Contacts of the strand formed by residues 450 - 457 (chain C) in PDB entry 4PE5
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 THR 450 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C THR* 4.6 13.2 - - + -
438C GLY* 3.7 18.7 - - - +
439C PRO 5.5 0.3 - - - -
449C HIS* 1.3 72.1 + - - +
451C VAL* 1.3 69.5 + - - +
452C PRO* 4.7 1.8 - - + +
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Residues in contact with VAL 451 (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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437C THR* 4.3 2.9 - - - -
438C GLY 2.7 42.6 + - - +
439C PRO 4.5 0.2 - - - -
440C ASN* 3.5 37.7 - - + +
450C THR* 1.3 81.9 - - - +
452C PRO* 1.3 76.9 - - + +
453C GLN* 3.7 4.1 + - + +
1I NAG 4.2 23.6 - - - +
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Residues in contact with PRO 452 (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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414C THR* 3.3 22.7 + - + +
435C ILE* 3.8 23.6 - - + -
437C THR* 3.8 22.0 - - + -
450C THR 4.7 1.1 - - - +
451C VAL* 1.3 93.2 - - + +
453C GLN* 1.3 60.2 + - - +
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Residues in contact with GLN 453 (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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411C VAL* 3.8 24.5 - - + -
412C LYS 3.9 7.4 - - - +
413C PRO* 4.9 4.0 - - + -
414C THR* 3.7 7.5 - - - +
435C ILE* 3.3 10.9 - - - +
436C CYS* 2.9 36.1 + - - +
438C GLY* 5.6 1.1 - - - +
451C VAL* 3.7 5.1 + - + +
452C PRO* 1.3 74.4 - - - +
454C CYS* 1.3 68.6 + - - +
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Residues in contact with CYS 454 (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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410C TYR 3.3 3.3 - - - +
411C VAL* 3.4 1.3 - - - -
412C LYS* 2.9 45.8 + - + +
413C PRO 4.5 1.6 - - - +
414C THR* 3.6 31.6 - - - -
419C THR* 4.0 1.3 - - - -
420C CYS* 2.0 52.3 - - + -
433C LYS* 4.8 1.8 - - + -
434C VAL 3.8 2.2 - - - -
435C ILE* 5.7 3.6 - - - -
436C CYS* 3.7 2.5 - - - -
453C GLN* 1.3 78.4 - - - +
455C CYS* 1.3 60.8 + - - +
456C TYR* 4.0 1.1 + - + +
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Residues in contact with CYS 455 (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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402C THR* 4.5 9.6 - - - -
409C VAL* 4.5 9.0 - - + -
410C TYR 3.2 4.0 - - - +
411C VAL* 3.7 22.7 - - - -
433C LYS* 3.4 1.1 - - - -
434C VAL* 2.9 41.5 + - + +
436C CYS* 2.0 47.2 - - + -
454C CYS* 1.3 72.1 - - - +
456C TYR* 1.3 62.9 + - - +
460C ILE* 3.7 22.1 - - + +
476C VAL* 4.9 0.4 - - + -
478C LEU* 6.1 2.0 - - - -
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Residues in contact with TYR 456 (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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410C TYR* 2.9 41.3 + - + +
431C VAL* 4.5 9.9 - - + -
432C LYS 3.5 19.5 - - - +
433C LYS* 4.0 9.6 - - + -
454C CYS* 4.0 1.7 + - + +
455C CYS* 1.3 75.1 - - - +
457C GLY* 1.3 58.4 + - - +
460C ILE* 3.6 10.9 - - - +
792C TRP* 4.5 2.0 - - + -
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Residues in contact with GLY 457 (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 PHE 3.2 10.3 - - - -
410C TYR* 4.7 1.1 - - - -
456C TYR* 1.3 75.7 - - - +
458C PHE* 1.3 65.2 + - - -
459C CYS 3.6 0.7 - - - -
460C ILE* 3.6 6.9 - - - +
461C ASP* 2.8 30.6 + - - +
792C TRP* 3.5 29.9 - - - -
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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