Contacts of the strand formed by residues 481 - 488 (chain C) in PDB entry 1EQR
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 TYR 481 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C LYS* 5.1 2.0 - - - -
287C ARG* 5.6 3.1 - - - -
477C VAL* 3.4 5.4 - - - +
478C ILE 2.8 28.2 + - - +
479C ASN* 3.6 21.5 - - + -
480C GLY* 1.3 83.0 - - - +
482C GLU* 1.3 53.2 + - - +
483C VAL* 2.7 24.0 + - + +
537C ARG* 3.2 56.8 + - + +
541C LEU* 3.5 30.3 - - + -
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Residues in contact with GLU 482 (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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282C ASP* 5.1 5.4 - - - +
283C LYS* 4.5 19.7 - - + +
475C ASP* 3.3 32.1 - - + +
476C MET 3.9 4.9 - - - -
477C VAL* 4.5 8.4 - - + +
480C GLY 4.1 1.8 + - - -
481C TYR* 1.3 70.0 - - - +
483C VAL* 1.3 57.9 + - - +
484C GLY 3.3 11.4 - - - +
485C GLY* 5.6 0.5 + - - -
537C ARG* 4.9 7.3 + - - +
903C MG 2.1 31.0 - - - -
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Residues in contact with VAL 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C MET* 2.9 42.9 + - + +
478C ILE* 4.1 12.6 - - + -
481C TYR* 2.7 22.6 + - + +
482C GLU* 1.3 73.3 - - - +
484C GLY* 1.3 56.9 + - - +
533C PHE* 3.3 11.4 - - + -
534C GLY* 2.9 27.9 + - - +
537C ARG* 4.7 13.2 - - + -
538C LEU* 3.8 21.7 - - + +
541C LEU* 3.6 31.0 - - + -
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Residues in contact with GLY 484 (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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475C ASP* 3.3 8.3 - - - +
476C MET* 2.7 33.9 + - - +
482C GLU* 3.3 10.2 - - - +
483C VAL* 1.3 85.0 - - - +
485C GLY* 1.3 55.6 + - - -
531C LEU* 4.3 3.4 - - - -
532C ALA 3.3 13.0 - - - -
533C PHE* 3.9 11.0 - - - -
534C GLY 4.6 0.2 - - - -
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Residues in contact with GLY 485 (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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448C HIS* 5.0 2.7 - - - -
474C TYR 3.2 13.0 - - - -
475C ASP* 3.4 8.5 - - - -
482C GLU* 5.7 0.7 - - - -
484C GLY* 1.3 75.2 - - - -
486C GLY* 1.3 58.5 + - - -
531C LEU* 3.7 14.8 - - - +
532C ALA* 2.9 28.9 + - - +
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Residues in contact with GLY 486 (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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448C HIS* 3.3 19.8 - - - -
449C HIS* 5.5 1.3 - - - -
474C TYR* 3.1 22.2 + - - -
475C ASP* 4.3 0.4 + - - -
485C GLY* 1.3 75.6 - - - -
487C SER* 1.3 67.2 + - - -
489C ARG* 4.1 6.5 - - - -
530C GLY 3.6 13.2 - - - -
531C LEU* 3.7 8.5 - - - +
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Residues in contact with SER 487 (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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448C HIS* 4.7 1.6 - - - -
449C HIS* 3.6 2.1 - - - -
452C THR* 3.0 35.4 + - - +
472C ASN 3.1 16.6 - - - -
473C ALA* 3.8 4.3 - - - -
474C TYR* 3.3 17.8 + - - -
486C GLY* 1.3 75.6 - - - -
488C VAL* 1.3 65.4 + - - +
489C ARG* 3.0 23.9 + - - +
529C ALA* 3.4 0.5 - - - -
530C GLY 3.2 22.8 + - - -
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Residues in contact with VAL 488 (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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239C MET 5.4 3.1 - - - +
240C THR* 4.9 0.7 - - - -
241C ALA* 3.8 23.1 - - + +
452C THR* 3.8 3.3 - - - -
453C SER* 3.1 31.6 + - - +
472C ASN* 3.1 40.7 + - + +
474C TYR* 4.5 0.2 - - + -
487C SER* 1.3 76.1 - - - +
489C ARG* 1.3 72.1 + - - +
491C HIS* 6.0 1.6 - - - +
527C PRO* 6.1 2.9 - - + -
528C HIS 3.6 9.9 - - - +
529C ALA* 3.5 17.9 - - + -
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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