 - - - -
599x VAL* 1.3 76.6 - - - +
601x GLN* 1.3 62.9 + - - +
603x HIS* 3.3 20.6 - - + +
604x VAL* 3.9 5.9 + - - +
628x LEU* 6.1 6.3 - - + +
631x ARG* 5.3 17.9 - - + +
632x CYS* 6.0 1.8 - - - +
635x LEU* 5.5 7.8 - - + +
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Residues in contact with GLN 601 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597x VAL 3.6 13.1 + - - +
598x SER* 3.2 10.7 + - - +
600x LEU* 1.3 75.1 - - - +
602x ILE* 1.3 60.3 + - - +
603x HIS 3.1 1.7 + - - -
604x VAL* 3.4 3.2 + - - +
605x THR* 2.8 38.3 + - - -
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Residues in contact with ILE 602 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598x SER 2.9 12.8 + - - +
599x VAL* 3.3 13.2 + - - +
601x GLN* 1.3 75.8 - - - +
603x HIS* 1.3 65.5 + - - +
605x THR* 5.0 1.1 - - - -
606x GLN* 3.1 37.8 + - + +
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Residues in contact with HIS 603 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599x VAL 3.2 9.8 + - - +
600x LEU* 3.3 20.2 - - - +
601x GLN 3.1 0.2 - - - -
602x ILE* 1.3 79.0 - - - +
604x VAL* 1.3 59.3 + - - +
606x GLN 4.2 5.9 - - - +
635x LEU* 5.9 6.5 - - + -
668x ARG* 5.5 13.6 - - + +
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Residues in contact with VAL 604 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600x LEU 3.9 5.5 + - - +
601x GLN* 3.4 4.9 + - - +
603x HIS* 1.3 80.0 - - + +
605x THR* 1.3 64.1 + - - +
606x GLN 3.4 5.1 + - - +
635x LEU* 6.2 2.5 - - + -
639x ILE* 5.4 12.3 - - + -
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Residues in contact with THR 605 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601x GLN* 2.8 26.2 + - - -
602x ILE* 5.1 0.4 - - - -
604x VAL* 1.3 73.3 - - - +
606x GLN* 1.3 57.7 + - - +
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Residues in contact with GLN 606 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602x ILE* 3.1 30.7 + - + +
603x HIS 4.2 4.9 - - - +
604x VAL 4.2 6.6 - - - +
605x THR* 1.3 79.1 - - - +
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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