Contacts of the helix formed by residues 609 - 615 (chain G) in PDB entry 5JLH
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 609 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293G ARG* 5.8 7.2 - - - +
565G ASP* 4.3 8.1 + - - +
607G ALA 3.2 1.0 + - - -
608G ASN* 1.3 84.4 - - + +
610G TRP* 1.3 64.2 + - - +
611G LEU* 3.3 3.1 - - - +
612G MET* 3.5 34.8 + - + +
613G LYS* 3.2 33.3 + - + +
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Residues in contact with TRP 610 (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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489G SER* 3.9 11.3 - - - +
490G PHE* 3.6 49.6 - + + +
493G LEU* 3.9 36.1 - - + -
550G LEU* 6.1 1.6 - - + -
554G LEU* 4.1 16.0 - - + +
565G ASP* 4.8 3.9 + - - +
568G PHE* 4.0 24.2 - + + -
594G PHE* 4.0 26.0 - + - -
605G TYR* 4.0 15.3 - + + -
606G LYS 2.6 24.5 + - - -
607G ALA* 3.0 27.2 + - - +
608G ASN 3.1 15.4 + - - -
609G GLU* 1.3 77.3 - - - +
611G LEU* 1.3 66.9 + - + +
613G LYS* 3.3 8.7 + - + +
614G ASN* 3.0 24.9 + - - +
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Residues in contact with LEU 611 (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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554G LEU* 3.8 18.6 - - + +
557G GLU* 3.6 28.7 - - + -
558G CYS* 3.8 18.2 - - + +
563G ALA* 3.6 25.8 - - + +
564G THR* 3.4 34.8 - - - +
565G ASP* 3.7 8.7 - - + +
568G PHE* 4.7 3.6 - - + -
609G GLU* 3.3 0.6 - - - -
610G TRP* 1.3 78.1 - - + +
612G MET* 1.3 67.0 + - + +
614G ASN* 3.4 3.6 + - - +
615G MET* 3.2 29.1 + - + +
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Residues in contact with MET 612 (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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293G ARG* 3.8 33.0 + - - +
434G GLU* 5.2 13.9 - - - +
438G PHE* 4.0 33.5 - - + -
441G GLU* 5.1 4.6 - - - +
445G LYS* 5.3 0.9 + - - -
609G GLU* 3.5 32.3 + - + +
610G TRP 3.2 0.4 - - - -
611G LEU* 1.3 85.5 - - + +
613G LYS* 1.3 60.4 + - - +
614G ASN 3.4 0.5 + - - -
615G MET* 3.4 17.5 + - - +
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Residues in contact with LYS 613 (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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289G SER* 4.9 5.1 - - - -
293G ARG* 4.5 31.9 - - + +
294G GLN 5.5 7.7 + - - +
445G LYS* 3.6 10.3 + - - +
489G SER* 3.1 37.2 + - - -
490G PHE* 3.7 30.1 - - + +
491G GLU* 4.1 16.0 + - - +
608G ASN 4.6 9.9 + - - -
609G GLU* 3.2 26.1 + - + +
610G TRP* 3.3 6.2 + - + +
612G MET* 1.3 75.5 - - - +
614G ASN* 1.3 61.0 + - - +
670G VAL* 3.4 21.4 - - - +
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Residues in contact with ASN 614 (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 PHE* 4.6 1.1 - - + -
554G LEU* 3.3 31.2 + - + +
555G ASP* 2.7 36.7 + - - +
558G CYS* 4.2 5.5 - - + +
610G TRP 3.0 16.0 + - - +
611G LEU* 3.7 6.3 - - - +
613G LYS* 1.3 77.0 - - - +
615G MET* 1.3 61.2 + - - +
616G ASP 3.3 0.7 + - - -
669G THR* 3.4 12.5 - - - +
670G VAL* 3.0 26.8 + - + +
671G GLY* 3.2 24.8 + - - -
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Residues in contact with MET 615 (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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435G GLN* 6.0 4.5 - - + -
438G PHE* 3.7 51.1 - - + +
441G GLU* 5.6 2.6 - - - +
442G ALA 5.7 0.5 + - - -
445G LYS* 3.7 14.0 + - - -
558G CYS* 3.1 48.2 - - + +
559G TRP* 4.5 7.9 - - + -
611G LEU* 3.2 16.9 + - + +
612G MET 3.4 7.0 + - - +
613G LYS 3.4 0.6 - - - -
614G ASN* 1.3 76.6 - - - +
616G ASP* 1.3 60.6 + - - +
617G PRO* 3.5 23.1 - - + +
666G MET* 6.1 3.1 - - + -
667G PHE 5.6 1.6 - - - +
669G THR* 5.3 1.6 - - - +
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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