Contacts of the helix formed by residues 549 - 560 (chain A) in PDB entry 1RQG
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A LYS* 4.9 1.6 - - - -
547A LYS 3.7 8.0 + - - -
548A VAL* 1.3 75.7 + - - +
550A ASP* 1.3 79.7 + - + +
551A ASP* 2.9 31.6 - - + +
552A GLN* 2.8 27.8 + - - +
553A ILE* 3.2 27.7 + - - +
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Residues in contact with ASP 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A LYS* 3.7 21.8 + - - +
549A THR* 1.3 77.7 - - + +
551A ASP* 1.3 68.0 + - - +
552A GLN 3.1 0.4 - - - -
553A ILE* 3.9 0.6 - - - +
554A ILE* 2.9 35.1 + - + +
577A TYR* 3.3 41.8 + - + -
585A VAL* 5.3 0.2 - - - -
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Residues in contact with ASP 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A THR* 2.9 18.4 - - + +
550A ASP* 1.3 82.4 - - - +
552A GLN* 1.3 58.3 + - + +
555A TYR* 3.0 28.9 + - - +
584A ARG* 4.0 13.2 + - - -
585A VAL* 3.6 37.6 - - - +
588A GLU* 3.9 15.6 - - - +
589A LYS* 5.2 10.2 - - + +
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A VAL* 4.2 23.6 + - + +
362A PHE* 4.0 21.8 - - + -
366A TYR* 6.1 0.2 - - - -
547A LYS 4.0 2.9 - - - +
548A VAL* 3.4 12.8 - - - +
549A THR* 2.8 42.8 + - - +
550A ASP 3.1 0.6 - - - -
551A ASP* 1.3 78.3 - - + +
553A ILE* 1.3 61.6 + - - +
555A TYR* 3.1 8.8 + - - +
556A PHE* 2.8 29.5 + - - +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A PHE* 4.4 9.4 - - + -
385A PHE* 3.9 41.5 - - + +
386A SER* 5.4 0.4 - - - -
388A PHE* 5.2 2.0 - - + -
389A LYS* 3.4 37.5 - - + -
548A VAL* 4.3 8.5 - - + -
549A THR 3.2 13.1 + - - +
550A ASP 3.4 1.1 + - - +
552A GLN* 1.3 75.7 - - - +
554A ILE* 1.3 58.7 + - - +
556A PHE* 3.1 7.0 + - - +
557A ILE* 2.8 54.7 + - + +
576A TYR* 5.5 0.9 - - + -
577A TYR* 3.5 23.6 - - + +
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Residues in contact with ILE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ASP* 2.9 23.6 + - + +
553A ILE* 1.3 74.0 - - - +
555A TYR* 1.3 66.1 + - - +
556A PHE 3.1 0.3 + - - -
557A ILE* 3.2 6.6 + - - +
558A LEU* 2.7 33.3 + - + +
573A LEU* 4.3 6.1 - - + -
577A TYR* 3.6 41.1 - - + -
581A ASP* 4.7 3.8 - - + +
582A VAL* 3.7 46.0 - - + +
585A VAL* 3.7 31.6 - - + -
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Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A VAL* 3.7 31.4 - - + -
551A ASP 3.0 20.3 + - - +
552A GLN* 3.1 6.3 + - - +
554A ILE* 1.3 78.7 - - - +
556A PHE* 1.3 55.8 + - - +
558A LEU* 3.9 4.2 - - - +
559A ASN* 2.7 68.5 + - + +
560A TYR* 4.4 4.1 + + - -
585A VAL* 4.3 3.8 - - + +
589A LYS* 3.4 44.0 - - + -
590A PHE* 3.8 26.2 - + - -
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Residues in contact with PHE 556 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A ALA 5.8 0.2 - - - -
353A ILE* 4.3 9.6 - - + -
354A TRP 5.4 1.1 - - - -
357A GLU* 3.9 5.6 - - + -
358A PHE* 3.5 44.0 - + + -
361A VAL* 4.2 12.3 - - + -
362A PHE* 4.5 14.4 - + + -
385A PHE* 3.7 36.1 - + - -
552A GLN 2.8 12.9 + - - +
553A ILE* 3.4 10.5 - - - +
554A ILE 3.1 0.2 - - - -
555A TYR* 1.3 78.8 - - - +
557A ILE* 1.3 62.8 + - + +
560A TYR* 2.8 67.9 + + + +
561A MET* 3.8 20.9 - - + -
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Residues in contact with ILE 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A PHE* 4.2 28.0 - - + -
553A ILE* 2.8 45.8 + - + +
554A ILE* 3.7 2.7 - - - +
556A PHE* 1.3 72.8 - - - +
558A LEU* 1.3 56.6 + - - +
561A MET* 3.0 18.3 + - + +
562A ALA* 2.7 31.9 + - - +
569A ALA* 3.8 29.4 - - + +
572A LEU* 4.4 15.5 - - + -
573A LEU* 3.9 28.0 - - + +
576A TYR* 5.2 4.3 - - + -
577A TYR* 5.0 4.9 - - + -
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A ILE* 2.7 41.2 + - + +
555A TYR* 3.9 2.9 - - - +
557A ILE* 1.3 74.8 - - + +
559A ASN* 1.3 60.5 + - - +
562A ALA* 3.0 21.0 - - - +
563A LYS* 4.4 1.4 + - - +
573A LEU* 3.8 25.6 - - + -
582A VAL* 4.0 7.4 - - + -
585A VAL* 5.3 0.4 - - + -
586A ALA* 3.6 31.9 - - + -
590A PHE* 3.7 20.0 - - + -
597A VAL* 3.9 25.1 - - + +
598A LEU* 4.5 4.7 - - + -
600A ARG* 5.6 0.3 + - - -
601A VAL* 4.1 15.5 - - + -
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Residues in contact with ASN 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A TYR* 2.7 53.6 + - + +
558A LEU* 1.3 74.8 - - - +
560A TYR* 1.3 98.9 + - + +
563A LYS* 5.6 3.4 + - - +
590A PHE* 3.9 17.3 - - + -
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Residues in contact with TYR 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A GLU* 3.4 52.9 - - + +
360A ASP* 3.0 32.2 + - - +
361A VAL* 4.2 13.8 - - + +
555A TYR* 4.4 3.9 + + - -
556A PHE* 2.8 54.1 + + + +
559A ASN* 1.3 104.1 + - + +
561A MET* 1.3 68.9 + - + +
562A ALA 3.1 2.4 + - - -
563A LYS 3.1 20.6 + - - +
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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