Contacts of the helix formed by residues 541 - 553 (chain A) in PDB entry 4RG7
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A CYS* 3.3 32.8 - - - -
528A PHE* 3.7 16.5 - - - -
538A ARG* 3.8 2.7 - - - +
539A VAL 3.4 0.2 - - - -
540A GLU* 1.3 75.9 - - - +
542A MET* 1.3 61.0 + - - +
543A GLU* 2.9 8.4 + - - -
544A ILE* 3.1 16.8 + - - +
545A TYR 3.6 6.4 + - - -
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Residues in contact with MET 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A PHE* 5.5 0.4 - - - -
532A ARG* 5.6 6.5 - - + -
538A ARG* 4.3 5.1 + - - +
539A VAL* 3.2 16.9 + - - +
541A GLY* 1.3 76.0 - - - +
543A GLU* 1.3 65.6 + - - +
544A ILE 3.4 0.2 - - - -
545A TYR* 3.8 20.7 - - + +
546A SER* 3.0 25.1 + - - -
561A LEU* 6.4 0.4 - - + -
565A LEU* 3.7 34.7 - - + +
574A GLU* 5.0 0.9 - - - -
578A ALA* 4.9 0.3 - - - +
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Residues in contact with GLU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A VAL 3.7 4.6 + - - -
540A GLU 3.6 21.1 - - - +
541A GLY 4.0 1.3 - - - +
542A MET* 1.3 75.4 - - - +
544A ILE* 1.3 76.4 + - + +
546A SER* 2.9 22.5 + - - -
547A THR 4.1 0.7 + - - -
574A GLU* 3.7 26.9 - - + +
577A CYS* 5.0 5.0 - - + +
606A TYR* 3.0 39.4 + - - +
608A TYR* 3.9 22.7 - - + +
612A LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 544 (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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509A CYS 5.4 0.4 - - - +
513A ARG* 3.6 20.9 - - + -
516A PHE* 3.5 43.1 - - + -
528A PHE* 3.3 36.3 - - + -
541A GLY* 3.1 6.8 + - - +
543A GLU* 1.3 99.6 - - + +
545A TYR* 1.3 61.8 + - - +
546A SER 3.2 1.8 - - - -
547A THR* 3.1 9.8 + - - +
548A THR* 3.0 27.1 + - + +
608A TYR* 4.5 14.4 - - + -
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Residues in contact with TYR 545 (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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525A GLU* 4.5 9.2 - - + -
528A PHE* 3.4 56.8 - + + -
529A SER* 3.2 23.6 + - - -
531A VAL* 5.7 0.4 - - + -
532A ARG* 4.2 20.4 - - + -
541A GLY 3.6 0.2 + - - -
542A MET* 3.8 22.9 - - + +
544A ILE* 1.3 78.7 - - - +
546A SER* 1.3 65.2 + - - +
548A THR* 3.2 16.5 + - - -
549A LEU* 3.1 53.8 + - + +
557A ALA* 5.4 2.6 - - - +
561A LEU* 5.2 9.0 - - + -
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A MET 3.0 17.4 + - - -
543A GLU 2.9 13.7 + - - -
545A TYR* 1.3 77.6 - - - +
547A THR* 1.3 60.5 + - - +
549A LEU* 3.5 1.7 + - - -
550A TRP* 3.1 19.4 + - - +
558A LEU* 3.2 24.2 - - - +
561A LEU* 5.9 2.7 - - - -
565A LEU* 5.7 0.2 - - - -
577A CYS* 4.3 2.1 - - - +
578A ALA* 3.5 34.0 + - - -
581A ASN* 2.8 19.7 + - - -
612A LEU* 5.8 0.9 - - - +
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Residues in contact with THR 547 (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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516A PHE* 3.3 33.9 - - + -
543A GLU 4.7 0.4 - - - -
544A ILE* 3.1 10.1 + - - +
546A SER* 1.3 80.8 + - - +
548A THR* 1.3 64.8 + - - +
