Contacts of the helix formed by residues 542 - 551 (chain B) in PDB entry 1RL3
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 ASN 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 4.7 10.6 - - - +
540B ASP* 3.0 9.6 + - - +
541B ASP* 1.3 91.2 + - - +
543B GLU* 1.3 55.9 + - + +
544B ARG 3.3 0.4 - - - -
545B SER* 3.3 9.2 - - - -
546B ASP* 2.3 29.7 - - - +
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Residues in contact with GLU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B HIS 3.7 5.4 - - - +
539B LEU* 3.1 18.5 - - + -
540B ASP* 2.4 70.1 + - - +
542B ASN* 1.3 63.4 - - - +
544B ARG* 1.3 66.8 + - - +
545B SER 2.9 2.7 - - - -
546B ASP* 2.8 23.9 + - - +
547B ILE* 3.0 17.0 + - - +
632B ILE* 3.4 36.0 - - + +
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Residues in contact with ARG 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 2.7 44.8 + - - -
121A LYS* 4.2 9.1 - - - +
124A ALA* 6.1 1.2 - - - +
530B ILE* 5.2 3.5 - - + +
531B GLU* 5.9 3.1 - - - +
539B LEU* 3.6 23.0 - - + +
540B ASP 3.5 16.9 + - - +
541B ASP* 3.2 45.5 + - - +
543B GLU* 1.3 78.2 - - - +
545B SER* 1.3 58.2 + - - +
547B ILE* 3.5 2.6 + - - +
548B PHE* 3.1 46.8 + - + -
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Residues in contact with SER 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TYR* 3.4 23.4 - - - +
121A LYS* 3.2 41.0 - - - +
541B ASP 4.4 1.1 - - - -
542B ASN 3.3 13.8 + - - -
543B GLU 2.9 0.2 - - - -
544B ARG* 1.3 79.1 - - - +
546B ASP* 1.3 61.4 + - - +
548B PHE* 3.6 2.6 + - - +
549B ASP* 2.9 37.5 + - - +
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Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B VAL 5.6 1.0 - - - +
513B ARG* 6.2 3.4 - - - -
542B ASN 2.3 30.7 - - - +
543B GLU* 2.8 14.8 + - - +
545B SER* 1.3 71.7 + - - +
547B ILE* 1.3 57.9 + - - +
549B ASP* 3.5 7.1 - - - +
550B ALA* 2.6 38.6 + - - +
631B ARG* 3.5 29.8 + - - +
632B ILE* 3.9 8.7 - - + +
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Residues in contact with ILE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ILE* 4.1 4.0 - - + -
536B PHE* 3.6 25.4 - - + -
539B LEU* 4.1 20.2 - - + -
543B GLU 3.0 14.5 + - - +
544B ARG 3.8 5.6 - - - +
546B ASP* 1.3 74.2 - - - +
548B PHE* 1.3 59.6 + - - +
550B ALA* 3.0 2.6 + - - +
551B MET* 2.6 60.9 + - + +
624B ILE* 4.3 15.5 - - + -
628B SER 4.9 0.4 - - - +
632B ILE* 3.2 38.8 - - + -
633B LEU* 4.5 11.4 - - + -
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Residues in contact with PHE 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.8 43.7 - + + -
518B LYS* 2.7 36.6 + - - -
523B MET* 4.1 15.0 - - + -
526B LEU* 3.2 28.4 - - + +
527B ALA* 3.3 50.0 - - + -
530B ILE* 3.8 22.9 - - + -
531B GLU* 5.2 3.1 - - - -
544B ARG* 3.1 42.8 + - + +
545B SER 3.7 5.2 - - - +
547B ILE* 1.3 79.5 - - - +
549B ASP* 1.3 54.9 + - - +
551B MET 3.8 0.7 + - - -
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Residues in contact with ASP 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASP* 3.5 17.8 - - - +
120A TYR* 3.2 26.9 + - - +
121A LYS* 5.5 2.1 + - - +
513B ARG* 6.1 1.6 - - - -
514B LYS 5.6 0.9 - - - +
515B VAL* 4.0 24.2 - - - +
516B ILE* 2.8 41.3 + - - +
518B LYS* 3.6 4.5 + - - +
545B SER* 2.9 28.5 + - - +
546B ASP* 3.5 8.2 - - - +
548B PHE* 1.3 82.1 - - - +
550B ALA* 1.3 50.1 + - - +
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Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B LYS* 4.0 25.7 - - + +
516B ILE* 3.8 6.0 - - - +
546B ASP 2.6 22.1 + - - +
547B ILE* 3.8 4.5 - - + +
549B ASP* 1.3 70.8 - - - +
551B MET* 1.3 66.6 + - - +
552B PHE* 4.0 9.2 - - - -
624B ILE* 4.2 9.0 - - + +
625B ASP* 4.2 5.8 - - - +
628B SER* 3.7 30.7 - - - +
631B ARG* 5.2 2.5 - - - +
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Residues in contact with MET 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B ILE* 3.0 17.7 - - - +
518B LYS* 3.3 10.2 - - - -
526B LEU* 3.4 42.8 - - + -
529B ALA* 6.4 0.2 - - + -
530B ILE* 3.4 28.3 - - + -
536B PHE* 3.4 27.4 - - + -
547B ILE* 2.6 33.4 + - + +
548B PHE 3.8 0.2 + - - -
549B ASP 3.5 0.6 - - - -
550B ALA* 1.3 77.4 - - - +
552B PHE* 1.3 59.7 + - - +
574B VAL* 5.6 2.9 - - + -
622B TRP* 4.4 18.2 - - + +
623B GLY 3.4 15.9 - - - +
624B ILE* 4.1 16.8 - - + -
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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