Contacts of the strand formed by residues 479 - 483 (chain A) in PDB entry 5IXC
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 GLU 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LEU* 3.5 6.8 - - - +
466A ASN* 3.0 35.2 + - + +
467A VAL 3.9 21.4 - - - +
478A LYS* 1.3 77.6 - - - +
480A TRP* 1.3 61.3 + - - +
481A VAL* 3.7 1.2 + - + -
490A PHE* 3.6 28.3 - - + -
492A LYS* 3.7 25.4 - - + +
493A TYR* 2.6 38.7 + - + +
604A ASN* 5.6 1.0 + - - -
606A LEU* 5.7 0.2 - - - +
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Residues in contact with TRP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 3.9 15.5 - - + -
463A LEU* 3.6 31.6 - - + -
464A SER* 3.5 9.4 - - - -
465A LEU* 3.7 41.3 - - + +
478A LYS 5.3 2.7 + - - -
479A GLU* 1.3 74.2 - - - +
481A VAL* 1.3 62.0 + - - +
490A PHE* 3.7 5.0 - - - +
491A LEU* 3.3 44.2 + - + +
492A LYS* 4.7 6.9 + - - +
649A ALA* 4.9 1.3 - - + -
653A ASN* 4.0 37.9 - - + -
654A THR 4.7 1.3 - - - -
657A PRO* 3.9 25.1 - - + +
689A TYR* 4.2 21.0 - + - -
693A ARG* 5.5 2.2 - - - -
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 3.6 2.9 - - - -
464A SER* 2.7 44.8 + - - +
466A ASN* 4.2 23.6 - - + -
479A GLU 4.4 0.7 - - - +
480A TRP* 1.3 74.2 - - - +
482A GLU* 1.3 64.1 + - - +
483A PHE* 3.4 32.9 - - + -
488A VAL* 4.3 7.2 - - + -
489A GLY* 3.4 16.6 - - - +
490A PHE* 3.8 35.4 - - + -
502A PHE* 5.3 3.4 - - + -
605A PHE* 5.7 0.7 - - + -
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 3.8 13.8 - - + +
462A TYR 3.7 4.0 - - - +
463A LEU* 3.8 9.4 - - + -
480A TRP 4.1 1.2 + - - -
481A VAL* 1.3 72.0 - - - +
483A PHE* 1.3 66.6 + - - +
484A SER* 5.0 1.7 - - - +
487A GLU 4.0 3.0 - - - +
488A VAL* 3.3 4.2 - - - +
489A GLY 2.8 39.4 + - - +
491A LEU* 3.8 20.3 - - + +
496A PHE* 4.4 2.3 - - + -
658A SER* 2.4 30.2 + - - +
661A ARG* 3.0 20.6 + - - -
664A ARG* 2.6 43.5 + - - -
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Residues in contact with PHE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 4.2 6.1 - - + -
461A LEU* 3.5 4.9 - - - -
462A TYR* 2.7 59.2 + - + +
464A SER* 3.9 10.8 - - - -
481A VAL* 3.4 33.7 - - + -
482A GLU* 1.3 78.3 - - - +
484A SER* 1.3 60.5 + - - +
487A GLU 4.0 1.6 - - - -
488A VAL* 3.6 26.9 - - + -
502A PHE* 3.9 34.3 - + - -
523A LEU* 4.1 15.3 - - + -
526A ILE* 4.9 7.9 - - + -
527A TRP* 3.4 37.7 - + + -
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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
------------------------------------------------------------
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