Contacts of the strand formed by residues 474 - 481 (chain C) in PDB entry 1JIQ
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 474 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASP 4.5 1.6 - - - +
57C LYS* 3.0 31.3 + - - +
58C ASN* 3.4 16.5 - - - +
404C CYS* 3.2 14.6 - - + +
406C PHE* 3.7 14.1 - - + -
433C THR* 3.4 28.5 + - + +
436C LEU* 3.5 32.5 - - + -
472C ARG 4.1 4.3 + - - +
473C PRO* 1.3 80.8 - - - +
475C ASN* 1.3 65.1 + - - +
476C SER* 4.8 0.5 + - - -
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Residues in contact with ASN 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C VAL* 5.9 0.7 - - + -
54C ASP 3.6 4.5 - - - +
55C TYR* 3.3 16.2 - - - +
58C ASN* 2.8 28.7 + - - +
320C LEU* 3.6 27.2 + - + +
323C LEU* 3.7 11.5 - - - +
336C HIS* 5.1 4.0 - - - -
404C CYS 2.9 6.6 + - - +
405C ASP* 3.0 28.7 + - - +
406C PHE* 2.8 29.2 + - - +
474C THR* 1.3 74.7 - - - +
476C SER* 1.3 62.7 + - - +
477C ILE* 4.1 8.1 - - + -
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Residues in contact with SER 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU 3.5 2.6 - - - +
54C ASP* 2.9 39.3 + - - +
57C LYS* 4.3 2.6 + - - -
406C PHE 3.4 4.7 - - - -
429C PHE* 3.9 14.0 - - - -
433C THR* 3.6 27.4 + - - +
474C THR* 4.8 0.7 + - - -
475C ASN* 1.3 72.0 + - - +
477C ILE* 1.3 60.9 + - - +
478C VAL* 4.0 1.1 + - - -
545D LEU* 3.8 36.2 - - - +
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Residues in contact with ILE 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 4.1 22.2 - - + -
52C LEU 3.3 3.6 - - - +
53C VAL* 4.5 16.2 - - + -
320C LEU* 4.4 15.9 - - + -
405C ASP* 4.7 9.4 - - + -
406C PHE 2.8 10.8 + - - +
407C LEU* 3.2 17.0 - - + -
408C ILE 3.1 23.2 + - - -
429C PHE* 4.4 0.6 - - - -
475C ASN* 4.8 3.4 - - + -
476C SER* 1.3 78.5 - - - +
478C VAL* 1.3 62.2 + - - +
479C PHE* 3.6 13.4 - - + -
490C LEU* 4.3 11.9 - - + -
493C MET* 4.1 17.5 - - + -
494C TYR* 3.5 25.1 - - + +
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Residues in contact with VAL 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 3.4 2.3 - - - +
52C LEU* 2.7 40.3 + - + +
408C ILE* 3.3 17.0 - - + +
410C VAL* 3.6 26.9 - - + -
429C PHE* 3.9 22.4 - - + -
477C ILE* 1.3 77.1 - - - +
479C PHE* 1.3 63.8 + - - +
545D LEU* 3.8 30.1 - - + -
548D PHE* 3.7 19.8 - - + -
549D ILE* 4.3 10.5 - - + -
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Residues in contact with PHE 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C HIS 3.1 11.7 - - - +
51C ILE* 4.4 3.8 - - + -
345C LEU* 4.5 11.4 - - + -
407C LEU* 4.1 12.3 - - + -
408C ILE 3.1 24.4 + - - -
409C PRO* 3.1 32.0 - - + +
410C VAL* 2.7 33.8 + - - -
477C ILE* 3.6 17.3 - - + -
478C VAL* 1.3 79.3 - - - +
480C THR* 1.3 57.9 - - - +
481C LYS 4.3 4.3 - - - -
482C LEU* 4.0 17.9 - - + -
486C MET* 3.8 33.2 - - + -
490C LEU* 3.7 28.9 - - + -
548D PHE* 4.7 0.9 - - - -
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Residues in contact with THR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLY* 3.6 10.0 - - - -
50C HIS 2.9 27.8 + - - -
410C VAL* 3.2 9.3 + - - +
411C GLN* 2.8 45.6 + - - +
479C PHE* 1.3 72.6 - - - +
481C LYS* 1.3 59.3 + - - +
486C MET* 4.6 1.6 - - - +
548D PHE* 5.0 0.4 - - - -
552D GLN* 2.7 35.8 + - + +
555D ALA* 4.1 4.3 - - + -
557D VAL* 3.4 26.2 - - + -
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Residues in contact with LYS 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C HIS 5.6 0.7 - - - +
174C TYR* 4.5 4.7 - - - -
409C PRO* 4.2 2.2 - - - -
411C GLN* 3.7 35.8 + - + +
412C THR 4.5 13.2 + - - -
413C GLN* 3.8 31.6 + - - +
479C PHE* 3.3 5.9 + - - -
480C THR* 1.3 81.3 - - - +
482C LEU* 1.3 60.8 + - - +
483C THR* 3.0 19.4 + - + +
486C MET* 3.3 19.8 - - - +
557D VAL* 3.8 32.1 - - + +
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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