Contacts of the helix formed by residues 420 - 428 (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 SER 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C VAL 4.7 0.4 - - - -
416C ALA* 4.0 13.5 - - - -
417C PRO* 3.7 8.4 + - - -
418C VAL 3.8 0.2 - - - -
419C ILE* 1.3 77.8 - - - +
421C LYS* 1.3 65.6 + - - +
422C GLU* 2.7 29.1 + - - +
423C THR* 3.1 25.3 + - - -
424C VAL* 3.0 20.7 + - - +
565C LEU* 5.2 0.7 - - - +
566C THR* 3.7 16.9 + - - -
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Residues in contact with LYS 421 (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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412C VAL* 3.7 31.1 + - + +
413C ASP* 4.0 26.2 - - + +
416C ALA* 4.3 7.4 - - + +
420C SER* 1.3 74.8 - - - +
422C GLU* 1.3 76.6 + - - +
424C VAL* 3.2 3.8 + - - +
425C GLU* 3.0 52.1 + - - +
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Residues in contact with GLU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C SER* 2.7 23.3 + - - +
421C LYS* 1.3 92.8 + - + +
423C THR* 1.3 63.0 + - - +
425C GLU* 3.2 16.8 + - - +
426C PHE* 3.0 36.1 + - + -
565C LEU* 4.5 14.8 - - + +
566C THR* 4.9 1.7 + - - -
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Residues in contact with THR 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ILE* 3.8 14.4 - - + -
420C SER* 3.1 29.4 + - - -
422C GLU* 1.3 75.1 - - - +
424C VAL* 1.3 56.1 + - - +
426C PHE* 4.5 1.1 - - - +
427C HIS* 2.7 46.9 + - + +
561C HIS 4.1 13.5 - - - +
562C ALA 3.7 23.3 - - - +
563C TYR* 5.4 1.8 - - - -
565C LEU* 3.8 27.8 + - + +
566C THR* 4.3 5.4 + - - -
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Residues in contact with VAL 424 (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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408C LEU* 3.5 32.5 - - + -
410C TYR* 5.3 2.7 - - + -
412C VAL* 3.3 37.9 - - + +
415C LEU* 4.9 11.7 - - + -
419C ILE* 3.7 23.6 - - + +
420C SER 3.0 14.9 + - - +
421C LYS 3.5 3.1 - - - +
423C THR* 1.3 74.5 - - - +
425C GLU* 1.3 60.6 + - - +
427C HIS* 4.6 1.8 - - - -
428C HIS* 2.8 33.5 + - + +
429C GLY 3.2 4.7 + - - -
478C PHE* 5.4 5.8 - - + -
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Residues in contact with GLU 425 (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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412C VAL* 4.6 19.0 - - + +
421C LYS* 3.0 44.2 + - + +
422C GLU* 3.5 22.2 + - - +
424C VAL* 1.3 77.0 - - - +
426C PHE* 1.3 61.8 + - + +
429C GLY* 3.0 26.8 - - - +
430C LYS* 3.4 7.3 + - - +
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Residues in contact with PHE 426 (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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422C GLU* 3.0 33.4 + - + +
423C THR* 4.1 2.0 - - - +
425C GLU* 1.3 79.0 - - + +
427C HIS* 1.3 62.9 + - - +
430C LYS* 2.9 44.9 + - + +
431C HIS* 2.8 30.2 + - + -
565C LEU* 4.0 17.7 - - + -
764D TYR* 3.7 14.6 - - - +
768D GLN* 3.5 50.9 - - + -
769D ASN* 3.7 6.3 - - - -
770D ARG* 6.3 0.4 - - - -
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Residues in contact with HIS 427 (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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419C ILE* 5.5 1.8 - - + +
423C THR* 2.7 32.2 + - + +
424C VAL* 4.2 0.4 - - - +
426C PHE* 1.3 72.9 - - - +
428C HIS* 1.3 58.2 + - - +
431C HIS* 3.3 13.7 - - + +
432C LEU* 3.0 26.0 + - - +
474C HIS* 3.0 12.8 + + - -
477C TYR* 3.7 22.8 + + - -
478C PHE* 3.7 13.8 - + + -
557C ASP* 2.9 17.7 - - - -
561C HIS* 3.1 15.0 + + + +
562C ALA* 3.6 26.7 + - + +
592C MN 2.2 29.5 + - - -
764D TYR* 5.0 0.6 + - - -
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Residues in contact with HIS 428 (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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405C LEU* 3.3 57.7 - - + +
406C ILE* 2.6 38.4 + - + -
407C SER* 5.1 0.9 - - - -
408C LEU* 3.5 38.7 - - + +
424C VAL* 2.8 21.3 + - + +
427C HIS* 1.3 76.7 - - - +
429C GLY* 1.3 67.1 + - - +
432C LEU* 3.4 8.0 - - + +
433C LYS 3.4 8.5 + - - -
478C PHE* 3.7 23.1 - + + -
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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