Contacts of the helix formed by residues 439 - 444 (chain B) in PDB entry 4R95
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 ASP 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278B CYS* 4.9 0.9 - - - -
354B ASN* 4.2 6.9 + - - -
438B LEU* 1.4 84.6 - - - +
440B MET* 1.3 64.0 + - - +
441B GLU* 3.3 4.3 - - - +
442B ASP* 3.1 39.1 - - + +
443B CYS* 3.8 6.1 + - - -
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Residues in contact with MET 440 (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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263B ILE* 3.9 1.6 - - - +
265B VAL* 3.7 19.1 - - + -
349B MET* 3.4 41.5 - - + +
350B GLY 5.1 0.2 - - - +
352B VAL 4.3 3.4 - - - +
353B THR* 5.2 0.4 - - - -
354B ASN* 3.7 15.7 + - - +
355B GLN 3.2 43.1 - - - +
356B SER* 4.1 2.2 - - - -
437B THR* 3.6 39.9 - - + +
438B LEU 4.3 0.2 - - - +
439B ASP* 1.3 72.7 - - - +
441B GLU* 1.4 57.3 + - - +
442B ASP 3.1 2.0 - - - -
443B CYS* 2.8 36.5 + - - +
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Residues in contact with GLU 441 (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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255B ARG* 5.3 2.3 + - - -
263B ILE* 5.1 3.5 - - - +
279B LYS* 5.0 0.2 + - - -
349B MET* 3.8 11.5 - - + +
439B ASP* 3.3 2.0 - - - -
440B MET* 1.4 76.1 - - - +
442B ASP* 1.4 62.3 + - - +
444B GLY* 3.4 15.6 + - - +
446B ASN* 5.8 1.0 + - - -
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Residues in contact with ASP 442 (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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278B CYS* 4.5 3.4 - - - -
279B LYS* 2.8 40.4 + - - +
439B ASP* 3.1 36.8 + - + +
441B GLU* 1.4 78.2 - - - +
443B CYS* 1.3 57.3 + - - +
444B GLY 3.2 1.1 - - - -
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Residues in contact with CYS 443 (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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263B ILE* 3.6 14.8 - - + -
264B ILE 3.8 1.6 - - - +
265B VAL* 4.0 16.4 - - - -
278B CYS* 2.0 51.8 - - + -
279B LYS* 3.4 15.1 - - - +
282B ASN* 2.9 26.7 + - - +
437B THR* 6.2 0.4 - - - -
438B LEU 5.7 1.1 - - - -
439B ASP 4.1 3.6 - - - -
440B MET* 2.8 27.5 + - - +
442B ASP* 1.3 75.2 - - - +
444B GLY* 1.3 62.1 + - - +
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Residues in contact with GLY 444 (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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255B ARG* 3.6 21.7 + - - -
263B ILE* 4.2 15.9 - - - +
279B LYS* 2.8 24.9 + - - -
282B ASN* 4.8 2.9 - - - -
440B MET 4.0 1.8 + - - -
441B GLU 3.4 10.7 + - - +
442B ASP 3.2 1.7 - - - +
443B CYS* 1.3 79.2 - - - +
445B TYR* 1.3 63.1 + - - -
446B ASN* 4.1 2.9 + - - -
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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