Contacts of the helix formed by residues 445 - 452 (chain K) in PDB entry 6D6Q
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 SER 445 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLU 3.4 7.2 + - - -
179A GLU* 2.9 37.8 + - - -
180A ARG* 3.6 9.9 - - - -
181A ASP* 3.7 10.3 - - - -
443K PRO 3.5 3.8 + - - -
444K PHE* 1.3 73.3 - - - +
446K GLN* 1.3 65.7 + - - +
447K ALA* 4.5 0.7 - - - +
448K VAL* 3.3 25.4 + - - +
449K LEU* 3.1 24.0 + - - +
522K GLU* 4.8 3.4 - - - +
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Residues in contact with GLN 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO 4.4 14.1 + - - +
178A GLU* 3.8 11.9 + - + -
181A ASP* 3.9 7.9 + - - +
445K SER* 1.3 71.5 - - - +
447K ALA* 1.3 68.2 + - - +
449K LEU* 3.1 19.0 + - - +
450K SER* 3.1 25.5 + - - +
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Residues in contact with ALA 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 2.9 36.2 + - + +
179A GLU* 4.9 2.2 - - - -
445K SER* 4.5 1.3 - - - +
446K GLN* 1.3 75.7 - - - +
448K VAL* 1.3 65.7 + - - +
450K SER* 3.1 20.9 + - - -
451K PHE* 3.5 16.5 + - + -
518K ALA* 4.8 15.5 - - + -
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Residues in contact with VAL 448 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K PHE* 4.2 21.5 - - + -
445K SER* 3.3 29.1 + - - +
446K GLN 3.1 0.6 - - - -
447K ALA* 1.3 78.1 - - - +
449K LEU* 1.3 66.7 + - + +
450K SER 2.9 1.7 + - - -
451K PHE* 3.1 14.0 + - - +
452K LEU* 3.7 9.0 + - + +
518K ALA* 4.3 14.4 - - + +
519K LEU* 3.3 38.5 - - + +
522K GLU* 3.7 28.9 - - + -
541K PRO* 5.1 3.6 - - + -
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Residues in contact with LEU 449 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K PHE* 3.6 30.5 - - + +
445K SER 3.1 23.6 - - - +
446K GLN* 3.1 21.5 + - - +
448K VAL* 1.3 80.1 - - + +
450K SER* 1.3 61.8 + - - +
452K LEU* 3.2 43.2 + - + +
541K PRO* 4.8 8.7 - - + -
543K LEU* 6.0 1.8 - - + -
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Residues in contact with SER 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446K GLN* 3.1 17.5 + - - +
447K ALA* 3.3 14.6 - - - -
448K VAL 2.9 1.4 + - - -
449K LEU* 1.3 78.2 - - - +
451K PHE* 1.3 73.5 + - - +
452K LEU 3.0 11.3 + - - +
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Residues in contact with PHE 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447K ALA* 4.2 12.8 - - + -
448K VAL 3.1 8.2 + - - +
450K SER* 1.3 86.6 - - - +
452K LEU* 1.3 61.2 + - - +
453K PRO* 3.7 1.4 - - - +
512K PHE 5.4 3.5 - - - +
516K GLY 5.4 0.2 - - - -
517K ASN* 3.1 45.3 - - + +
518K ALA* 3.4 27.4 - - + -
519K LEU* 4.4 11.4 - - + -
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Residues in contact with LEU 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448K VAL 3.7 7.9 + - - +
449K LEU* 3.3 42.7 - - + +
450K SER 3.0 10.1 + - - +
451K PHE* 1.3 84.3 - - - +
453K PRO* 1.3 78.4 - - + +
454K LYS* 3.7 1.4 + - - +
519K LEU* 4.7 17.0 - - + -
541K PRO* 4.3 17.5 - - + -
543K LEU* 4.1 21.1 - - + -
544K LEU* 3.4 38.4 - - + -
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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