Contacts of the helix formed by residues 553 - 560 (chain C) in PDB entry 1WSU
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 LEU 553 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518C LEU* 3.3 36.6 - - + -
519C LEU* 3.9 19.3 - - + -
522C LEU* 3.4 30.5 - - + -
551C GLU 3.3 1.6 - - - +
552C GLU* 1.3 90.3 - - + +
554C LEU* 1.3 61.5 + - + +
555C HIS 3.3 0.2 - - - -
556C TYR* 2.8 30.6 + - + +
557C LEU* 3.2 10.8 + - - +
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Residues in contact with LEU 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LEU* 5.0 12.1 - - + -
526C TYR* 3.6 27.1 - - + +
536C PHE* 3.5 37.7 - - + -
539C VAL* 5.2 2.2 - - + -
551C GLU* 3.8 12.7 + - - +
553C LEU* 1.3 79.9 - - + +
555C HIS* 1.3 64.5 + - - +
557C LEU* 3.0 14.0 + - + +
558C VAL* 2.9 27.5 + - - +
563C LEU* 3.7 22.2 - - + +
571C TYR* 3.2 34.5 - - + -
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Residues in contact with HIS 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C GLU* 3.1 33.2 + - + +
552C GLU 4.5 2.7 - - - +
554C LEU* 1.3 78.6 - - - +
556C TYR* 1.3 60.7 + - - +
558C VAL* 3.4 14.2 + - + +
559C ARG* 3.1 41.7 + - + +
571C TYR* 5.4 0.4 - - - -
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Residues in contact with TYR 556 (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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519C LEU* 3.6 37.4 - - + +
552C GLU 4.0 7.7 + - - +
553C LEU* 2.8 17.2 + - + +
555C HIS* 1.3 79.7 - - - +
557C LEU* 1.3 67.1 + - + -
559C ARG* 3.1 38.1 + - - +
560C GLU* 2.8 65.1 + - + +
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Residues in contact with LEU 557 (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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519C LEU* 4.0 31.6 - - + +
522C LEU* 4.1 32.8 - - + -
523C GLU* 4.6 5.8 - - - +
553C LEU 3.8 9.4 - - - +
554C LEU* 3.0 8.3 + - + +
556C TYR* 1.3 86.5 - - + +
558C VAL* 1.3 64.0 + - - +
560C GLU* 3.1 9.5 + - - -
561C GLY 3.1 0.2 + - - -
562C VAL* 2.9 49.5 + - + -
563C LEU* 3.3 34.5 + - + -
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Residues in contact with VAL 558 (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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554C LEU* 2.9 28.3 + - + +
555C HIS* 3.4 16.6 - - + +
557C LEU* 1.3 76.0 - - - +
559C ARG* 1.3 60.6 + - - +
560C GLU 3.3 0.9 + - - -
561C GLY* 3.3 10.9 + - - -
563C LEU* 3.4 31.9 - - + +
564C VAL* 4.7 8.1 - - + +
565C LYS* 4.8 12.1 - - + +
571C TYR* 5.1 11.7 - - + -
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Residues in contact with ARG 559 (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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552C GLU 5.4 1.6 + - - -
555C HIS* 3.1 33.3 + - + +
556C TYR* 3.1 54.8 + - - +
558C VAL* 1.3 78.9 - - - +
560C GLU* 1.3 70.0 + - - +
561C GLY 3.4 0.4 + - - -
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Residues in contact with GLU 560 (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 TYR* 2.8 71.5 + - + +
557C LEU 3.1 6.2 + - - +
559C ARG* 1.3 94.7 + - - +
561C GLY* 1.3 59.0 + - - +
562C VAL* 3.2 18.5 + - + +
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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