Contacts of the strand formed by residues 421 - 425 (chain G) in PDB entry 1I43
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 LEU 421 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212G PRO* 3.5 32.5 - - + -
213G PHE* 3.7 27.1 - - + -
338G TYR* 4.2 9.6 - - + -
363G SER* 4.0 24.7 - - - -
364G PHE 3.8 10.3 - - - +
365G GLU* 4.4 7.8 - - + +
398G GLN* 3.6 15.6 - - - +
399G PRO* 3.8 27.5 - - + +
400G ALA 5.3 0.2 + - - -
417G ILE* 4.4 8.7 - - + -
418G MET* 3.2 21.7 + - + +
420G ASN* 1.3 81.7 - - - +
422G VAL* 1.3 70.7 + - - +
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Residues in contact with VAL 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362G VAL 3.9 0.3 - - - +
363G SER* 3.3 3.5 - - - -
364G PHE* 2.9 62.0 + - + +
366G VAL* 4.5 8.3 - - + -
373G THR* 3.3 33.9 - - + -
376G PHE* 4.4 5.8 - - + -
377G VAL* 4.3 10.8 - - + -
396G VAL* 4.2 15.9 - - + -
397G ASP 3.7 8.7 - - - +
398G GLN* 4.2 6.7 - - + -
399G PRO* 4.4 0.2 - - - -
420G ASN 3.7 2.7 - - - +
421G LEU* 1.3 78.1 - - - +
423G ARG* 1.3 67.5 + - - +
424G PHE 3.8 0.7 + - - -
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Residues in contact with ARG 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G ASN* 3.5 24.8 + - - +
212G PRO* 4.4 8.8 - - + +
239G PHE* 4.8 8.6 - - - -
361G ALA* 5.1 7.9 - - + -
362G VAL 3.9 3.4 - - - +
363G SER* 3.3 20.4 - - - +
386G ALA 5.1 0.8 + - - -
387G PRO 4.9 0.6 - - - -
388G SER 3.6 23.6 + - - +
389G PHE* 4.1 19.9 - - - +
395G ILE* 3.9 1.3 - - - +
396G VAL* 3.5 6.2 - - - +
397G ASP* 3.0 63.1 + - - +
399G PRO* 4.0 13.7 - - + +
421G LEU* 5.8 0.2 - - + -
422G VAL* 1.3 72.4 - - - +
424G PHE* 1.3 67.4 + - - +
425G SER* 4.0 2.7 + - - +
606G PMC 3.3 43.0 + - - -
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Residues in contact with PHE 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360G GLY 3.8 0.2 - - - +
361G ALA* 3.6 2.8 - - - +
362G VAL 2.7 44.0 + - - +
364G PHE* 3.9 24.5 - + + -
376G PHE* 5.4 0.4 - + - -
380G LEU* 4.1 9.2 - - + -
383G PRO* 3.6 25.4 - - + -
394G SER* 4.2 9.2 - - - -
395G ILE 3.8 3.6 - - - -
396G VAL* 3.4 23.3 - - + -
422G VAL 3.8 0.4 + - - -
423G ARG* 1.3 75.0 - - - +
425G SER* 1.3 71.1 + - - +
426G PHE* 3.3 43.8 + + + -
434G LEU* 4.5 7.2 - - + -
438G ILE* 3.8 31.6 - - + -
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Residues in contact with SER 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G PHE* 5.6 1.6 - - - -
317G GLN* 5.4 0.3 + - - -
360G GLY 4.0 4.6 + - - -
361G ALA* 4.6 4.5 - - - +
388G SER 4.5 1.1 - - - -
389G PHE* 3.1 36.4 - - - +
390G GLY* 3.2 13.5 + - - -
391G GLY 4.9 0.9 + - - -
393G GLU 5.0 2.3 + - - -
394G SER* 3.3 4.2 - - - -
395G ILE* 2.8 44.0 + - - +
423G ARG* 4.0 5.7 + - - -
424G PHE* 1.3 72.5 - - - +
426G PHE* 1.3 65.8 + - - +
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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