Contacts of the strand formed by residues 418 - 423 (chain A) in PDB entry 6G4N
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 THR 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A ILE* 3.4 13.8 - - + +
321A LEU* 4.2 8.5 - - + -
408A VAL* 3.4 33.0 - - + -
411A TYR* 4.0 8.0 - - - -
412A THR* 3.0 24.0 + - - +
415A GLY* 5.7 0.2 - - - -
417A GLY* 1.3 77.6 + - - -
419A TYR* 1.3 67.4 + - - +
494A LEU* 3.5 9.1 - - - +
495A PHE* 2.7 52.6 + - + -
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Residues in contact with TYR 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLN* 5.2 0.2 - - + -
319A ILE 3.1 15.0 + - - -
320A LEU* 3.4 11.9 - - + +
321A LEU* 2.8 32.0 + - - +
417A GLY* 4.7 4.0 - - - -
418A THR* 1.3 79.1 - - - +
420A LEU* 1.3 60.4 + - - +
476A PHE* 4.0 8.5 - + - -
480A GLY 3.7 14.6 + - - -
481A ASN* 3.4 22.1 + - - +
482A PRO* 3.5 32.8 - - + -
483A ASN* 4.5 2.2 - - - -
492A TRP* 3.5 46.1 - + + +
493A PRO 3.7 9.0 - - - -
494A LEU* 3.2 42.5 - - + +
495A PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LEU* 3.1 11.0 - - + +
322A GLY* 4.9 1.6 - - - -
404A LEU* 4.4 9.0 - - + -
405A MET* 3.6 26.2 - - + -
408A VAL* 3.8 28.9 - - + -
418A THR 4.2 1.2 + - - -
419A TYR* 1.3 73.0 - - - +
421A TYR* 1.3 69.4 + - - +
492A TRP* 3.3 17.8 + - - +
493A PRO 5.3 0.2 + - - -
495A PHE* 4.2 19.3 - - + +
501A LYS 4.8 1.2 + - - -
502A PHE* 3.2 46.7 - - + +
503A ILE 3.5 2.3 + - - -
516A LEU* 3.5 31.6 - - + -
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Residues in contact with TYR 421 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LEU 4.4 0.9 - - - -
225A GLN* 3.1 38.4 + - + +
320A LEU* 4.0 8.1 - - + -
321A LEU* 2.9 26.9 + - - -
322A GLY* 3.1 41.7 + - - -
323A VAL* 3.3 14.0 + - - +
420A LEU* 1.3 86.5 - - - +
422A PHE* 1.3 64.4 + - - +
423A PHE* 3.7 23.3 - + + -
443A GLU* 3.8 8.8 + - + +
473A TRP* 3.5 30.9 - + - -
492A TRP* 3.7 12.6 - + + -
503A ILE* 3.6 9.6 - - + +
505A LEU* 3.7 24.5 - - + -
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A VAL* 3.5 23.1 - - + -
324A ASN 3.9 4.7 - - - -
325A LYS* 3.7 41.3 - - + -
401A ILE* 4.7 8.5 - - + -
421A TYR* 1.3 76.4 - - - +
423A PHE* 1.3 60.4 + - - +
424A ASN* 3.2 35.8 + - + +
502A PHE* 3.8 22.7 - + + -
503A ILE 3.1 5.5 + - - -
504A ASP* 3.6 13.1 - - - +
505A LEU 3.1 19.8 + - - -
516A LEU* 3.9 22.7 - - + -
517A ARG* 5.8 2.5 - - + -
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Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A VAL 2.8 10.1 + - - +
324A ASN* 3.2 25.7 - - - +
325A LYS 3.0 24.9 + - - -
421A TYR* 3.7 15.7 - - + -
422A PHE* 1.3 73.0 - - - +
424A ASN* 1.3 59.5 + - - +
425A HIS* 3.8 26.2 - - + -
438A VAL* 3.8 12.0 - - + +
442A TYR* 4.2 4.7 - - + -
443A GLU* 3.8 24.5 - - + -
446A PHE* 3.8 29.6 - + + -
465A LEU* 4.2 12.1 - - + -
469A ILE* 4.0 22.9 - - + -
505A LEU* 3.7 25.1 - - + -
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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