Contacts of the strand formed by residues 434 - 439 (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 VAL 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420C CYS* 5.5 1.6 - - - -
433C LYS* 1.3 75.8 - - - +
435C ILE* 1.3 71.4 + - + +
436C CYS 3.2 0.5 + - - -
453C GLN 4.5 0.2 - - - -
454C CYS* 3.8 2.6 - - - -
455C CYS* 2.9 43.9 + - + +
460C ILE* 3.7 30.7 - - + -
463C LEU* 5.5 0.7 - - + -
474C TYR* 3.6 32.8 - - + +
476C VAL* 3.7 21.5 - - + +
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Residues in contact with ILE 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C THR* 5.7 3.6 - - + -
418C GLY 4.8 14.4 - - - +
419C THR* 6.4 0.9 - - - -
420C CYS* 5.8 2.0 - - - -
434C VAL* 1.3 81.6 - - - +
436C CYS* 1.3 61.1 + - - +
437C THR* 4.2 5.4 + - + +
452C PRO* 3.8 27.8 - - + -
453C GLN 3.3 10.5 - - - +
454C CYS* 4.9 5.8 - - - +
476C VAL* 3.4 13.0 + - - +
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Residues in contact with CYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C VAL* 4.4 3.1 - - - -
435C ILE* 1.3 73.7 - - - +
437C THR* 1.3 63.7 + - - +
438C GLY* 3.5 2.4 + - - -
453C GLN* 2.9 41.3 + - - +
454C CYS 3.7 5.2 - - - -
455C CYS* 2.0 60.3 - - + -
476C VAL* 3.3 24.2 - - + +
477C HIS* 4.5 5.2 - - - -
478C LEU* 5.0 3.2 - - + +
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Residues in contact with THR 437 (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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435C ILE* 5.0 5.4 - - + +
436C CYS* 1.3 69.9 - - - +
438C GLY* 1.3 57.9 + - - +
450C THR* 4.6 14.9 - - + +
451C VAL 3.7 6.1 - - - -
452C PRO* 3.8 24.0 - - + -
476C VAL 3.4 7.5 + - - +
477C HIS* 3.4 17.0 - - - +
478C LEU* 2.9 24.3 + - - +
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C CYS 3.5 3.4 + - - -
437C THR* 1.3 74.1 - - - +
439C PRO* 1.3 76.6 - - - +
449C HIS 4.3 0.7 - - - -
450C THR* 4.4 7.4 - - - +
451C VAL* 2.7 36.5 + - - +
453C GLN* 5.6 1.3 - - - +
478C LEU* 3.8 10.8 - - - -
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Residues in contact with PRO 439 (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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438C GLY* 1.3 87.9 - - - +
440C ASN* 1.3 62.6 + - - +
441C ASP 4.5 11.4 - - - +
449C HIS 3.1 15.3 - - - +
450C THR* 4.7 0.4 - - - -
451C VAL* 4.8 0.3 - - - +
478C LEU* 4.1 7.9 - - + +
479C VAL 3.9 22.7 - - - +
480C ALA* 4.8 11.0 - - - +
481C ASP 5.0 4.3 - - - +
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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
------------------------------------------------------------
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