Contacts of the helix formed by residues 541 - 546 (chain G) in PDB entry 4KYI
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 PRO 541 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G ALA* 4.1 29.6 - - + +
332G ILE* 4.5 16.2 - - + -
335G PHE* 3.9 27.6 - - + -
539G TRP 3.6 1.1 - - - +
540G ALA* 1.3 88.2 - - + +
542G ILE* 1.3 63.1 + - - +
543G GLU* 3.3 8.3 - - + +
544G TRP* 2.9 44.8 + - + +
545G VAL* 3.6 4.0 + - - +
553G ALA* 6.1 3.4 - - - -
555G ASP* 5.1 6.7 - - + +
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Residues in contact with ILE 542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G ALA* 5.2 2.0 - - - +
362G GLU* 3.5 43.8 + - + +
363G LYS 3.2 36.1 - - - +
364G VAL* 4.0 9.9 - - + +
422G TYR* 5.3 2.9 - - + +
498G LEU* 5.5 3.4 - - + -
501G LYS* 4.5 11.7 - - + +
540G ALA 3.6 2.1 + - - -
541G PRO* 1.3 69.6 - - - +
543G GLU* 1.3 83.4 + - - +
544G TRP 3.1 5.4 - - - -
545G VAL* 3.3 22.1 - - + +
546G VAL* 3.3 24.3 - - + +
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Residues in contact with GLU 543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328G ALA* 4.6 23.5 - - + +
331G ALA* 5.1 8.3 - - + -
362G GLU* 5.9 0.7 - - - -
541G PRO* 3.3 8.2 - - + -
542G ILE* 1.3 96.8 - - + +
544G TRP* 1.3 58.5 + - - +
546G VAL* 4.4 8.3 - - - +
547G SER* 3.3 19.2 + - - -
555G ASP* 4.2 13.1 - - - +
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Residues in contact with TRP 544 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490G ILE* 4.2 10.8 - - + -
493G GLU* 4.8 12.6 - - + -
494G LYS* 3.1 57.3 - - + -
497G ALA* 5.4 0.6 - - - +
540G ALA* 3.6 14.6 - - + +
541G PRO* 2.9 43.6 + - + +
542G ILE 3.1 0.6 - - - -
543G GLU* 1.3 79.7 - - - +
545G VAL* 1.3 81.7 + - + +
546G VAL 3.1 2.0 - - - -
547G SER* 3.1 10.6 + - - -
549G PHE* 3.9 15.9 - + + -
551G GLY 3.1 26.0 - - - -
552G PRO* 3.6 27.4 - - + -
553G ALA 5.0 6.1 - - - -
555G ASP* 3.7 31.9 - - + +
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Residues in contact with VAL 545 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418G MET* 3.3 25.8 - - - +
494G LYS* 3.6 29.3 - - - +
497G ALA* 3.9 26.5 - - + -
498G LEU* 4.7 10.8 - - + +
501G LYS* 4.7 7.6 - - - -
540G ALA* 4.5 3.1 - - + -
541G PRO 3.6 4.3 - - - +
542G ILE* 3.3 37.0 - - + +
544G TRP* 1.3 99.5 - - + +
546G VAL* 1.3 64.6 + - + +
547G SER 3.4 0.4 - - - +
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Residues in contact with VAL 546 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G THR 4.7 1.7 - - - +
413G PHE* 4.2 21.3 - - + -
418G MET* 4.6 12.6 - - - -
422G TYR* 4.0 49.4 - - + +
498G LEU* 4.7 3.4 - - + -
542G ILE* 3.3 18.2 - - + +
543G GLU* 4.4 9.4 - - - +
545G VAL* 1.3 91.1 - - + +
547G SER* 1.3 61.6 + - - +
548G LEU* 4.6 3.8 - - - +
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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