550A TRP* 3.0 23.1 - - - +
551A HIS* 3.1 20.9 + - + +
581A ASN* 3.5 10.1 + - - +
608A TYR* 3.3 24.0 + - - +
612A LEU* 3.4 19.0 - - - +
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Residues in contact with THR 548 (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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516A PHE* 3.7 25.6 - - + -
521A TYR* 4.8 17.2 - - - +
524A ALA* 4.8 4.9 - - + -
525A GLU* 4.3 11.4 - - - +
528A PHE* 4.4 8.3 - - + -
544A ILE* 3.0 24.1 + - + +
545A TYR* 3.2 26.3 + - - -
547A THR* 1.3 71.1 - - - +
549A LEU* 1.3 67.9 + - - +
550A TRP 3.0 5.1 + - - -
551A HIS* 3.1 15.4 + - - +
552A LEU* 3.1 19.8 + - - +
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Residues in contact with LEU 549 (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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525A GLU* 5.0 9.9 - - + -
545A TYR* 3.1 51.4 + - + +
546A SER* 3.6 8.3 - - - +
548A THR* 1.3 81.8 + - - +
550A TRP* 1.3 60.4 + - - +
552A LEU* 4.1 7.2 - - + -
553A GLN* 3.2 2.6 + - - -
554A LYS* 3.1 39.4 + - + +
557A ALA* 3.7 41.5 - - + +
558A LEU* 3.9 23.9 - - + +
561A LEU* 4.5 4.5 - - + -
585A LEU* 6.0 0.2 - - - +
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Residues in contact with TRP 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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546A SER 3.1 11.5 + - - +
547A THR* 3.0 25.4 - - - +
548A THR 3.0 0.4 - - - -
549A LEU* 1.3 77.3 - - - +
551A HIS* 1.3 102.8 + + - +
553A GLN* 3.3 17.0 + - - +
558A LEU* 4.2 5.4 - - + -
581A ASN* 3.1 25.4 - - + +
584A SER* 2.1 39.5 + - - -
585A LEU* 3.7 16.1 - - + +
615A HIS* 6.6 0.7 - - + -
681A ILE* 4.1 19.1 - - + -
684A VAL* 3.9 26.8 - - + +
685A GLN* 4.9 13.5 - - + -
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Residues in contact with HIS 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE* 4.1 8.2 - + - -
521A TYR* 3.6 44.5 + + + -
547A THR* 3.1 36.9 + - + +
548A THR* 3.1 4.7 + - - +
550A TRP* 1.3 106.4 - + - +
552A LEU* 1.3 62.2 + - - +
553A GLN* 3.1 14.1 + - - +
677A LEU* 4.0 24.5 + - - +
680A HIS* 4.1 24.3 + - + -
681A ILE* 4.3 8.9 + - + -
684A VAL* 5.2 3.5 - - - +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A TYR* 3.4 53.2 - - + +
522A MET* 4.2 9.0 - - + +
525A GLU* 4.3 14.6 - - + -
548A THR* 3.1 16.9 + - - +
549A LEU* 4.2 9.6 - - + +
551A HIS* 1.3 74.2 - - - +
553A GLN* 1.3 72.2 + - - +
554A LYS* 3.6 7.8 + - + +
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Residues in contact with GLN 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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549A LEU 3.2 5.7 + - - -
550A TRP 3.3 12.8 + - - +
551A HIS 3.1 13.8 + - - +
552A LEU* 1.3 83.7 - - - +
554A LYS* 1.3 60.2 + - - +
555A ASP* 3.6 7.1 + - - +
585A LEU* 5.9 5.8 - - - -
680A HIS* 6.0 2.6 - - - -
684A VAL* 4.5 25.0 + - + +
687A ALA* 5.3 7.1 - - - +
688A LEU* 6.0 2.6 - - - +
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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