Contacts of the helix formed by residues 599 - 606 (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 GLY 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ILE* 6.0 1.3 - - - -
571B ASN 3.7 8.0 - - - +
572B PHE* 4.4 1.6 - - - -
573B TYR* 5.3 0.4 - - - -
598B PHE* 1.3 83.3 - - - +
600B GLU* 1.3 58.7 + - - +
603B LEU* 3.3 14.0 - - - +
609B ARG* 2.8 25.6 + - - -
801B PCG 2.9 34.2 + - - -
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Residues in contact with GLU 600 (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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572B PHE* 4.1 11.9 - - + -
597B SER* 4.5 5.5 + - - -
598B PHE* 3.3 12.9 + - - -
599B GLY* 1.3 76.5 - - - +
601B LEU* 1.3 83.3 + - + +
603B LEU* 3.1 6.8 + - - +
604B ILE* 2.7 48.4 + - + +
629B TYR* 3.5 27.1 - - + +
637B THR* 5.0 0.4 - - + -
641B ARG* 3.2 25.0 + - - +
660B TRP* 3.1 23.2 + - - -
801B PCG 3.2 13.0 + - - -
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Residues in contact with LEU 601 (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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599B GLY 3.4 0.8 - - - -
600B GLU* 1.3 108.4 - - + +
602B ALA* 1.3 69.4 + - - +
603B LEU 3.1 0.2 + - - -
604B ILE* 3.2 0.6 + - + -
605B TYR* 3.0 51.1 + - + +
607B THR* 4.4 4.4 + - - +
610B ALA* 5.1 2.2 - - + -
641B ARG* 3.9 13.9 - - - +
660B TRP* 3.9 10.1 - - + -
663B LEU* 5.6 2.5 - - + -
801B PCG 3.1 55.6 + - + +
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Residues in contact with ALA 602 (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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569B GLY* 4.2 10.0 - - - -
601B LEU* 1.3 77.6 - - - +
603B LEU* 1.3 59.4 + - - +
606B GLY* 2.8 30.0 + - - -
607B THR* 3.5 26.8 + - - +
608B PRO 3.8 3.1 - - - +
609B ARG* 3.6 23.1 - - - +
801B PCG 3.2 27.1 + - - +
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Residues in contact with LEU 603 (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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569B GLY* 3.4 39.0 - - - +
570B ASP 3.6 4.5 - - - +
571B ASN* 3.2 34.8 - - - +
572B PHE* 3.3 13.7 - - + +
599B GLY 3.3 14.8 - - - +
600B GLU* 3.4 5.4 - - - +
601B LEU 3.0 0.4 - - - -
602B ALA* 1.3 79.3 - - - +
604B ILE* 1.3 61.8 + - - +
606B GLY* 3.9 4.0 + - - -
609B ARG* 3.8 2.2 - - - +
626B ARG* 3.6 33.3 + - + +
629B TYR* 4.4 13.0 - - + -
630B ARG* 3.4 26.1 + - + +
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Residues in contact with ILE 604 (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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600B GLU* 2.7 34.4 + - + +
603B LEU* 1.3 73.4 - - - +
605B TYR* 1.3 77.9 + - + +
629B TYR* 3.5 34.3 - - + +
630B ARG* 4.4 7.2 + - - -
634B MET* 3.7 31.5 - - + +
637B THR* 3.8 19.3 - - + -
638B LEU* 3.7 31.6 - - + -
641B ARG* 4.5 4.7 - - - +
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Residues in contact with TYR 605 (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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601B LEU* 3.0 41.4 + - + +
604B ILE* 1.3 96.8 - - + +
606B GLY* 1.3 62.2 - - - +
607B THR* 3.5 23.5 - - + +
638B LEU* 3.2 23.7 - - + +
641B ARG* 4.9 5.2 + - - -
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Residues in contact with GLY 606 (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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602B ALA 2.8 15.0 + - - -
603B LEU 3.9 3.9 + - - -
604B ILE 3.7 1.6 - - - -
605B TYR* 1.3 78.0 - - - +
607B THR* 1.3 64.1 + - - +
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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