Contacts of the helix formed by residues 442 - 447 (chain B) in PDB entry 4A9C
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 442 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B TRP* 4.4 15.5 - - + -
438B PRO* 4.4 4.0 - - + -
439B PRO* 3.8 33.4 - - + +
440B LYS 4.0 3.5 + - - +
441B ASN* 1.3 77.2 - - - +
443B THR* 1.4 62.6 + - - +
444B SER 3.4 2.9 - - - -
445B TRP* 3.3 27.5 + - + +
446B PHE* 3.5 35.0 + - + -
484B LEU* 5.2 13.0 - - + -
488B GLY* 6.2 0.4 - - - -
713B ILE* 4.1 18.8 - - + -
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Residues in contact with THR 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ASN* 3.2 29.5 + - - -
442B VAL* 1.4 73.8 + - - +
444B SER* 1.4 55.7 + - - +
446B PHE* 3.2 14.8 + - + +
447B THR* 2.7 41.1 + - + +
492B LEU* 3.8 28.7 - - + -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ASN* 4.4 3.7 + - - -
442B VAL 3.4 0.6 - - - -
443B THR* 1.4 77.4 - - - +
445B TRP* 1.3 60.7 + - - +
447B THR* 3.4 7.9 - - - -
448B SER* 3.2 2.6 + - - -
449B LYS* 2.8 54.9 + - - +
710B THR* 3.6 6.2 - - - +
712B ASP* 2.6 40.1 + - - -
713B ILE* 4.7 1.1 - - - -
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Residues in contact with TRP 445 (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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427B PHE* 3.2 23.0 - + - -
429B GLY* 3.5 32.4 - - - -
430B THR 3.7 2.9 - - - +
431B TRP* 3.8 38.4 - + + -
442B VAL* 3.3 20.5 + - + +
443B THR 3.2 0.6 - - - -
444B SER* 1.3 79.3 - - - +
446B PHE* 1.4 74.9 + + - +
448B SER 3.5 4.0 + - - -
469B PHE* 3.8 25.8 - + + -
471B THR* 4.2 16.6 - - + -
481B TRP* 5.7 2.5 - - - -
485B LEU* 4.9 7.4 - - + -
710B THR* 3.6 7.2 - - + +
713B ILE* 3.9 14.3 - - + +
720B PRO* 3.7 23.2 - - + +
721B VAL 3.1 28.9 + - - -
722B PHE* 3.7 10.6 - + + +
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Residues in contact with PHE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 3.7 20.7 - - - -
442B VAL* 3.5 39.3 - - + -
443B THR* 3.2 14.3 + - + +
445B TRP* 1.4 88.8 - + - +
447B THR* 1.3 57.0 + - - +
448B SER* 3.3 1.8 + - - -
464B HIS* 4.3 8.8 + - - -
467B TYR* 4.2 15.3 + - + -
469B PHE* 3.5 39.9 - + - -
484B LEU* 5.4 1.8 - - + -
485B LEU* 4.4 14.6 - - + -
488B GLY* 4.0 35.4 - - - -
489B LEU* 4.5 6.5 - - + -
492B LEU* 3.8 25.2 - - + +
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Residues in contact with THR 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B THR* 2.7 28.7 + - + +
444B SER* 3.4 11.8 + - - -
446B PHE* 1.3 75.5 - - - +
448B SER* 1.4 68.3 + - - +
449B LYS* 3.7 29.3 + - + +
455B LEU* 3.9 16.0 - - - +
457B GLU* 5.9 0.4 - - - +
461B THR* 3.9 20.1 - - + +
464B HIS* 5.8 1.3 - - - -
492B LEU* 3.6 32.5 - - + -
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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