Contacts of the helix formed by residues 547 - 559 (chain G) in PDB entry 2A07
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 THR 547 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509F TYR* 3.4 9.1 + - - -
543G ARG 5.3 2.7 - - - +
544G ASN* 3.3 29.8 + - - +
546G ALA* 1.3 85.5 - - + +
548G TRP* 1.3 65.0 + - - +
549G LYS* 3.1 4.2 + - - -
550G ASN* 3.3 10.4 + - - +
551G ALA* 3.0 22.1 + - - +
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Residues in contact with TRP 548 (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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509F TYR* 3.7 26.5 - - + -
531F TYR* 3.5 35.9 - + - -
534F PHE* 3.4 29.2 - + + -
535F THR* 3.5 23.6 - - + -
538F PHE* 3.6 39.8 - + + +
544G ASN 3.3 9.8 + - - +
545G ALA 3.4 25.6 + - - -
546G ALA 3.8 0.2 - - - -
547G THR* 1.3 77.2 - - - +
549G LYS* 1.3 113.6 + - + +
552G VAL* 2.8 37.9 + - + +
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Residues in contact with LYS 549 (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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531F TYR* 4.0 33.7 + - + +
535F THR* 4.7 3.4 + - - -
546G ALA 5.3 2.2 + - - +
547G THR 3.1 1.6 + - - -
548G TRP* 1.3 122.1 - - + +
550G ASN* 1.3 66.4 + - - +
552G VAL* 3.4 2.9 + - - +
553G ARG* 3.2 42.6 + - - +
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Residues in contact with ASN 550 (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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547G THR* 3.3 10.1 + - - +
549G LYS* 1.3 79.3 - - - +
551G ALA* 1.3 60.5 + - - +
553G ARG* 2.5 36.2 + - - +
554G HIS* 2.9 29.5 + - - +
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Residues in contact with ALA 551 (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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509F TYR* 3.2 45.5 - - + +
547G THR* 3.0 17.0 + - - +
548G TRP 3.7 0.4 - - - +
550G ASN* 1.3 77.6 - - - +
552G VAL* 1.3 56.8 + - - +
554G HIS* 3.4 6.1 + - - +
555G ASN* 2.8 37.5 + - - +
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Residues in contact with VAL 552 (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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509F TYR* 4.4 5.2 - - + -
513F ILE* 4.1 13.9 - - + -
527F LEU* 4.6 0.4 - - + -
530F ILE* 4.0 20.2 - - + -
531F TYR* 4.3 14.4 - - + -
534F PHE* 3.6 41.5 - - + -
548G TRP* 2.8 28.4 + - + +
549G LYS 3.7 4.0 - - - +
551G ALA* 1.3 73.7 - - - +
553G ARG* 1.3 66.4 + - - +
555G ASN* 3.3 2.0 + - - +
556G LEU* 2.9 45.7 + - + +
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Residues in contact with ARG 553 (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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527F LEU* 4.5 15.7 - - + -
531F TYR* 2.7 50.1 + - + +
549G LYS* 3.2 28.3 + - - +
550G ASN* 2.5 43.0 + - - +
552G VAL* 1.3 78.1 - - - +
554G HIS* 1.3 62.8 + - - +
556G LEU* 3.5 9.1 + - - +
557G SER* 3.2 23.4 + - - -
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Residues in contact with HIS 554 (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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550G ASN 2.9 17.5 + - - +
551G ALA* 3.6 7.9 - - - +
552G VAL 3.2 0.2 - - - -
553G ARG* 1.3 77.0 - - - +
555G ASN* 1.3 66.9 + - - +
557G SER* 3.2 9.6 + - - -
558G LEU* 2.8 60.1 + - + +
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Residues in contact with ASN 555 (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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509F TYR* 3.6 28.0 - - - +
510F ALA* 3.9 14.6 + - - +
513F ILE* 3.9 15.5 - - + -
551G ALA* 2.8 29.4 + - - +
552G VAL 3.8 3.4 - - - +
554G HIS* 1.3 84.4 - - - +
556G LEU* 1.3 64.0 + - - +
558G LEU* 4.3 2.9 - - - -
559G HIS* 2.9 59.6 + - + +
562G PHE* 3.7 3.6 - - + -
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Residues in contact with LEU 556 (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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513F ILE* 3.9 29.8 - - + -
527F LEU* 3.6 30.5 - - + -
530F ILE* 4.4 5.8 - - + -
552G VAL* 2.9 30.6 + - + +
553G ARG* 3.8 6.5 - - - +
554G HIS 3.3 0.2 - - - -
555G ASN* 1.3 77.7 - - - +
557G SER* 1.3 51.5 + - - +
559G HIS 3.6 0.9 - - - +
562G PHE* 3.7 14.1 - - + +
573G TRP* 3.5 57.3 - - + +
604G MG 2.4 31.0 - - - -
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Residues in contact with SER 557 (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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553G ARG 3.2 10.8 + - - -
554G HIS* 3.2 16.0 + - - -
556G LEU* 1.3 78.9 - - - +
558G LEU* 1.3 63.0 + - - +
573G TRP* 5.0 6.5 - - - -
604G MG 4.1 5.8 - - - -
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Residues in contact with LEU 558 (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 HIS* 2.8 48.0 + - + +
555G ASN* 4.0 3.4 - - - +
557G SER* 1.3 81.3 + - - +
559G HIS* 1.3 88.8 + - + +
560G LYS* 3.7 6.9 + - - +
583G ARG* 5.5 1.1 + - - +
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Residues in contact with HIS 559 (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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510F ALA* 4.8 9.0 - - + +
555G ASN* 2.9 52.2 + - + +
556G LEU 3.6 2.4 - - - +
558G LEU* 1.3 97.6 - - + +
560G LYS* 1.3 60.5 + - - +
561G CYS* 3.8 22.7 - - - -
562G PHE* 3.2 16.5 + + + +
583G ARG* 2.8 35.4 + - - +
604G MG 2.4 25.2 - - - -
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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