Contacts of the helix formed by residues 654 - 659 (chain B) in PDB entry 4RIB
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 PRO 654 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B THR* 5.5 3.6 - - + +
652B ASP 3.7 2.0 - - - +
653B LEU* 1.3 98.0 - - + +
655B LEU* 1.3 66.4 + - - +
656B PHE* 3.4 32.5 - - + -
657B LEU* 3.1 19.4 + - + -
658B ARG* 2.8 20.4 + - - +
857B ASP* 5.2 4.7 - - - +
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Residues in contact with LEU 655 (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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653B LEU 3.8 0.4 + - - -
654B PRO* 1.3 70.7 - - - +
656B PHE* 1.3 60.2 + - - +
657B LEU 2.8 7.6 + - - -
658B ARG* 3.0 43.0 + - - +
659B CYS* 3.5 11.6 + - - +
664B TRP* 4.0 26.8 - - + -
701B PRO* 4.0 28.5 - - + -
737B GLU* 5.9 1.3 - - - +
872B THR* 4.0 23.8 - - + -
873B ASP* 6.6 0.4 - - + -
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Residues in contact with PHE 656 (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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654B PRO* 3.4 31.9 - - + -
655B LEU* 1.3 76.6 - - - +
657B LEU* 1.3 65.7 + - + +
659B CYS* 3.9 7.3 - - - -
660B PHE* 3.5 17.8 - - - -
855B ILE* 6.1 0.9 - - + -
856B PRO 3.7 8.3 - - - -
857B ASP* 3.7 34.8 - - + -
858B VAL* 3.4 21.8 - - + -
868B LEU* 3.3 39.1 - - + +
869B ASP* 3.8 21.3 - - + -
872B THR* 3.9 11.8 - - + +
874B SER* 4.4 10.3 - - - -
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Residues in contact with LEU 657 (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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593B THR* 4.7 3.8 - - - -
595B ILE* 4.6 12.3 - - + +
653B LEU* 3.7 32.9 - - + +
654B PRO* 3.1 17.8 + - + +
655B LEU 2.8 1.6 + - - -
656B PHE* 1.3 97.8 - - + +
658B ARG* 1.3 63.0 + - - +
659B CYS 3.0 2.7 - - - -
660B PHE* 2.8 39.0 + - + +
661B THR* 4.3 2.3 - - - +
857B ASP* 4.0 32.1 - - + +
860B ARG* 4.3 14.6 - - - +
868B LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 658 (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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650B HIS 3.7 19.1 - - - +
651B GLU 3.7 11.5 + - - -
652B ASP 5.1 0.4 + - - -
653B LEU* 3.0 26.6 + - - +
654B PRO* 2.8 12.9 + - - +
655B LEU* 3.0 28.7 + - - +
657B LEU* 1.3 76.5 - - - +
659B CYS* 1.3 57.3 + - - +
660B PHE 3.0 4.9 + - - -
661B THR* 3.2 27.6 + - + +
664B TRP* 3.5 18.8 - - + +
697B ARG 4.5 2.6 + - - -
698B ILE* 2.8 63.2 + - - +
699B TYR* 4.5 8.1 - - + -
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Residues in contact with CYS 659 (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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558B MET* 5.2 4.0 - - - +
559B GLU* 5.9 0.2 - - - -
605B TYR* 4.6 0.9 + - - -
655B LEU 3.5 5.3 + - - +
656B PHE* 3.9 10.8 - - - -
657B LEU 3.0 1.0 - - - -
658B ARG* 1.3 77.0 - - - +
660B PHE* 1.3 92.8 + - - +
661B THR 3.4 3.1 + - - -
664B TRP* 3.2 50.7 - - + +
665B ILE* 4.3 10.4 - - - +
668B ARG* 5.7 0.2 + - - -
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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