Contacts of the helix formed by residues 435 - 439 (chain B) in PDB entry 3UO8
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 ARG 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B TYR* 3.7 4.9 - - - -
433B PRO* 5.4 1.6 - - + +
434B TYR* 1.3 83.8 - - - +
436B SER* 1.3 61.8 + - - +
437B GLU* 3.2 36.4 + - - +
438B ASN* 2.9 29.0 + - - +
439B CYS* 3.6 9.6 - - - -
468B ASN* 3.8 8.3 - - - +
470B TYR* 3.3 26.2 + - + +
471B ASP* 3.9 8.2 + - + +
472B ASP* 4.3 16.6 + - - +
473B THR* 4.7 8.2 + - - -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ARG* 4.8 0.3 + - - -
417B TYR* 3.3 9.7 + - - -
424B PHE* 3.6 28.4 - - - -
435B ARG* 1.3 75.0 - - - +
437B GLU* 1.3 64.0 + - - +
439B CYS* 3.1 23.6 + - - +
471B ASP* 2.9 28.1 + - - -
473B THR* 3.3 21.7 + - - +
475B PRO* 5.8 3.1 - - - -
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B GLU* 3.1 21.1 - - - +
392B ARG* 4.1 4.5 + - - +
435B ARG* 3.3 45.8 + - - +
436B SER* 1.3 84.4 + - - +
438B ASN* 1.3 70.2 + - - +
439B CYS 3.3 1.3 - - - -
473B THR* 4.4 4.9 + - - -
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Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B GLU* 3.6 18.6 - - - +
427B PRO* 3.1 25.6 - - - +
429B ASP* 5.2 0.2 - - - +
430B ALA* 4.7 4.1 - - + +
431B PRO* 3.5 40.5 - - + +
434B TYR* 3.8 3.3 - - + +
435B ARG* 2.9 35.9 + - - +
437B GLU* 1.3 91.7 - - - +
439B CYS* 1.3 63.0 + - - +
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Residues in contact with CYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ARG* 2.9 18.2 + - - -
417B TYR* 4.0 5.2 - - - -
424B PHE* 4.1 15.9 - - + -
425B MET 3.2 18.6 - - - +
426B VAL* 3.9 18.2 - - - -
427B PRO* 4.0 3.6 - - - -
434B TYR* 3.8 22.2 - - - -
435B ARG 3.6 14.6 - - - +
436B SER* 3.1 15.9 + - - +
437B GLU 3.3 0.6 - - - -
438B ASN* 1.3 87.0 - - - +
440B LEU* 1.3 66.1 + - - +
441B CYS 4.0 1.4 + - - -
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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