Contacts of the strand formed by residues 536 - 540 (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 ASN 536 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358M ARG* 4.2 19.6 + - - +
391M TRP* 3.0 42.4 + - + +
394M GLY 4.4 11.4 - - - +
395M ASP 4.8 2.7 - - - +
396M ASN* 3.3 18.8 - - - +
508M GLN 2.8 21.4 + - - +
509M PHE* 3.3 10.9 - - + -
510M MET* 3.3 16.0 + - - +
534M VAL* 4.5 2.3 - - - +
535M ALA* 1.3 88.8 - - - +
537M ARG* 1.3 68.4 + - - +
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Residues in contact with ARG 537 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396M ASN* 3.2 36.0 - - + +
397M GLY 4.3 0.6 - - - +
509M PHE* 4.8 3.5 - - - -
510M MET* 3.6 22.1 - - + +
529M LEU 3.2 23.9 + - - -
530M ASN* 2.9 30.1 + - - +
532M PHE 4.4 2.0 + - - -
534M VAL* 3.5 27.6 - - + +
536M ASN* 1.3 80.6 - - - +
538M MET* 1.3 71.7 + - - +
539M LEU* 5.5 3.6 - - + -
558M PHE* 2.6 61.6 + - + -
559M LEU* 4.7 11.0 - - + +
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Residues in contact with MET 538 (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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386M TRP* 4.5 7.4 - - + -
387M MET* 3.7 47.1 - - + +
390M LEU* 6.0 1.1 - - + -
396M ASN* 5.4 0.4 - - - -
397M GLY 3.3 34.3 - - - +
399M LEU* 4.3 15.9 - - - -
411M THR* 6.4 0.2 - - + -
414M PHE* 5.6 1.6 - - + -
509M PHE* 3.8 24.0 - - + -
510M MET 2.9 14.4 + - - +
511M ALA* 3.6 11.4 - - - -
512M VAL* 3.7 4.2 + - - +
537M ARG* 1.3 81.1 - - - +
539M LEU* 1.3 66.1 + - - +
540M ILE* 3.7 23.3 - - + +
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Residues in contact with LEU 539 (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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397M GLY 3.6 5.8 + - - +
398M ILE* 3.4 36.8 - - + +
399M LEU* 2.6 33.3 + - - +
512M VAL* 3.7 22.9 - - + -
515M ALA* 4.5 12.1 - - + -
518M LEU* 5.1 3.8 - - + -
537M ARG* 5.5 3.6 - - + -
538M MET* 1.3 77.7 - - - +
540M ILE* 1.3 58.4 + - - +
541M THR* 3.8 3.1 - - + -
555M LEU* 3.7 35.0 - - + +
558M PHE* 4.0 32.5 - - + -
559M LEU* 5.8 5.2 - - + -
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Residues in contact with ILE 540 (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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387M MET* 5.8 0.2 - - + -
399M LEU* 3.6 23.3 - - + -
407M LYS* 3.7 46.1 - - + +
411M THR* 4.1 18.6 - - + +
440M TRP* 6.2 4.0 - - + -
511M ALA* 4.1 11.2 - - + -
512M VAL* 3.3 26.8 + - - +
513M ASP* 3.7 10.3 - - + +
514M GLU 3.3 18.2 + - - -
515M ALA 4.9 0.2 - - - -
538M MET* 3.7 33.0 - - + +
539M LEU* 1.3 72.1 - - - +
541M THR* 1.3 62.6 + - - +
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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