Contacts of the strand formed by residues 469 - 478 (chain C) in PDB entry 5IXM
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 TRP 469 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464C PRO* 3.4 20.8 - - - +
465C ILE* 3.5 10.9 + - + +
466C ALA* 3.3 35.0 - - + +
467C ASP 3.5 1.5 - - - +
468C ARG* 1.3 87.0 - - + +
470C ALA* 1.3 66.7 + - - +
491C LEU* 4.1 40.8 - - + -
492C GLN 3.6 7.9 - - - -
493C TYR* 3.3 33.2 - + + -
494C ASN* 5.8 0.4 - - - -
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Residues in contact with ALA 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ASP 5.9 1.3 - - - +
462C SER* 5.7 1.3 - - - +
463C TRP 3.5 12.1 - - - +
464C PRO* 4.1 4.5 - - + -
465C ILE* 4.5 2.0 - - - +
469C TRP* 1.3 79.9 - - - +
471C ILE* 1.3 61.3 + - - +
472C VAL* 4.5 0.4 + - - -
491C LEU* 3.5 6.9 - - - +
492C GLN* 2.9 44.8 + - + +
494C ASN* 5.6 0.9 - - - +
541C THR* 4.3 22.2 - - + -
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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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461C ALA 4.1 0.5 - - - +
462C SER* 3.4 2.9 + - - -
463C TRP* 2.9 46.6 + - + +
465C ILE* 3.6 28.9 - - + -
470C ALA* 1.3 75.2 - - - +
472C VAL* 1.3 75.3 + - - +
489C VAL* 5.0 10.5 - - + -
490C GLY 3.2 14.6 - - - +
491C LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 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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461C ALA 3.2 5.8 - - - +
462C SER* 3.4 29.2 - - - +
470C ALA 5.6 0.2 - - - -
471C ILE* 1.3 83.4 - - - +
473C GLY* 1.3 59.5 + - - +
488C LEU* 4.3 13.5 - - + -
489C VAL* 3.6 2.9 - - - +
490C GLY* 2.8 50.0 + - - +
541C THR* 3.6 26.0 - - + +
544C MET* 3.9 22.0 - - + -
545C LEU* 3.8 14.1 - - + -
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Residues in contact with GLY 473 (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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459C THR 4.6 0.2 - - - -
460C THR* 3.3 6.5 - - - +
461C ALA* 2.9 34.7 + - - +
472C VAL* 1.3 76.2 - - - +
474C ALA* 1.3 64.4 + - - +
488C LEU* 3.2 12.1 - - - -
489C VAL* 4.7 1.6 - - - -
545C LEU* 4.3 1.3 - - - +
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Residues in contact with ALA 474 (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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459C THR 3.3 10.3 - - - +
460C THR* 4.1 13.7 - - + +
473C GLY* 1.3 75.7 - - - +
475C TYR* 1.3 61.3 + - - +
476C TYR* 4.3 11.6 - - + -
486C SER* 3.8 1.7 + - - +
487C GLN* 3.2 6.1 + - - +
488C LEU* 2.8 55.4 + - + -
545C LEU* 5.1 3.1 - - + +
550C LEU 5.8 1.8 - - - +
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Residues in contact with TYR 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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457C VAL 3.8 1.3 - - - +
458C GLY* 3.3 2.4 - - - -
459C THR* 2.9 44.9 + - - +
474C ALA* 1.3 73.7 - - - +
476C TYR* 1.3 64.4 + - - +
477C TYR* 3.2 45.7 - + + -
484C PRO* 3.2 25.1 - - + +
486C SER 3.6 0.9 - - - -
487C GLN* 3.9 38.1 - - + -
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Residues in contact with TYR 476 (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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427C GLN* 4.4 10.0 + - - -
429C ASN* 3.4 26.8 + - - -
456C GLN* 3.4 30.1 - - + -
457C VAL 3.4 1.1 - - - -
458C GLY* 3.6 12.8 - - - -
459C THR 4.4 2.5 - - - -
460C THR* 3.4 24.2 + - - -
474C ALA* 4.5 9.6 - - + -
475C TYR* 1.3 82.8 - - - +
477C TYR* 1.3 61.3 + - - +
484C PRO* 3.6 4.7 - - - +
485C ALA* 2.9 28.3 + - + -
486C SER* 2.9 25.4 + - - +
550C LEU* 3.5 49.0 + - + -
551C PRO 5.2 2.6 + - - -
552C TYR* 5.6 3.1 - - - -
67D VAL 5.1 1.8 - - - -
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Residues in contact with TYR 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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219A TRP* 3.5 36.3 - + + -
7B THR* 3.7 20.2 + - + +
456C GLN* 3.4 7.9 - - - +
457C VAL* 2.8 42.3 + - + +
475C TYR* 3.2 40.8 - + + -
476C TYR* 1.3 73.8 - - - +
478C ASP* 1.3 87.6 + - - +
479C THR* 3.6 4.2 + - + +
482C LYS* 2.8 24.2 + - - -
483C GLN* 3.3 18.6 - - - -
484C PRO* 3.7 11.6 - - + +
485C ALA* 5.3 0.7 - - - -
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Residues in contact with ASP 478 (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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455C SER 3.5 15.5 + - - +
456C GLN* 4.8 2.9 - - + +
476C TYR 4.3 0.6 + - - -
477C TYR* 1.3 72.9 - - - +
479C THR* 1.3 63.4 + - - +
480C LYS* 3.3 15.3 + - - +
481C ALA* 3.3 26.9 + - + +
482C LYS* 2.9 22.2 + - - -
483C GLN* 2.9 31.1 + - + +
485C ALA* 4.5 11.2 - - + +
508C ILE* 6.1 1.6 - - + -
69D ILE 6.1 1.1 - - - -
70D PHE 5.8 0.7 - - - -
71D ARG* 4.5 15.2 + - - +
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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