Contacts of the strand formed by residues 467 - 472 (chain C) in PDB entry 3EI4
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 GLN 467 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C ASN* 3.7 1.0 - - - +
463C VAL* 2.7 38.4 + - + +
465C HIS* 3.5 27.1 + - - +
466C GLN* 1.3 80.1 - - - +
468C LEU* 1.3 68.3 + - - +
478C LEU* 3.5 22.7 - - + +
479C VAL 3.2 15.3 - - - +
480C SER* 4.3 6.2 - - - +
481C GLN* 3.7 3.8 - - - +
487C VAL* 3.6 16.2 - - - +
521C ILE* 3.6 5.7 - - - +
522C HIS 3.6 11.1 + - - +
523C PRO* 3.9 0.8 - - - +
524C GLN* 3.0 37.4 + - - +
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Residues in contact with LEU 468 (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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413C LEU* 3.7 19.7 - - + -
414C ARG 4.0 0.4 - - - +
415C SER* 5.0 2.2 - - - -
448C LEU* 3.4 30.7 - - + -
451C PHE* 4.0 15.0 - - + -
461C GLY 3.7 2.9 - - - +
462C ASN* 3.3 27.1 - - - +
463C VAL* 4.5 0.7 - - - -
467C GLN* 1.3 79.3 - - - +
469C ILE* 1.3 58.7 + - - +
478C LEU* 3.5 7.5 - - - +
479C VAL* 2.6 44.9 + - + +
481C GLN* 3.2 31.2 - - + +
484C LYS* 3.6 15.0 - - + -
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Residues in contact with ILE 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C PHE* 3.6 5.6 - - - -
459C PHE* 3.4 25.8 - - + -
460C CYS* 3.1 19.9 - - - +
461C GLY 3.1 17.9 + - - +
463C VAL* 3.4 20.1 - - + +
468C LEU* 1.3 74.6 - - - +
470C GLN* 1.3 63.6 + - - +
471C ILE* 3.8 19.1 - - + -
476C VAL* 3.9 10.1 - - + -
477C ARG 3.3 10.5 - - - +
478C LEU* 4.5 4.0 - - + +
503C CYS* 3.7 8.3 - - - -
508C VAL* 3.5 32.3 - - + -
521C ILE* 4.4 8.5 - - + -
526C LEU* 4.9 4.0 - - + -
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Residues in contact with GLN 470 (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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433C THR* 4.2 1.2 + - - -
450C GLY 3.9 0.4 + - - -
451C PHE* 3.3 40.4 - - + +
452C VAL* 2.9 49.3 - - - +
455C GLN 5.5 0.5 - - - +
457C THR* 3.0 26.6 + - - +
459C PHE 3.7 3.6 - - - +
460C CYS* 4.3 3.8 - - + -
469C ILE* 1.3 75.1 - - - +
471C ILE* 1.3 60.1 + - - +
472C THR* 3.4 11.1 + - - +
477C ARG* 2.6 61.6 + - + +
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Residues in contact with ILE 471 (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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457C THR* 3.8 0.9 - - - -
458C PHE* 2.9 24.7 + - + -
459C PHE* 2.8 25.7 + - + +
469C ILE* 3.8 19.3 - - + -
470C GLN* 1.3 71.2 - - - +
472C THR* 1.3 68.9 + - - +
475C SER 3.7 2.7 - - - -
476C VAL* 3.8 14.6 - - + +
498C ILE* 4.2 2.7 - - + -
501C ALA* 3.6 30.3 - - + -
502C SER 4.1 4.3 - - - +
503C CYS* 3.9 23.3 - - + -
508C VAL* 3.8 24.5 - - + -
510C VAL* 3.7 15.5 - - + -
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Residues in contact with THR 472 (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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452C VAL* 4.3 13.7 - - + -
455C GLN* 3.0 39.9 + - - +
456C GLN 3.1 12.9 + - - -
457C THR* 4.3 1.8 - - - +
458C PHE* 4.2 4.4 - - - -
470C GLN* 3.4 13.2 + - - +
471C ILE* 1.3 80.4 - - - +
473C SER* 1.3 71.4 + - - +
474C ALA* 3.8 2.5 - - + +
475C SER* 3.0 48.7 + - - +
477C ARG* 4.8 1.1 - - - -
498C ILE* 3.6 10.7 - - - +
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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