Contacts of the strand formed by residues 454 - 463 (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 ILE 454 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ARG* 3.6 22.4 - - + +
432C TYR* 3.1 14.2 - - - +
433C ALA* 2.9 45.3 + - + +
438C ILE* 4.5 0.4 - - + -
453C GLY* 1.3 83.1 - - - +
455C SER* 1.3 62.6 + - - +
456C GLN* 4.3 7.9 - - + +
480C LYS* 5.6 0.7 - - - -
68D SER* 4.2 20.9 - - - +
69D ILE 3.5 25.1 - - - +
70D PHE* 4.0 11.2 - - + -
76D ALA* 3.7 23.3 - - + -
77D GLU* 4.4 2.7 - - - +
107D PHE* 4.4 8.1 - - + -
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Residues in contact with SER 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C TYR* 2.8 26.9 + - - -
431C ARG 3.2 5.4 - - - -
432C TYR* 4.5 1.8 - - - -
453C GLY 4.3 0.2 - - - -
454C ILE* 1.3 77.0 - - - +
456C GLN* 1.3 59.2 + - - +
478C ASP* 3.5 10.4 + - - +
479C THR* 2.8 48.1 + - - +
480C LYS* 3.8 26.4 - - - +
606C C8E 3.7 7.4 + - - -
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Residues in contact with GLN 456 (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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429C ASN* 3.8 8.5 + - - +
430C TYR* 3.2 7.5 - - - -
431C ARG* 2.9 42.8 + - + +
454C ILE* 4.3 10.0 - - + +
455C SER* 1.3 73.7 - - - +
457C VAL* 1.3 64.0 + - - +
458C GLY 4.2 0.2 + - - -
476C TYR* 3.4 37.7 - - + -
477C TYR 3.4 11.2 - - - +
478C ASP* 5.3 2.5 - - + -
485C ALA* 4.9 5.2 - - + +
550C LEU* 3.9 10.5 - - - +
67D VAL 2.8 26.0 + - - -
68D SER* 3.3 22.5 - - - -
69D ILE* 3.6 12.0 + - - +
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Residues in contact with VAL 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 6.1 0.2 - - + -
219A TRP* 5.7 0.9 - - + -
222A ILE* 5.8 7.2 - - + -
429C ASN 3.5 8.3 - - - +
430C TYR* 3.5 23.8 - - + -
456C GLN* 1.3 74.4 - - - +
458C GLY* 1.3 64.8 + - - +
459C THR* 5.4 3.1 - - - +
475C TYR* 3.8 1.2 - - - +
476C TYR* 3.4 2.9 - - - +
477C TYR* 2.8 39.7 + - + +
479C THR* 3.7 21.5 - - + -
606C C8E 4.0 34.1 - - + +
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Residues in contact with GLY 458 (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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428C LEU* 3.3 6.8 - - - +
429C ASN* 2.9 54.2 + - - +
457C VAL* 1.3 79.4 - - - +
459C THR* 1.3 65.9 + - - -
475C TYR 3.3 7.2 - - - -
476C TYR* 3.6 10.5 - - - -
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Residues in contact with THR 459 (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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426C ILE* 5.2 3.8 - - + -
427C GLN 3.3 8.3 - - - +
428C LEU* 4.3 18.0 - - + +
457C VAL* 5.4 4.0 - - - +
458C GLY* 1.3 77.2 + - - -
460C THR* 1.3 75.6 + - - +
461C ALA* 5.5 3.1 - - + -
473C GLY 5.3 0.2 - - - -
474C ALA* 3.3 1.4 - - - +
475C TYR* 2.9 43.5 + - - +
476C TYR* 4.4 1.4 - - - -
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Residues in contact with THR 460 (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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425C MET* 3.2 16.0 - - + +
426C ILE* 3.5 2.8 - - - +
427C GLN* 2.9 42.5 + - - -
429C ASN* 5.6 0.2 + - - -
458C GLY 5.3 0.2 - - - -
459C THR* 1.3 82.3 + - - +
461C ALA* 1.3 66.1 + - - +
473C GLY 3.3 14.6 - - - +
474C ALA* 4.1 7.2 - - + +
476C TYR* 3.4 23.6 + - - -
545C LEU* 3.9 25.6 - - + -
552C TYR* 4.4 13.8 - - + -
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Residues in contact with ALA 461 (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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425C MET* 3.1 14.4 - - - +
426C ILE* 4.6 11.7 - - + -
459C THR* 5.5 4.3 - - + -
460C THR* 1.3 79.0 - - - +
462C SER* 1.3 63.3 + - - +
463C TRP* 4.3 4.0 - - + +
471C ILE 4.5 0.4 - - - -
472C VAL* 3.2 5.6 - - - +
473C GLY* 2.9 35.4 + - - +
545C LEU* 4.2 3.0 - - - +
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Residues in contact with SER 462 (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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423C ASP* 2.7 27.6 + - - +
424C ARG* 3.2 0.7 - - - -
425C MET* 2.9 40.1 + - - -
461C ALA* 1.3 76.6 - - - +
463C TRP* 1.3 59.7 + - - +
470C ALA* 5.7 1.2 - - - +
471C ILE 3.4 5.8 + - - -
472C VAL* 3.4 19.5 - - - +
541C THR* 3.7 16.9 + - - +
545C LEU* 4.3 15.0 - - - -
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Residues in contact with TRP 463 (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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360A PHE* 5.3 0.2 - + - -
603A C8E 3.4 52.5 - - + +
605A C8E 4.6 9.4 - - - -
418C TYR* 3.9 24.0 - + - -
423C ASP 4.1 1.3 - - - -
424C ARG* 3.1 46.5 - - + +
425C MET 3.7 7.9 - - - -
426C ILE* 3.7 33.2 - - + -
461C ALA* 5.8 3.6 - - + -
462C SER* 1.3 87.6 + - - +
464C PRO* 1.3 90.7 - - + +
465C ILE* 4.7 6.7 - - + -
470C ALA* 4.3 2.9 - - - +
471C ILE* 2.9 44.3 + - + +
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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