Contacts of the helix formed by residues 448 - 453 (chain B) in PDB entry 3H44
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 GLU 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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878A THR* 5.8 3.4 - - - -
879A GLU* 3.4 37.6 - - + +
880A GLU 5.9 0.7 - - - -
55B THR* 5.2 3.1 - - - +
326B TYR* 3.9 18.7 + - - -
444B TYR* 4.4 4.1 - - + +
445B PRO* 2.9 33.4 + - - +
447B GLU* 1.3 89.7 - - + +
449B VAL* 1.3 58.4 + - - +
450B LEU 3.4 1.1 - - - -
451B THR* 3.5 15.9 - - - +
452B ALA* 2.9 32.5 + - + +
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Residues in contact with VAL 449 (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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54B ILE* 4.1 10.8 - - + -
76B LEU* 4.3 17.5 - - + -
437B ILE* 4.6 9.8 - - + +
440B ILE* 4.1 25.2 - - + +
441B LEU* 3.6 38.8 - - + +
444B TYR* 3.8 23.8 - - + +
445B PRO 4.0 2.7 - - - +
446B LEU* 3.4 15.5 - - - +
447B GLU 3.7 0.2 - - - -
448B GLU* 1.3 76.3 - - - +
450B LEU* 1.3 83.7 + - + +
451B THR 3.0 1.4 + - - -
452B ALA* 3.5 7.8 + - - +
453B GLU 4.6 1.7 + - - -
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Residues in contact with LEU 450 (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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54B ILE* 3.6 19.9 - - + +
55B THR 3.3 20.0 - - - +
56B LYS* 4.1 9.6 - - + -
60B ASP* 5.6 0.4 - - - +
64B TYR* 3.5 45.5 - - + -
76B LEU* 4.4 4.7 - - + -
422B PHE* 3.3 18.7 - - + -
425B LYS* 5.3 2.4 - - - -
433B TYR* 3.3 25.1 - - + +
437B ILE* 3.9 22.4 - - + -
448B GLU 3.4 0.2 - - - -
449B VAL* 1.3 88.6 - - + +
451B THR* 1.3 58.0 + - - +
453B GLU 5.3 0.2 + - - -
454B TYR* 4.6 6.9 - - - -
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Residues in contact with THR 451 (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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878A THR* 4.7 8.2 - - + +
55B THR* 3.7 31.7 - - + +
422B PHE* 3.4 30.1 - - + -
448B GLU* 3.4 24.1 + - - +
449B VAL 3.0 0.2 - - - -
450B LEU* 1.3 78.5 - - - +
452B ALA* 1.3 67.1 + - - +
453B GLU 3.3 2.5 - - - -
454B TYR* 2.9 4.3 + - - -
455B LEU* 2.9 47.3 + - + +
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Residues in contact with ALA 452 (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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326B TYR* 4.7 13.1 - - + +
444B TYR* 3.2 48.4 + - + -
448B GLU* 2.9 21.6 + - + +
449B VAL 3.5 4.5 + - - +
451B THR* 1.3 77.9 - - - +
453B GLU* 1.3 62.7 + - - +
454B TYR 3.2 0.5 + - - -
455B LEU 3.5 16.2 - - - +
456B LEU* 5.7 0.9 - - - +
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Residues in contact with GLU 453 (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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418B ASN* 5.2 1.7 + - - -
436B LYS* 3.4 30.4 + - - -
440B ILE* 3.5 29.2 - - + +
444B TYR* 3.6 22.0 + - - +
449B VAL 4.6 3.2 + - - -
450B LEU 5.3 0.2 + - - -
451B THR 3.3 0.4 - - - -
452B ALA* 1.3 78.9 - - - +
454B TYR* 1.3 68.4 + - + +
456B LEU* 6.1 0.4 - - - +
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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