Contacts of the helix formed by residues 333 - 338 (chain C) in PDB entry 4PS1
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 ILE 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C GLY* 2.9 22.8 + - - +
322C ILE* 4.1 5.6 - - - +
323C ILE* 4.3 13.5 - - + +
331C ALA 4.2 0.4 - - - +
332C PRO* 1.3 70.3 - - - +
334C TYR* 1.3 63.8 + - - +
336C LEU* 3.0 21.3 + - + +
337C THR* 3.0 22.1 + - + +
357C ILE* 4.2 17.5 - - + -
361C GLN* 3.7 32.8 - - - +
401C LEU* 4.3 28.9 - - + -
403C MET* 3.7 21.5 - - + -
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Residues in contact with TYR 334 (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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332C PRO* 3.1 4.4 - - + +
333C ILE* 1.3 81.5 - - - +
335C GLU* 1.3 58.9 + - + +
337C THR* 3.6 10.8 - - - -
338C SER* 2.7 56.6 + - - -
341C THR* 5.5 0.9 - - - +
396C GLU* 3.4 24.0 + - - -
501C DTT 3.8 34.8 - - + -
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Residues in contact with GLU 335 (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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293C TYR* 3.7 23.8 - - + +
332C PRO* 2.9 34.9 + - + +
334C TYR* 1.3 84.3 - - + +
336C LEU* 1.3 59.5 + - - +
338C SER* 3.8 5.5 + - - -
339C GLN* 2.7 40.1 + - - +
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Residues in contact with LEU 336 (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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292C ILE* 3.9 14.1 - - + -
293C TYR* 3.5 28.3 - - + -
296C LEU* 3.7 31.3 - - + +
314C ILE* 3.6 30.5 - - + -
323C ILE* 4.0 24.5 - - + -
331C ALA* 4.1 7.4 - - + -
332C PRO 3.6 12.8 - - - +
333C ILE* 3.0 13.8 + - + +
335C GLU* 1.3 76.1 - - - +
337C THR* 1.3 67.3 + - + +
339C GLN* 3.3 18.5 + - - +
340C PHE* 3.7 5.7 - - - -
355C PHE* 4.1 6.7 - - + -
357C ILE* 5.5 0.9 - - + -
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Residues in contact with THR 337 (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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333C ILE* 3.0 25.6 + - + +
334C TYR* 3.4 14.6 + - - -
336C LEU* 1.3 76.9 - - + +
338C SER* 1.3 59.9 + - - +
339C GLN 3.0 5.8 + - - -
340C PHE* 3.1 12.1 + - - +
355C PHE* 3.8 39.0 - - + -
357C ILE* 6.1 0.2 - - + -
399C PHE* 3.3 24.1 - - + -
401C LEU* 4.4 10.8 - - + -
501C DTT 3.5 25.3 + - - +
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Residues in contact with SER 338 (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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334C TYR* 2.7 54.1 + - - -
335C GLU* 3.8 5.4 + - - -
336C LEU 3.3 0.2 - - - -
337C THR* 1.3 76.7 + - - +
339C GLN* 1.3 72.6 + - - +
340C PHE 3.1 3.1 + - - -
341C THR* 3.7 14.0 - - - +
344C LYS* 3.4 21.6 + - - +
501C DTT 3.8 12.3 - - - -
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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