Contacts of the helix formed by residues 497 - 506 (chain R) in PDB entry 6CNB
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 ARG 497 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213R TRP* 3.3 17.8 - - + -
216R GLU* 6.2 0.2 - - - -
496R ILE* 1.3 76.5 - - - +
498R LEU* 1.3 63.0 + - - +
499R GLU* 3.4 21.3 + - - +
500R GLY* 3.9 24.7 - - - -
501R LEU* 3.6 17.3 + - - +
562R GLU 4.5 2.0 + - - -
563R PHE* 3.1 60.1 + - + +
564R ARG* 4.1 11.5 + - - +
565R LYS* 3.8 34.1 - - - +
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Residues in contact with LEU 498 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216R GLU* 3.2 40.7 - - + +
496R ILE* 3.7 15.3 + - + -
497R ARG* 1.3 71.7 - - - +
499R GLU* 1.3 68.9 + - - +
500R GLY 3.2 0.4 - - - -
501R LEU* 2.9 18.0 + - + +
502R ALA* 3.2 13.9 + - - +
511R TYR* 4.1 10.2 - - + +
517R PRO 4.8 5.8 - - - +
519R LEU* 3.6 44.2 - - + +
532R ILE* 3.6 30.1 - - + +
534R VAL* 3.7 17.3 - - + -
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Residues in contact with GLU 499 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R LEU* 4.6 17.5 - - + +
213R TRP* 4.5 6.9 - - - -
215R PHE* 6.4 2.7 - - + -
216R GLU* 3.9 20.4 + - - +
497R ARG* 3.4 25.3 + - - +
498R LEU* 1.3 79.3 + - - +
500R GLY* 1.3 61.7 + - - +
502R ALA* 4.7 1.4 - - - +
503R PHE* 3.2 22.0 + - - +
511R TYR* 5.8 4.7 - - - -
565R LYS* 5.5 2.3 - - - -
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Residues in contact with GLY 500 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497R ARG* 3.9 22.9 + - - +
498R LEU 3.2 0.2 - - - -
499R GLU* 1.3 87.4 - - - +
501R LEU* 1.3 56.1 + - - +
503R PHE* 3.3 13.7 - - - +
504R SER* 2.6 38.8 + - - -
563R PHE* 4.5 0.4 - - - -
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Residues in contact with LEU 501 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496R ILE* 4.8 8.1 - - + -
497R ARG* 3.6 15.7 + - - +
498R LEU* 2.9 24.8 + - + +
500R GLY* 1.3 74.3 - - - +
502R ALA* 1.3 54.7 + - - +
504R SER* 2.8 4.0 + - - -
505R HIS* 2.7 41.8 + - + +
509R SER* 3.7 23.1 - - - +
519R LEU* 3.7 23.3 - - + -
521R TYR* 5.5 1.8 - - + -
532R ILE* 5.4 4.3 - - + -
556R ILE* 6.4 1.8 - - + -
559R VAL* 4.5 12.3 - - + +
560R LEU* 5.1 11.2 - - + -
563R PHE* 3.4 32.1 - - + -
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Residues in contact with ALA 502 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R THR* 4.9 0.5 + - - -
172R GLU* 5.2 6.8 - - - +
175R LEU* 5.4 8.1 - - + -
498R LEU 3.2 6.6 + - - +
499R GLU 4.8 1.6 - - - +
501R LEU* 1.3 81.2 - - - +
503R PHE* 1.3 61.6 + - - +
506R GLY* 3.1 22.2 - - - -
509R SER* 4.2 17.0 - - - +
511R TYR* 3.5 42.6 - - + +
519R LEU* 4.4 1.6 - - + -
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Residues in contact with PHE 503 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172R GLU* 5.7 9.3 - - + +
175R LEU* 4.1 24.8 - - + +
499R GLU 3.2 22.2 + - - +
500R GLY* 3.1 12.9 + - - +
502R ALA* 1.3 78.8 - - - +
504R SER* 1.3 60.1 + - - +
506R GLY 4.7 0.2 - - - -
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Residues in contact with SER 504 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500R GLY 2.6 18.7 + - - -
501R LEU 2.8 3.9 + - - -
503R PHE* 1.3 79.3 - - - +
505R HIS* 1.3 66.8 + - - -
506R GLY 3.2 7.7 + - - -
507R THR* 4.9 3.5 + - - +
562R GLU* 5.2 0.3 + - - -
563R PHE* 3.6 26.1 - - - -
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Residues in contact with HIS 505 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501R LEU* 2.7 16.9 + - + +
504R SER* 1.3 78.5 + - - +
506R GLY* 1.3 51.9 + - - -
507R THR* 2.7 21.1 + - - -
508R PHE* 2.9 8.2 + - + +
509R SER* 2.8 33.6 + - - +
521R TYR* 4.9 5.2 - + + -
559R VAL* 3.4 32.9 - - + +
562R GLU* 3.5 21.0 + - - -
563R PHE* 3.2 40.6 - + - -
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Residues in contact with GLY 506 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171R THR* 2.3 33.5 + - - -
172R GLU* 5.6 2.0 - - - -
502R ALA 3.1 21.3 + - - -
503R PHE 4.7 0.2 - - - -
504R SER 3.2 4.6 + - - -
505R HIS* 1.3 75.9 - - - +
507R THR* 1.3 61.9 + - - +
509R SER* 2.7 25.5 + - - +
510R SER* 5.4 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