Contacts of the helix formed by residues 657 - 664 (chain B) in PDB entry 4RS6
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 LEU 657 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B VAL* 3.2 48.0 - - + +
479B LEU* 4.6 4.7 - - + +
482B CYS* 4.1 18.6 - - + -
634B ILE* 5.2 9.0 - - + -
641B TYR* 3.1 30.0 + - + +
642B LEU 4.7 1.8 - - - +
643B LEU* 3.9 34.3 - - + +
655B PHE 3.5 2.0 + - - -
656B ARG* 1.3 69.4 - - - +
658B THR* 1.3 65.1 + - - +
660B LEU* 3.3 13.4 + - + +
661B LEU* 3.0 23.1 + - - +
673B MET* 4.9 2.2 - - + -
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Residues in contact with THR 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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640B GLU* 4.5 9.9 + - + +
641B TYR 4.9 0.4 + - - -
656B ARG* 3.7 19.4 - - - +
657B LEU* 1.3 79.0 - - - +
659B THR* 1.3 61.5 + - - +
661B LEU* 3.1 29.4 - - + +
662B MET* 3.1 23.8 + - + +
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Residues in contact with THR 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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493B PRO* 4.0 25.6 - - + -
495B GLU* 3.6 42.4 + - + +
655B PHE* 5.1 1.3 - - + -
656B ARG* 3.1 28.8 + - - +
658B THR* 1.3 74.7 + - - +
660B LEU* 1.3 67.4 + - - +
661B LEU 2.9 1.5 + - - -
662B MET* 3.1 4.6 + - - +
663B SER* 2.8 34.5 + - - +
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Residues in contact with LEU 660 (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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482B CYS* 3.9 9.2 - - - -
486B MET* 3.1 17.1 - - + +
493B PRO* 4.2 12.1 - - + -
643B LEU* 3.8 32.3 - - + -
655B PHE* 4.1 25.4 - - + -
656B ARG 3.3 2.7 + - - +
657B LEU* 3.3 13.2 + - + +
659B THR* 1.3 79.7 - - - +
661B LEU* 1.3 58.0 + - - +
664B GLY 3.0 41.4 + - - +
665B CYS* 3.5 24.2 - - + -
669B LEU* 4.4 5.4 - - + -
673B MET* 4.3 16.2 - - + -
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Residues in contact with LEU 661 (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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481B GLY 4.6 4.0 - - - +
482B CYS* 3.9 25.5 - - + +
485B ASN* 3.7 31.8 - - + +
486B MET* 3.2 27.2 - - - +
487B PRO* 3.5 0.9 - - - +
657B LEU* 3.0 11.8 + - + +
658B THR* 3.1 24.0 - - + +
659B THR 2.9 0.2 - - - -
660B LEU* 1.3 78.7 - - - +
662B MET* 1.3 85.6 + - + +
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Residues in contact with MET 662 (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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487B PRO* 3.6 12.3 - - - +
658B THR* 3.2 20.9 - - + +
659B THR* 3.1 5.0 + - - +
661B LEU* 1.3 101.5 - - + +
663B SER* 1.3 65.1 + - - +
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Residues in contact with SER 663 (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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487B PRO* 3.6 11.2 - - - +
489B ALA* 3.9 9.5 - - - +
493B PRO* 3.9 24.0 - - - +
659B THR* 2.8 23.3 + - - +
662B MET* 1.3 82.8 - - - +
664B GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 664 (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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486B MET* 4.0 5.6 - - - -
487B PRO* 3.8 24.3 - - - +
489B ALA* 4.0 3.8 - - - -
491B CYS 4.5 1.3 - - - -
493B PRO* 3.6 11.6 - - - +
660B LEU* 3.0 29.2 + - - +
663B SER* 1.3 79.4 - - - +
665B CYS* 1.3 65.3 + - - +
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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