Contacts of the helix formed by residues 445 - 451 (chain B) in PDB entry 6FEQ
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 445 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442B VAL* 3.1 17.2 + - + +
444B ALA* 1.3 78.1 - - - +
446B GLU* 1.3 62.0 + - - +
447B LEU 3.1 1.6 + - - -
448B PHE 3.9 1.2 + - - -
449B VAL* 3.3 27.8 + - + +
524B ALA* 4.2 12.6 - - + +
528B ALA* 3.7 26.3 - - + +
534B VAL* 4.2 12.8 - - + +
537B ALA* 4.0 18.4 - - + -
538B THR* 4.1 17.7 - - - +
541B MET* 4.1 26.0 - - + -
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Residues in contact with GLU 446 (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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394B ALA* 5.3 11.0 - - - +
443B SER* 3.3 22.1 + - - +
444B ALA 3.2 0.2 - - - -
445B VAL* 1.3 78.0 - - - +
447B LEU* 1.3 62.8 + - - +
449B VAL* 4.3 1.8 - - - -
450B VAL* 3.3 37.7 + - + +
451B GLU* 5.7 0.2 - - - +
534B VAL* 5.5 8.1 - - + +
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Residues in contact with LEU 447 (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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443B SER 4.4 0.4 + - - -
444B ALA* 3.2 18.9 + - + +
445B VAL 3.1 1.8 + - - -
446B GLU* 1.3 80.5 - - - +
448B PHE* 1.3 81.2 + - + +
451B GLU* 3.9 22.7 + - - +
473B LYS* 3.8 15.7 - - + +
474B LEU* 4.8 3.4 - - + -
477B ASP* 3.4 35.7 - - + +
478B LEU* 4.8 20.0 - - + -
525B LEU* 3.8 27.1 - - + -
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Residues in contact with PHE 448 (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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444B ALA 4.5 0.8 + - - -
445B VAL 3.9 2.6 + - - +
447B LEU* 1.3 96.3 - - + +
449B VAL* 1.3 64.7 + - + +
450B VAL 3.7 0.2 - - - -
451B GLU* 4.3 3.7 - - - +
452B LYS* 3.6 21.5 + - - +
469B TYR* 4.2 19.1 - + - -
470B PHE* 3.6 40.6 - + - -
473B LYS* 3.6 29.8 - - + -
474B LEU* 4.9 5.4 - - + -
525B LEU* 3.6 30.0 - - + +
528B ALA* 5.3 1.3 - - + -
529B ALA* 3.8 33.5 - - + +
530B GLY 5.6 2.4 + - - +
531B GLN 5.2 0.2 - - - +
644B ALA* 5.2 0.2 - - + -
648B LEU* 4.0 15.4 - - + +
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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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445B VAL* 3.3 25.9 + - + +
446B GLU 4.9 0.4 - - - +
447B LEU 3.4 0.6 - - - -
448B PHE* 1.3 78.7 - - - +
450B VAL* 1.3 66.4 + - + +
451B GLU 3.3 0.4 - - - -
452B LYS* 3.3 16.2 - - - +
528B ALA* 3.7 31.9 - - + +
531B GLN* 3.8 9.6 - - + +
532B SER* 3.6 33.7 - - - +
533B VAL 3.8 11.7 - - - +
534B VAL* 4.0 18.2 - - + -
537B ALA* 6.0 0.4 - - + -
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Residues in contact with VAL 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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446B GLU* 3.3 39.3 + - + +
447B LEU 5.0 0.2 - - - +
449B VAL* 1.3 78.8 - - + +
451B GLU* 1.3 67.6 + - + +
452B LYS 3.2 4.1 + - - -
453B LYS* 4.7 2.6 + - - +
454B LEU 5.4 0.3 + - - -
534B VAL* 5.2 9.9 - - + -
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Residues in contact with GLU 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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131B MET* 4.8 5.8 - - - +
383B ARG* 4.6 4.6 + - - -
387B ASN* 3.9 19.6 + - - +
447B LEU* 3.9 18.0 + - + +
448B PHE 4.2 3.8 + - - +
449B VAL 3.3 0.4 - - - -
450B VAL* 1.3 85.4 - - + +
452B LYS* 1.3 57.9 + - - +
453B LYS 3.5 1.3 - - - -
454B LEU* 3.3 36.7 + - - +
455B PHE* 2.9 27.9 + - - +
469B TYR* 3.9 16.3 + - - +
473B LYS* 4.3 16.9 + - - +
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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