Contacts of the helix formed by residues 583 - 591 (chain C) in PDB entry 1UES
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 583 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480C GLN 3.1 19.4 + - - +
482C ARG* 3.2 25.0 - - + +
485C LYS* 3.7 27.7 - - - +
581C ILE 3.5 1.4 + - - -
582C VAL* 1.3 73.0 - - - +
584C TRP* 1.3 62.0 + - - +
585C ASP* 3.1 25.9 + - - +
586C ILE* 2.9 41.8 + - + +
587C VAL* 3.2 12.5 + - - +
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Residues in contact with TRP 584 (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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485C LYS* 5.1 1.0 - - - +
486C GLY* 3.5 25.4 + - - +
487C GLY 3.4 17.8 + - - -
488C ALA 4.1 0.7 - - - -
489C PRO* 3.5 30.5 - - + -
490C LYS* 3.8 8.7 - - - +
493C LEU* 3.9 13.0 - - + -
497C ILE* 4.7 2.0 - - + -
504C PHE* 3.7 27.4 - + - -
507C PHE* 4.5 7.4 - + - -
526C LEU* 4.7 5.2 - - + -
554C LEU* 4.0 20.0 - - + -
579C TRP* 3.8 19.7 + + - -
582C VAL* 3.4 24.4 + - + +
583C ASP* 1.3 72.5 + - - +
585C ASP* 1.3 53.1 + - - +
586C ILE 3.3 0.2 - - - -
587C VAL* 3.6 32.8 - - + -
588C GLU* 2.7 55.7 + - - +
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Residues in contact with ASP 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C LYS* 5.0 8.4 - - - -
490C LYS* 2.8 26.3 + - - -
583C ASP* 3.0 16.5 + - - +
584C TRP* 1.3 78.4 + - - +
586C ILE* 1.3 60.3 + - + +
588C GLU* 3.9 8.7 - - - +
589C SER* 3.0 27.9 + - - -
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Residues in contact with ILE 586 (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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479C THR* 3.7 27.1 - - - +
480C GLN* 4.3 7.0 - - + +
482C ARG* 3.8 22.0 - - - +
583C ASP* 2.9 40.5 + - + +
585C ASP* 1.3 77.0 - - + +
587C VAL* 1.3 64.0 + - - +
589C SER* 2.5 27.8 + - - +
590C ARG* 3.3 29.7 + - + +
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Residues in contact with VAL 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C GLN* 4.8 11.2 - - + -
493C LEU* 3.7 10.8 - - + -
526C LEU* 4.8 1.1 - - + -
553C LEU* 3.7 35.9 - - + +
554C LEU* 4.1 14.8 - - + -
582C VAL* 4.0 21.1 - - + -
583C ASP 3.2 13.0 + - - +
584C TRP* 3.6 31.2 - - + +
586C ILE* 1.3 76.8 - - - +
588C GLU* 1.3 62.5 + - - +
590C ARG* 3.0 16.9 + - - +
591C TYR* 3.3 9.9 + - - +
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Residues in contact with GLU 588 (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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489C PRO* 3.6 0.7 - - - +
490C LYS* 2.8 63.2 + - - +
491C GLY* 5.6 1.5 - - - -
493C LEU* 4.0 30.7 - - + +
584C TRP* 2.7 33.8 + - + +
585C ASP* 3.9 7.8 - - - +
587C VAL* 1.3 73.1 - - - +
589C SER* 1.3 59.5 + - - +
591C TYR* 3.3 24.0 + - + +
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Residues in contact with SER 589 (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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585C ASP 3.0 16.3 + - - -
586C ILE* 2.5 25.6 + - - +
587C VAL 3.0 0.4 - - - -
588C GLU* 1.3 78.6 - - - +
590C ARG* 1.3 61.4 + - - +
591C TYR 3.4 4.5 - - - +
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Residues in contact with ARG 590 (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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476C LEU* 3.0 48.9 + - + +
479C THR* 3.2 15.4 + - - -
480C GLN* 3.1 35.9 + - - +
525C TRP* 5.8 1.4 - - - -
551C ASN* 2.8 27.6 - - - +
552C PRO 3.7 13.6 + - - +
553C LEU* 3.1 40.9 + - + +
554C LEU* 4.1 0.8 - - - +
555C THR* 5.8 0.4 - - - +
586C ILE* 3.6 24.0 - - + +
587C VAL* 3.0 7.2 + - - +
589C SER* 1.3 78.9 - - - +
591C TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 591 (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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492C LYS* 3.6 45.7 + - + +
493C LEU* 3.5 47.1 - - + -
496C ALA* 3.5 14.4 - - + +
528C SER* 3.8 15.7 + - - -
532C GLY* 2.7 32.8 + - - -
534C LEU* 3.6 19.1 - - + -
551C ASN* 5.2 0.6 - - - +
553C LEU* 3.5 26.0 - - + -
587C VAL 3.3 6.3 + - - +
588C GLU* 3.3 21.4 + - + +
589C SER 4.0 5.0 - - - +
590C ARG* 1.3 84.1 - - - +
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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