Contacts of the strand formed by residues 427 - 436 (chain R) in PDB entry 1G4W
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 LYS 427 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365R LEU* 4.3 28.7 - - + -
366R GLU* 6.3 0.7 - - + -
423R SER* 3.5 0.7 - - - -
424R CYS* 2.9 32.1 + - + +
426R GLU* 1.3 84.0 - - + +
428R ARG* 1.3 81.7 + - - +
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Residues in contact with ARG 428 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365R LEU* 4.4 2.3 - - - +
422R LEU 3.3 8.7 - - - +
423R SER* 3.7 22.1 + - - -
424R CYS 4.0 4.8 - - - +
425R GLY 2.7 26.7 + - - -
426R GLU* 3.5 12.7 + - - +
427R LYS* 1.3 103.8 + - - +
429R TYR* 1.3 67.9 + - - +
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Residues in contact with TYR 429 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364R LEU 3.8 14.8 - - - -
365R LEU* 4.0 26.2 - - + +
368R GLU* 3.1 55.7 + - + +
369R CYS 2.8 26.1 + - - -
370R SER* 4.5 2.6 - - - -
420R MET 3.5 1.6 - - - +
421R GLN* 4.6 0.7 - - - -
422R LEU* 2.8 44.6 + - + +
428R ARG* 1.3 79.7 - - - +
430R THR* 1.3 73.3 + - - +
431R ILE* 3.9 14.1 - - + -
462R ASN* 4.8 7.6 + - - -
475R HIS* 5.0 1.4 + - - -
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Residues in contact with THR 430 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419R ASN* 2.9 37.2 - - - +
420R MET 3.1 11.7 - - - +
421R GLN* 3.2 23.8 - - + +
429R TYR* 1.3 86.4 - - - +
431R ILE* 1.3 63.7 + - - +
432R PRO* 4.2 5.1 - - + +
462R ASN* 5.3 2.6 - - - +
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Residues in contact with ILE 431 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364R LEU* 4.1 14.1 - - + -
369R CYS* 3.5 35.4 - - + +
371R CYS* 3.5 23.3 - - - +
372R LEU* 3.6 11.0 - - + +
420R MET* 2.9 46.7 + - + +
422R LEU* 4.2 21.3 - - + -
429R TYR* 3.9 12.3 - - + -
430R THR* 1.3 76.2 - - - +
432R PRO* 1.3 77.4 - - + +
433R VAL* 3.6 1.0 - - + +
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Residues in contact with PRO 432 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370R SER 3.2 24.9 - - - +
371R CYS* 3.3 9.4 - - + +
372R LEU 2.9 23.7 + - - -
417R GLN* 4.7 10.5 - - - +
418R TYR 3.6 11.0 - - - +
419R ASN* 4.3 13.6 - - - +
430R THR* 4.2 5.4 - - + +
431R ILE* 1.3 86.6 - - + +
433R VAL* 1.3 59.5 + - - +
434R LEU* 5.9 0.9 - - + -
461R SER* 3.6 28.9 - - - +
462R ASN* 4.4 7.4 - - - +
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Residues in contact with VAL 433 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372R LEU* 3.3 31.2 - - + +
374R VAL* 4.5 3.4 - - + -
390R PHE* 4.2 22.4 - - + -
416R ASP 4.6 0.2 - - - -
417R GLN* 3.1 10.7 - - - +
418R TYR* 2.9 48.5 + - + -
420R MET* 3.7 31.0 - - + -
431R ILE* 3.6 11.0 - - + +
432R PRO* 1.3 79.9 - - - +
434R LEU* 1.3 72.8 + - - +
435R HIS 4.7 0.2 - - - +
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Residues in contact with LEU 434 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371R CYS* 5.0 6.1 - - + -
372R LEU 2.7 14.0 + - - +
373R VAL* 3.4 12.8 - - + +
374R VAL 2.9 26.7 + - - +
415R ILE* 4.0 17.7 - - + -
416R ASP 3.9 0.4 - - - -
417R GLN* 3.6 36.1 - - + +
432R PRO* 5.6 0.9 - - + -
433R VAL* 1.3 81.1 - - - +
435R HIS* 1.3 59.4 + - - +
436R VAL* 3.9 3.9 + - + -
454R LEU* 5.6 4.3 - - + -
457R ARG* 3.6 34.5 - - + +
458R VAL* 3.7 26.0 - - + +
461R SER* 4.5 9.9 - - - +
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Residues in contact with HIS 435 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374R VAL* 3.4 20.2 - - + +
376R THR 2.9 23.6 + - - -
377R SER 4.7 0.8 - - - -
378R GLU* 3.9 15.5 - - - -
381R MET* 3.7 15.3 - - - -
390R PHE* 3.4 36.2 - + + -
391R ARG* 3.9 3.4 + - - -
415R ILE* 3.5 6.1 - - - +
416R ASP* 2.8 45.7 + - + +
418R TYR* 4.3 5.4 + - + -
433R VAL* 4.1 1.1 - - + -
434R LEU* 1.3 72.0 - - - +
436R VAL* 1.3 75.5 + - - +
437R LYS* 3.7 22.4 + - + +
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Residues in contact with VAL 436 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373R VAL* 4.9 2.0 - - + -
374R VAL 2.9 10.3 + - - +
375R LEU* 3.7 30.2 - - + +
376R THR 3.7 9.9 - - - +
414R ALA 3.7 4.9 - - - +
415R ILE* 4.8 7.2 - - + +
434R LEU* 4.8 5.4 - - + +
435R HIS* 1.3 84.2 - - - +
437R LYS* 1.3 62.3 + - - +
438R ASN* 3.7 17.0 - - - +
439R TRP* 3.9 24.9 + - + -
445R LEU* 4.8 1.3 - - + -
454R LEU* 3.5 42.8 - - + -
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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