Contacts of the strand formed by residues 459 - 466 (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 LEU 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLU* 3.7 38.4 - - + +
293A PHE* 3.5 21.6 - - + -
355A THR 3.0 11.3 + - - +
356A TYR* 3.6 16.4 - - + -
357A PHE 2.7 32.1 + - - +
371A TYR* 4.1 0.2 - - - -
452A LEU* 3.6 28.9 - - + -
458A PRO* 1.3 70.1 - - - +
460A PRO* 1.3 70.5 - - + +
461A LEU* 4.2 14.3 - - + +
484A SER* 4.4 4.7 - - - +
485A PRO* 4.2 10.3 - - + -
486A TYR* 3.8 18.2 - - + -
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Residues in contact with PRO 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A PHE 3.2 6.5 - - - +
367A MET* 4.1 5.2 - - + -
371A TYR* 3.5 41.1 - - + +
448A GLN* 3.7 13.9 - - - +
452A LEU* 4.0 5.8 - - + -
458A PRO 3.4 9.0 - - - +
459A LEU* 1.3 93.9 - - + +
461A LEU* 1.3 60.7 + - - +
462A TYR* 3.9 19.0 - - + +
483A PHE 3.8 0.4 - - - +
484A SER* 3.5 24.8 - - - -
485A PRO* 3.7 12.1 - - + +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A TYR* 3.9 20.4 - - + -
357A PHE 2.6 12.7 + - - +
358A SER* 3.2 7.0 - - - -
359A GLY 3.1 26.0 + - - +
367A MET* 3.5 3.5 - - - +
459A LEU* 4.2 14.6 - - + +
460A PRO* 1.3 80.2 - - - +
462A TYR* 1.3 62.1 + - - +
463A LEU* 3.7 0.9 + - - +
482A GLU* 3.8 9.6 - - + +
483A PHE 3.5 3.1 - - - +
484A SER* 3.9 14.8 - - - -
658A SER* 3.7 21.9 + - - +
659A MET* 3.9 15.3 - - + -
664A ARG* 3.6 44.0 - - - +
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A GLY 3.9 3.8 - - - -
364A THR* 3.8 15.3 - - + -
367A MET* 3.5 38.8 + - + -
368A ALA* 3.9 6.7 - - - -
371A TYR* 4.0 1.0 - - - +
445A LEU* 3.8 14.6 - - + -
448A GLN* 2.8 38.3 + - - -
460A PRO* 3.9 23.6 - - + +
461A LEU* 1.3 71.9 - - - +
463A LEU* 1.3 59.7 + - - +
482A GLU* 3.6 0.8 - - - -
483A PHE* 2.7 57.6 + - + +
527A TRP* 3.3 54.5 - + + -
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A GLY 3.1 17.5 + - - +
360A ILE* 4.0 23.9 - - + +
361A SER 4.6 3.6 + - - -
364A THR* 4.9 0.7 - - - +
461A LEU 3.7 1.1 + - - +
462A TYR* 1.3 73.0 - - - +
464A SER* 1.3 62.1 + - - +
480A TRP* 3.6 23.1 - - + -
481A VAL 3.7 15.0 - - - +
482A GLU* 3.8 12.6 - - + -
491A LEU* 4.2 13.5 - - + -
527A TRP* 4.8 7.8 - - - +
655A SER* 3.8 19.5 - - - -
657A PRO* 3.5 38.6 - - + -
658A SER* 3.6 22.7 - - - +
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Residues in contact with SER 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A LEU* 1.3 76.6 - - - +
465A LEU* 1.3 67.1 + - - +
466A ASN* 4.5 2.6 + - - -
480A TRP* 3.5 7.6 - - - -
481A VAL* 2.7 50.0 + - - +
483A PHE* 3.9 10.1 - - - -
526A ILE* 3.6 30.7 + - - +
527A TRP* 3.7 24.3 + - - +
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A SER* 1.3 75.6 + - - +
466A ASN* 1.3 62.9 + - - +
478A LYS* 3.8 35.2 - - + +
479A GLU 3.5 17.7 - - - +
480A TRP* 3.7 40.7 - - + +
526A ILE 5.6 0.7 - - - +
649A ALA* 3.7 44.2 - - + +
650A TYR* 3.7 26.8 - - + -
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Residues in contact with ASN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A SER* 3.9 3.2 + - - +
465A LEU* 1.3 77.6 - - - +
467A VAL* 1.3 73.7 + - - +
478A LYS* 3.5 14.5 - - - +
479A GLU* 3.0 36.9 + - - +
481A VAL* 4.2 21.2 - - + +
490A PHE* 5.5 4.4 - - + -
526A ILE* 4.0 22.0 - - - +
604A ASN* 5.6 6.3 - - - +
650A TYR* 4.8 1.1 - - - -
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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