Contacts of the strand formed by residues 432 - 436 (chain C) in PDB entry 4P3N
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 432 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C GLN* 3.6 22.4 - - - +
420C PHE* 3.9 25.6 - - + -
425C ARG* 4.2 24.5 - - - +
429C GLU* 3.6 21.3 + - + +
430C LEU* 3.7 13.2 - - + +
431C PRO* 1.3 72.5 - - - +
433C ARG* 1.3 63.3 + - - +
434C LEU* 3.8 27.8 - - + -
466C PHE* 2.9 45.6 + - + +
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Residues in contact with ARG 433 (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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367C ARG 3.8 10.0 + - - -
368C GLY* 3.1 33.2 + - - +
369C PHE* 3.7 44.7 - - + -
370C GLN* 3.0 27.3 + - - +
431C PRO* 3.9 24.5 + - - +
432C LEU* 1.3 77.7 - - - +
434C LEU* 1.3 67.0 + - - +
464C HIS 3.3 6.3 - - - +
465C ILE* 4.0 16.4 - - + +
475C GLU* 2.7 38.0 + - - -
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Residues in contact with LEU 434 (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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370C GLN* 3.4 10.1 - - + +
372C VAL* 4.3 19.1 - - + -
416C HIS* 3.8 26.2 - - + +
419C MET* 4.3 28.5 - - + -
420C PHE 4.9 2.7 - - - +
425C ARG* 6.0 1.3 - - - +
432C LEU* 3.8 29.8 + - + -
433C ARG* 1.3 79.6 - - - +
435C ALA* 1.3 60.3 + - - +
463C ALA* 3.3 2.3 - - - -
464C HIS 2.9 38.6 + - - +
466C PHE* 4.2 21.8 - - + -
346D LEU* 6.3 0.9 - - + -
347D PRO* 4.5 12.8 - - + -
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Residues in contact with ALA 435 (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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364C TYR* 3.4 41.5 - - + -
369C PHE* 4.6 6.3 - - + -
370C GLN 3.0 10.5 + - - +
371C GLU* 3.2 14.2 - - + +
372C VAL* 2.8 29.9 + - - +
433C ARG 4.1 0.6 + - - -
434C LEU* 1.3 74.3 - - - +
436C ASP* 1.3 60.8 + - - +
437C PHE* 5.8 0.2 - - + -
462C ASP 3.3 5.8 - - - +
463C ALA* 4.1 4.5 - - + +
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Residues in contact with ASP 436 (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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364C TYR* 5.5 0.2 - - - -
371C GLU* 4.9 0.7 - - - -
372C VAL* 3.7 15.0 - - - +
373C VAL* 4.8 0.7 - - - -
374C THR* 2.3 37.0 + - - +
412C ASN* 3.7 15.0 + - - +
416C HIS* 3.0 31.5 + - + +
435C ALA* 1.3 72.7 - - - +
437C PHE* 1.3 62.7 + - - +
438C GLY* 2.7 32.7 + - - -
460C GLN 3.6 1.7 - - - +
462C ASP* 2.7 38.8 + - - +
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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