Contacts of the helix formed by residues 548 - 562 (chain G) in PDB entry 3HR4
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 GLY 548 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545G THR* 2.7 26.4 + - - -
547G THR* 1.3 80.8 + - - +
549G LYS* 1.3 60.3 + - - +
550G SER 3.4 2.9 - - - -
551G GLU* 3.1 23.9 - - - +
552G ALA* 3.2 9.9 + - - +
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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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547G THR* 2.5 35.1 + - - +
548G GLY* 1.3 68.8 - - - +
550G SER* 1.3 59.0 + - - +
551G GLU 3.1 2.0 - - - -
552G ALA* 3.5 6.1 + - - +
553G LEU* 3.0 33.1 + - + +
626G LEU* 3.7 7.4 - - + -
661G GLU* 5.0 7.9 + - - -
665G GLN* 3.6 23.3 - - - +
999G FMN 2.8 52.6 + - - +
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Residues in contact with SER 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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543G PHE* 3.9 3.5 - - - +
544G ALA 3.3 23.1 - - - -
545G THR* 3.8 2.0 - - - -
548G GLY 3.4 0.2 - - - -
549G LYS* 1.3 73.2 - - - +
551G GLU* 1.3 59.8 + - - +
553G LEU* 3.9 1.3 - - - -
554G ALA* 3.0 31.7 + - - +
589G VAL* 4.0 19.4 - - - +
590G THR 3.8 2.3 - - - -
591G SER 3.3 16.8 + - - -
626G LEU* 3.1 22.3 - - - +
999G FMN 3.2 12.9 + - - -
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Residues in contact with GLU 551 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543G PHE* 2.8 45.9 - - - -
545G THR* 3.8 16.9 - - + +
548G GLY* 3.1 16.0 - - - +
550G SER* 1.3 80.3 - - - +
552G ALA* 1.3 64.3 + - - +
554G ALA* 3.7 0.7 - - - +
555G TRP* 2.8 55.3 + - + -
601G ASN* 5.2 0.7 - - - +
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Residues in contact with ALA 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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548G GLY 3.2 11.3 + - - +
549G LYS* 3.9 5.8 - - - +
551G GLU* 1.3 83.1 - - - +
553G LEU* 1.3 55.8 + - + +
555G TRP* 3.7 5.6 + - - +
556G ASP* 2.5 34.6 + - - +
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Residues in contact with LEU 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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549G LYS* 3.0 15.4 + - + +
550G SER* 4.3 3.6 - - - +
551G GLU 3.2 0.2 - - - -
552G ALA* 1.3 74.4 - - + +
554G ALA* 1.3 66.7 + - - +
555G TRP 3.1 1.6 - - - -
556G ASP* 3.0 8.5 + - - +
557G LEU 2.9 18.7 + - - -
589G VAL* 4.5 2.5 - - + -
624G PHE* 4.1 2.5 - - + -
626G LEU* 3.6 39.9 - - + -
665G GLN* 4.4 11.9 - - + +
666G GLU* 4.1 19.1 - - + +
669G PHE* 3.0 60.2 - - + -
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Residues in contact with ALA 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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541G ILE* 4.0 17.2 - - + +
543G PHE* 3.6 22.7 - - + -
550G SER 3.0 21.9 + - - +
551G GLU 3.7 2.7 - - - +
553G LEU* 1.3 76.8 - - - +
555G TRP* 1.3 63.1 + - - +
557G LEU* 3.1 18.9 + - - +
558G GLY* 3.1 10.2 + - - -
569G VAL* 4.2 9.9 - - + +
589G VAL* 4.1 16.3 - - + +
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Residues in contact with TRP 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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543G PHE* 4.3 5.6 - + - -
551G GLU* 2.8 57.4 + - + +
552G ALA* 4.0 6.7 - - - +
553G LEU 3.1 0.2 - - - -
554G ALA* 1.3 74.7 - - - +
556G ASP* 1.3 65.0 + - - +
558G GLY* 3.1 2.7 + - - +
559G ALA* 3.1 20.8 + - - +
569G VAL* 3.7 48.1 - - + +
