Contacts of the strand formed by residues 509 - 513 (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 PHE 509 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387M MET* 4.8 1.8 - - + -
391M TRP* 5.4 4.7 - + - -
411M THR* 4.9 3.1 - - + -
414M PHE* 3.8 33.4 - + - -
415M ILE* 4.0 28.0 - - + -
418M LEU* 5.1 9.4 - - + -
427M PRO 4.8 0.2 + - - -
428M HIS* 3.4 29.3 + + + +
429M ILE* 3.2 31.5 + - - +
430M ILE* 4.9 1.6 - - + -
507M TRP* 4.8 0.2 - - - +
508M GLN* 1.3 77.9 - - - +
510M MET* 1.3 63.5 + - - +
511M ALA* 3.7 24.0 - - + -
534M VAL* 5.5 1.6 - - - -
536M ASN* 3.3 18.2 - - + -
537M ARG 4.8 3.6 - - - -
538M MET* 3.8 33.9 - - + -
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Residues in contact with MET 510 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429M ILE* 3.3 23.1 - - + +
431M VAL* 5.0 9.0 - - + -
509M PHE* 1.3 79.2 - - - +
511M ALA* 1.3 67.5 + - - +
512M VAL* 5.7 3.1 - - + -
529M LEU* 4.1 50.9 - - + +
532M PHE* 4.5 10.1 - - + -
534M VAL* 3.9 27.4 - - + -
536M ASN 3.3 6.2 + - - +
537M ARG* 3.6 25.6 - - + +
538M MET* 2.9 30.8 + - - +
558M PHE* 5.0 3.6 - - - -
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Residues in contact with ALA 511 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411M THR* 4.1 11.0 - - + -
429M ILE 3.4 5.5 + - - -
430M ILE* 3.4 22.9 - - + +
431M VAL* 3.0 30.8 + - - +
440M TRP* 6.1 0.9 - - + -
509M PHE* 3.7 21.3 - - + -
510M MET* 1.3 74.8 - - - +
512M VAL* 1.3 62.2 + - - +
538M MET 3.6 4.9 - - - -
540M ILE* 4.1 14.1 - - + -
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Residues in contact with VAL 512 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M ILE* 5.5 0.4 - - - -
431M VAL* 3.6 22.4 - - + +
440M TRP* 5.9 1.6 - - - -
492M TYR* 3.6 24.0 - - + +
510M MET* 5.6 4.9 - - + +
511M ALA* 1.3 78.7 - - - +
513M ASP* 1.3 64.1 + - - +
515M ALA* 3.8 20.7 - - + +
518M LEU* 6.1 1.8 - - + -
529M LEU* 6.0 8.1 - - + -
538M MET 3.7 5.1 + - - +
539M LEU* 3.7 30.5 - - + -
540M ILE* 3.3 28.3 + - - +
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Residues in contact with ASP 513 (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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407M LYS* 4.8 6.2 - - - +
408M THR* 4.9 0.2 + - - -
430M ILE* 6.1 0.2 - - - +
431M VAL 3.9 6.4 + - - +
432M VAL* 5.3 1.7 - - + +
433M PRO* 4.3 13.5 - - + +
436M THR* 4.9 11.1 + - - +
440M TRP* 3.7 37.3 + - + -
492M TYR* 2.8 23.4 + - - -
512M VAL* 1.3 72.9 - - - +
514M GLU* 1.3 94.7 + - - +
540M ILE* 3.7 16.7 - - + +
776M LEU 5.3 0.2 - - - +
1501M ADP 4.2 16.5 + - - -
1502M BEF 4.2 2.1 - - - -
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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