Contacts of the helix formed by residues 593 - 604 (chain C) in PDB entry 1U0O
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 SER 593 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558C TYR* 3.5 10.9 - - - -
559C HIS 2.8 12.9 + - - +
560C ASP* 4.8 3.6 - - - -
591C VAL* 3.9 5.6 - - - +
592C ALA* 1.3 71.7 - - - +
594C THR* 1.3 61.1 + - - +
595C SER* 3.4 1.9 + - - -
596C GLU* 3.1 28.7 + - - +
597C VAL 3.4 14.9 + - - -
626C GLU* 2.4 32.3 + - - -
630C MET* 3.7 22.4 - - - +
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Residues in contact with THR 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C TYR* 3.8 15.3 - - + +
592C ALA 3.4 4.8 + - - +
593C SER* 1.3 71.0 - - - +
595C SER* 1.3 64.6 + - - +
597C VAL* 3.5 8.5 - - - +
598C LEU* 3.1 26.9 + - - +
620C LEU* 4.2 17.0 - - + -
622C THR* 3.5 31.0 - - + +
624C SER 5.4 2.7 - - - +
625C GLN* 6.4 0.4 - - - -
626C GLU* 2.8 28.9 + - + +
634C LEU* 3.6 16.8 - - - +
661C GLN* 4.6 5.0 + - - +
665C ILE* 4.9 2.9 - - + +
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Residues in contact with SER 595 (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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593C SER* 3.4 1.7 + - - -
594C THR* 1.3 73.1 + - - +
596C GLU* 1.3 67.6 + - - +
598C LEU* 3.1 15.5 + - - +
599C LYS 3.1 9.5 + - - -
626C GLU* 2.6 30.7 + - - -
630C MET* 3.3 16.8 + - - +
633C ASN* 4.2 9.7 + - - +
634C LEU* 3.4 37.5 - - - +
637C TYR* 3.3 12.7 - - - -
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Residues in contact with GLU 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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559C HIS 5.5 0.2 - - - +
560C ASP 3.7 23.3 - - - +
561C GLY* 5.5 1.8 - - - -
562C SER* 5.4 0.2 - - - -
593C SER* 3.1 23.7 + - - +
594C THR 3.2 0.2 - - - -
595C SER* 1.3 78.6 + - - +
597C VAL* 1.3 61.0 + - - +
598C LEU 3.0 4.7 - - - -
599C LYS* 3.1 49.6 + - - +
600C TYR* 3.1 11.1 + - - +
630C MET* 4.0 16.2 - - + +
633C ASN* 5.5 2.3 - - - +
637C TYR* 5.2 4.2 - - - -
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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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518C LEU* 3.6 35.8 - - + +
556C VAL* 4.6 2.2 - - + -
558C TYR* 3.5 52.9 - - + -
562C SER* 3.5 24.0 - - - +
593C SER 3.4 3.2 + - - +
594C THR* 3.5 15.3 - - - +
596C GLU* 1.3 78.3 - - - +
598C LEU* 1.3 51.2 + - - +
600C TYR* 3.6 3.5 - - + +
601C THR* 2.7 34.9 + - - +
620C LEU* 4.2 3.6 - - + -
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Residues in contact with LEU 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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518C LEU* 4.2 18.8 - - + -
594C THR 3.1 20.2 - - - +
595C SER* 3.1 8.9 + - - +
596C GLU 3.0 0.6 - - - -
597C VAL* 1.3 80.7 - - + +
599C LYS* 1.3 58.6 + - - +
600C TYR 3.2 0.2 - - - -
601C THR* 3.4 3.0 + - - +
602C LEU* 2.8 29.7 + - - +
618C THR* 4.6 4.0 - - + -
620C LEU* 4.7 7.9 - - + -
634C LEU* 3.9 17.5 - - + +
637C TYR* 4.2 9.1 - - + +
638C VAL* 3.9 25.8 - - + -
641C LEU* 3.7 27.3 - - + +
648C VAL* 4.3 16.8 - - + -
665C ILE* 4.6 11.0 - - + -
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Residues in contact with LYS 599 (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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595C SER 3.1 4.4 + - - +
596C GLU* 3.1 38.1 + - - +
598C LEU* 1.3 74.0 - - - +
600C TYR* 1.3 66.2 + - - +
602C LEU* 4.1 2.9 - - - -
603C PHE* 2.9 56.8 + - + +
637C TYR* 3.6 41.4 + - + +
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Residues in contact with TYR 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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556C VAL* 4.0 29.2 - - + -
562C SER* 3.7 39.0 + - - +
564C ALA* 3.7 18.2 - - + +
567C GLU* 5.6 1.4 + - - -
596C GLU 3.1 10.9 + - - +
597C VAL* 3.6 11.2 - - + +
598C LEU 3.2 0.4 - - - -
599C LYS* 1.3 79.1 - - - +
601C THR* 1.3 56.7 + - - +
604C GLN* 2.7 75.1 + - + +
605C ILE* 4.6 12.7 - - + +
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Residues in contact with THR 601 (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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516C VAL* 4.5 0.7 - - + -
518C LEU* 3.5 16.3 - - - +
597C VAL* 2.7 20.3 + - - +
598C LEU* 3.6 9.2 - - - -
600C TYR* 1.3 79.9 - - - +
602C LEU* 1.3 63.5 + - - +
605C ILE* 3.6 28.6 + - + +
606C PHE* 3.1 40.9 + - + -
618C THR* 3.7 30.5 - - + +
641C LEU* 4.1 7.9 - - + -
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Residues in contact with LEU 602 (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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598C LEU 2.8 21.4 + - - +
599C LYS* 3.7 4.3 - - - +
600C TYR 3.3 0.2 - - - -
601C THR* 1.3 76.5 - - - +
603C PHE* 1.3 93.3 + - + +
606C PHE* 3.5 19.7 - - + +
607C GLY* 3.6 1.7 + - - -
636C ARG 5.0 0.4 - - - +
637C TYR* 4.1 20.9 - - + +
640C GLY* 3.7 40.8 - - - +
641C LEU* 3.5 17.9 - - + +
644C LYS* 3.8 23.6 + - + -
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Residues in contact with PHE 603 (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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599C LYS* 2.9 55.9 + - + +
602C LEU* 1.3 101.5 - - + +
604C GLN* 1.3 82.3 + - + +
607C GLY* 3.8 12.4 - - - -
637C TYR* 4.3 9.0 - + - -
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Residues in contact with GLN 604 (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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600C TYR* 2.7 63.2 + - + +
602C LEU 3.5 1.0 - - - -
603C PHE* 1.3 105.6 + - + +
605C ILE* 1.3 70.0 + - - +
606C PHE 3.2 0.4 - - - -
607C GLY* 2.8 12.5 + - - -
608C LYS 4.7 0.5 + - - -
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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