Contacts of the helix formed by residues 544 - 556 (chain C) in PDB entry 1RR8
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 544 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462C ARG* 3.3 30.5 + - - +
465C TRP* 3.9 24.5 - - + -
480C TYR* 3.7 19.6 + - + +
523C TYR* 4.4 2.9 - - - +
543C VAL* 1.3 93.5 - - - +
545C LYS* 1.3 65.4 + - - +
546C ARG* 3.5 2.7 - - + +
547C VAL* 3.6 12.8 + - + +
548C PHE* 3.6 8.5 + - - +
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Residues in contact with LYS 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C TYR* 3.7 42.0 - - + +
544C GLU* 1.3 76.5 - - - +
546C ARG* 1.3 84.4 + - - +
548C PHE* 3.6 4.0 + - - +
549C LYS* 3.4 43.2 + - + +
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Residues in contact with ARG 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C ARG* 5.9 1.2 - - - +
465C TRP* 4.2 31.0 - - + +
466C LYS* 2.8 46.5 - - + +
544C GLU* 3.5 2.0 - - + +
545C LYS* 1.3 96.9 - - - +
547C VAL* 1.3 56.0 + - - +
549C LYS* 3.4 10.9 + - - +
550C ASN* 2.8 39.9 + - - +
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Residues in contact with VAL 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C TRP* 3.7 44.0 - - + +
477C VAL* 3.9 24.0 - - + -
480C TYR* 3.9 25.1 - - + -
481C PHE* 4.4 6.7 - - + -
543C VAL* 4.2 11.0 - - + -
544C GLU* 3.9 16.2 - - + +
545C LYS 3.4 0.6 - - - -
546C ARG* 1.3 73.6 - - - +
548C PHE* 1.3 60.1 + - - +
550C ASN* 3.3 9.3 + - - +
551C LEU* 3.0 31.3 + - + +
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Residues in contact with PHE 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C LEU* 3.8 26.3 - - + +
515C HIS 3.6 31.9 - - - -
516C PRO* 3.7 15.9 - - + -
523C TYR* 3.8 43.7 - + + -
524C VAL 3.5 22.4 - - - -
525C VAL* 4.3 6.3 - - + -
543C VAL* 4.1 3.8 - - + +
544C GLU 3.6 7.6 + - - +
545C LYS 3.6 8.9 + - - +
546C ARG 3.4 0.4 - - - -
547C VAL* 1.3 78.6 - - - +
549C LYS* 1.3 65.3 + - - +
551C LEU* 3.4 7.2 + - - +
552C GLN* 3.3 49.5 + - + +
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Residues in contact with LYS 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C ARG* 5.9 1.6 - - - +
523C TYR* 4.2 27.1 + - - -
545C LYS* 3.4 30.5 + - + +
546C ARG* 3.7 14.6 - - - +
547C VAL 3.3 0.4 - - - -
548C PHE* 1.3 80.3 - - + +
550C ASN* 1.3 60.7 + - - +
552C GLN* 3.6 20.0 + - - +
553C LEU* 3.4 30.1 + - + +
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Residues in contact with ASN 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C TRP* 3.3 36.5 + - - +
473C ARG* 2.8 41.0 + - - +
477C VAL* 4.0 9.7 - - + +
546C ARG* 2.8 25.8 + - - +
547C VAL* 3.4 7.1 - - - +
548C PHE 3.2 0.2 - - - -
549C LYS* 1.3 75.6 - - - +
551C LEU* 1.3 58.1 + - - +
552C GLN 3.2 0.2 - - - -
553C LEU* 3.1 7.1 + - - +
554C PHE* 3.1 53.2 + - + -
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Residues in contact with LEU 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C VAL* 4.0 21.5 - - + -
481C PHE* 3.9 28.7 - - + -
512C ILE* 4.1 18.4 - - + -
514C LEU* 4.0 20.0 - - + -
525C VAL* 3.9 28.7 - - + -
547C VAL* 3.0 25.7 + - + +
548C PHE* 3.4 5.6 + - - +
550C ASN* 1.3 73.8 - - - +
552C GLN* 1.3 59.3 + - - +
554C PHE* 3.4 9.2 + - + +
555C MET* 3.1 34.3 + - - +
564C LEU* 4.3 10.8 - - + -
565C PHE* 4.4 2.7 - - + -
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Residues in contact with GLN 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514C LEU* 3.8 20.2 - - + -
548C PHE* 3.3 38.6 + - + +
549C LYS* 3.6 25.4 + - - +
550C ASN 3.2 0.2 - - - -
551C LEU* 1.3 77.0 - - - +
553C LEU* 1.3 65.7 + - + +
555C MET* 3.5 3.6 + - - +
556C GLU* 3.4 29.3 + - - +
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Residues in contact with LEU 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C MET* 3.9 28.8 - - + +
473C ARG* 4.3 17.9 - - - +
549C LYS* 3.4 18.7 + - + +
550C ASN* 3.1 11.6 + - - +
552C GLN* 1.3 82.4 - - + +
554C PHE* 1.3 66.5 + - + +
556C GLU* 3.6 31.9 + - - +
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Residues in contact with PHE 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C MET* 3.9 27.6 - - + -
473C ARG* 4.0 4.0 - - + -
474C GLN* 3.4 47.3 - - + +
477C VAL* 3.9 15.3 - - + -
509C VAL* 4.8 0.2 - - - +
550C ASN* 3.1 45.4 + - + +
551C LEU* 3.4 12.1 + - + +
552C GLN 3.3 0.2 - - - -
553C LEU* 1.3 81.4 - - + +
555C MET* 1.3 59.5 + - - +
556C GLU 3.4 1.5 + - - -
558C LYS* 2.9 36.0 + - - +
564C LEU* 3.8 22.9 - - + +
565C PHE* 3.8 24.7 - + - -
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Residues in contact with MET 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C VAL* 3.7 36.4 - - + +
512C ILE* 3.6 41.5 - - + +
513C ASN* 5.1 3.1 - - - +
514C LEU* 3.4 32.8 - - + +
551C LEU 3.1 13.6 + - - +
552C GLN* 3.5 5.6 + - - +
553C LEU 3.4 0.4 - - - -
554C PHE* 1.3 77.6 - - - +
556C GLU* 1.3 62.2 + - - +
557C ASN 3.8 0.3 + - - -
558C LYS* 3.7 17.5 + - - +
564C LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552C GLN* 3.4 13.1 + - - +
553C LEU* 3.6 41.0 - - - +
554C PHE 3.4 3.8 - - - +
555C MET* 1.3 73.4 - - - +
557C ASN* 1.3 75.1 - - + +
558C LYS* 3.0 21.4 + - - +
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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