Contacts of the helix formed by residues 796 - 803 (chain M) in PDB entry 6G0L
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 GLN 796 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542M GLY 4.0 8.5 - - - +
544M PRO* 3.3 43.0 - - + +
546M GLN* 6.2 1.8 - - - +
794M ASN 3.7 0.6 + - - -
795M PRO* 1.3 73.1 - - + +
797M ALA* 1.3 59.0 + - - +
798M ASP* 3.1 4.7 - - - +
799M LEU* 3.2 25.8 + - + +
800M GLN* 2.9 37.7 + - + +
836M LYS 5.5 2.2 + - - -
837M MET* 3.5 38.3 - - - +
839M LEU 5.8 1.8 + - - -
840M GLU* 6.1 1.8 - - - +
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Residues in contact with ALA 797 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771M THR* 5.4 8.3 - - + -
792M ASP* 5.3 8.7 - - + +
794M ASN* 3.3 38.5 + - + +
795M PRO 2.8 4.9 + - - -
796M GLN* 1.3 78.7 - - - +
798M ASP* 1.3 61.5 - - - +
800M GLN* 3.8 9.6 - - - +
801M ALA* 2.9 28.6 + - - +
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Residues in contact with ASP 798 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788M ILE* 4.2 23.0 - - + +
791M SER* 3.6 23.6 + - - -
792M ASP* 4.4 17.5 + - - +
794M ASN 4.5 4.5 - - - +
796M GLN* 3.1 2.1 - - - +
797M ALA* 1.3 83.6 - - - +
799M LEU* 1.3 61.6 + - + +
801M ALA* 4.0 5.6 - - - +
802M MET* 2.9 41.4 + - + +
818M ARG* 3.9 25.2 + - - +
830M LEU* 5.5 1.0 - - - +
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Residues in contact with LEU 799 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796M GLN* 3.2 26.3 + - + +
798M ASP* 1.3 80.2 - - + +
800M GLN* 1.3 58.9 + - + +
802M MET* 3.6 22.5 + - + +
803M ALA* 3.1 24.9 + - - +
818M ARG* 6.3 0.7 - - - +
837M MET* 3.8 28.9 - - + -
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Residues in contact with GLN 800 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403M MET* 6.1 3.4 - - + -
514M GLU* 4.8 12.7 + - - +
516M HIS* 5.7 6.7 - - - +
541M THR* 5.2 1.0 + - - -
542M GLY* 3.2 35.8 + - - +
543M THR* 4.3 4.8 - - - +
544M PRO* 5.0 4.7 - - - +
775M GLY* 4.6 5.0 - - - +
796M GLN* 2.9 24.5 + - + +
797M ALA* 4.2 7.6 - - - +
799M LEU* 1.3 76.7 - - + +
801M ALA* 1.3 64.1 + - - +
803M ALA* 3.3 20.1 + - + +
804M ARG* 3.9 20.3 + - - +
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Residues in contact with ALA 801 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717M PHE* 3.4 45.0 - - + -
770M SER 5.6 1.1 - - - +
771M THR* 5.6 4.0 - - - +
775M GLY* 4.9 8.7 - - - +
788M ILE* 5.3 4.0 - - + -
792M ASP* 5.9 2.5 - - - +
797M ALA 2.9 21.0 + - - +
798M ASP* 3.2 8.7 + - - +
800M GLN* 1.3 74.9 - - - +
802M MET* 1.3 64.7 + - + +
803M ALA 3.1 2.1 + - - -
804M ARG* 3.3 14.0 + - - +
805M ALA 4.5 0.2 + - - -
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Residues in contact with MET 802 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611M GLU* 5.3 4.0 - - + -
786M VAL* 3.8 32.3 - - + -
788M ILE* 4.5 9.2 - - + -
798M ASP* 2.9 27.7 + - + +
799M LEU* 3.7 30.3 - - + +
801M ALA* 1.3 72.9 - - - +
803M ALA* 1.3 53.0 + - - +
804M ARG 3.1 3.1 - - - -
805M ALA* 3.1 4.7 + - - +
806M HIS* 2.7 42.9 + - + +
816M VAL* 3.6 37.9 - - + -
818M ARG* 5.6 5.6 - - - +
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Residues in contact with ALA 803 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402M GLU* 5.9 0.9 - - - +
403M MET* 4.0 26.7 - - + +
799M LEU 3.1 15.8 + - - +
800M GLN* 3.3 18.2 - - - +
801M ALA 3.1 0.4 - - - -
802M MET* 1.3 76.3 - - - +
804M ARG* 1.3 60.8 + - - +
805M ALA 3.3 0.4 - - - -
806M HIS* 3.8 11.7 - - - -
807M ARG* 3.2 31.5 + - - +
1502M BEF 4.8 2.7 - - - -
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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