Contacts of the strand formed by residues 517 - 521 (chain D) in PDB entry 6M04
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 GLU 517 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D ASP 3.3 16.8 - - - +
494D VAL* 3.3 17.8 - - + +
495D LEU* 3.0 52.3 + - - +
515D LEU* 3.4 12.2 + - - +
516D GLN* 1.3 82.2 - - + +
518D LEU* 1.3 65.0 + - - +
519D HIS* 2.6 37.0 + - - -
539D LEU* 3.7 4.8 - - - +
541D CYS* 3.2 29.5 - - - +
563D ARG* 3.6 10.1 - - - +
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Residues in contact with LEU 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D LEU* 3.7 31.4 - - + -
497D LEU* 3.8 19.3 - - + -
505D ILE* 5.3 13.2 - - + -
515D LEU* 5.8 3.1 - - + -
517D GLU* 1.3 78.8 - - - +
519D HIS* 1.3 61.2 + - - +
520D LEU* 4.0 21.4 + - + +
528D GLU* 5.2 9.6 - - - +
535D LEU* 5.7 4.0 - - + -
539D LEU* 3.8 24.2 - - + -
541D CYS 3.0 7.9 + - - -
542D LEU* 3.2 24.7 - - + +
543D HIS 3.5 2.6 + - - +
556D VAL* 5.6 4.3 - - + -
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Residues in contact with HIS 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D VAL* 5.9 1.3 - - + -
495D LEU* 3.1 27.0 + - - +
496D LYS* 3.2 13.9 - - + +
497D LEU* 2.7 34.5 + - - +
517D GLU* 2.6 32.8 + - - -
518D LEU* 1.3 72.8 - - - +
520D LEU* 1.3 57.7 + - - +
541D CYS* 4.2 7.7 - - - -
542D LEU 4.0 1.8 - - - -
543D HIS* 3.2 53.6 + + + -
566D TYR* 4.4 4.8 - + - -
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Residues in contact with LEU 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D LEU* 3.4 18.6 - - + -
518D LEU* 4.0 32.5 - - + +
519D HIS* 1.3 75.5 - - - +
521D CYS* 1.3 62.2 + - - +
522D HIS 5.1 0.4 - - - +
523D CYS* 3.5 43.3 - - + +
525D ALA* 6.5 1.1 - - + -
542D LEU* 6.0 0.2 - - + -
543D HIS* 2.5 27.7 + - - +
544D VAL* 3.3 32.4 - - + +
545D LYS* 3.0 19.4 + - - +
547D THR* 5.2 1.6 - - + -
553D PRO* 4.5 8.1 - - + -
555D TRP* 5.9 5.2 - - + +
556D VAL* 6.5 0.4 - - + -
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Residues in contact with CYS 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D LEU 2.9 18.0 + - - -
498D GLU* 3.6 15.9 - - - -
499D LEU* 2.9 26.8 + - - -
520D LEU* 1.3 77.6 - - - +
522D HIS* 1.3 67.5 + - - +
523D CYS* 3.2 2.6 - - - +
545D LYS* 3.3 31.4 - - + +
546D PHE* 3.7 24.7 - - + -
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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