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Residues in contact with ASP 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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552G ALA* 2.5 24.7 - - - +
553G LEU* 3.0 13.5 + - - +
555G TRP* 1.3 76.9 - - - +
557G LEU* 1.3 61.5 + - - +
559G ALA* 3.1 9.6 + - - +
560G LEU 3.1 16.6 + - - -
666G GLU* 5.6 1.7 - - - +
669G PHE* 4.0 8.6 - - + -
698G TYR* 2.6 30.1 + - + +
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Residues in contact with LEU 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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541G ILE* 3.9 7.6 - - + -
553G LEU 2.9 12.0 + - - +
554G ALA* 3.1 10.1 + - - +
556G ASP* 1.3 77.6 - - - +
558G GLY* 1.3 56.1 + - - +
560G LEU* 3.6 4.0 + - + +
561G PHE* 3.1 45.3 + - + +
587G LEU* 3.4 36.6 - - + -
589G VAL* 3.9 22.7 - - + -
669G PHE* 3.9 7.2 - - + -
672G TRP* 3.9 24.0 - - + -
673G ALA* 4.3 14.6 - - + -
676G THR* 4.5 2.5 - - + -
698G TYR* 3.2 6.5 + - - -
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Residues in contact with GLY 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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541G ILE* 3.5 19.7 - - - +
554G ALA 3.1 10.5 + - - -
555G TRP 3.1 4.8 + - - -
557G LEU* 1.3 74.3 - - - +
559G ALA* 1.3 60.0 + - - +
560G LEU 3.1 0.2 - - - -
561G PHE 3.1 1.9 + - - -
562G SER* 2.6 34.7 + - - -
567G PRO* 3.6 8.0 - - - +
569G VAL* 4.2 11.0 - - - -
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Residues in contact with ALA 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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555G TRP* 3.1 12.3 + - - +
556G ASP* 3.1 12.1 + - - +
558G GLY* 1.3 75.8 - - - +
560G LEU* 1.3 61.8 + - - +
562G SER* 3.3 20.9 + - - -
563G CYS* 3.9 8.8 - - - -
695G PRO* 5.1 13.6 - - + +
698G TYR* 5.7 0.7 - - + -
42H ASN* 4.9 1.2 - - - +
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Residues in contact with LEU 560 (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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556G ASP 3.1 9.3 + - - +
557G LEU* 3.7 8.5 - - + +
559G ALA* 1.3 78.0 - - - +
561G PHE* 1.3 61.6 + - + +
562G SER 3.1 1.5 + - - -
563G CYS* 3.3 21.4 - - - +
673G ALA* 3.8 32.5 - - + +
674G VAL* 4.4 3.4 - - + +
677G PHE* 3.5 35.9 - - + -
694G ILE* 3.7 24.2 - - + -
695G PRO* 5.0 3.4 - - - -
698G TYR* 3.3 47.0 - - + +
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Residues in contact with PHE 561 (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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539G VAL* 3.9 22.4 - - + -
541G ILE* 4.6 1.3 - - + -
557G LEU* 3.1 34.2 + - + +
558G GLY* 3.1 6.7 + - - +
560G LEU* 1.3 74.2 - - + +
562G SER* 1.3 56.2 + - - +
563G CYS 3.0 5.8 + - - -
564G ALA 3.6 1.0 + - - -
565G PHE* 3.0 51.0 + + - +
567G PRO* 3.8 13.4 - - + +
585G LEU* 3.8 22.7 - - + -
587G LEU* 3.7 24.7 - - + -
676G THR* 4.2 7.0 - - + -
677G PHE* 3.5 32.3 - + + -
680G ALA* 3.7 24.2 - - + -
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Residues in contact with SER 562 (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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536G ARG* 3.2 18.9 + - - -
558G GLY 2.6 21.1 + - - -
559G ALA* 3.4 13.8 + - - -
560G LEU 3.1 0.6 - - - -
561G PHE* 1.3 73.9 - - - +
563G CYS* 1.3 56.7 + - - +
564G ALA 3.0 11.2 + - - -
565G PHE 3.7 9.9 - - - +
567G PRO* 3.6 12.7 - - - +
42H ASN* 3.5 19.2 + - - -
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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