Contacts of the strand formed by residues 499 - 511 (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 ALA 499 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492C GLN* 3.9 20.2 - - - +
493C TYR 3.4 12.6 - - - +
494C ASN* 3.6 20.2 - - - +
498C TRP* 1.3 85.2 - - - +
500C VAL* 1.3 65.6 + - - +
501C ASN* 4.2 5.4 + - - +
528C ILE* 3.3 27.3 - - - +
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Residues in contact with VAL 500 (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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492C GLN* 3.4 4.5 - - - +
493C TYR* 2.9 60.7 + - + +
495C THR* 6.0 1.3 - - - +
498C TRP 5.9 0.4 - - - -
499C ALA* 1.3 76.9 - - - +
501C ASN* 1.3 63.2 + - - +
526C PHE* 3.8 27.1 - - + -
527C ASN 3.9 3.6 - - - -
528C ILE* 3.6 23.1 - - + -
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Residues in contact with ASN 501 (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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491C LEU 3.7 2.7 - - - -
492C GLN* 2.6 38.2 + - - +
499C ALA* 4.2 10.1 + - - +
500C VAL* 1.3 76.9 - - - +
502C LEU* 1.3 61.2 + - - +
525C GLY 4.0 0.3 - - - +
526C PHE* 2.9 23.7 - - - -
527C ASN* 2.9 44.8 + - - +
528C ILE 4.8 4.8 - - - -
541C THR 4.6 2.0 + - - +
543C GLN* 4.8 13.6 + - - +
544C MET* 3.6 24.5 - - + +
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Residues in contact with LEU 502 (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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490C GLY* 3.4 2.1 - - - -
491C LEU* 2.9 57.3 + - + +
501C ASN* 1.3 75.2 - - - +
503C GLY* 1.3 66.6 + - - +
524C ILE* 4.5 20.0 - - + -
525C GLY 3.4 16.4 - - - +
526C PHE* 4.4 13.7 - - + -
544C MET* 3.8 4.9 - - - +
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Residues in contact with GLY 503 (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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489C VAL 3.4 8.5 - - - -
490C GLY* 4.3 1.3 - - - -
502C LEU* 1.3 78.5 - - - +
504C TYR* 1.3 60.3 + - - -
523C LYS 3.9 0.4 - - - +
524C ILE* 3.1 10.0 - - - +
525C GLY 3.0 35.3 + - - -
544C MET* 4.7 6.7 - - - -
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Residues in contact with TYR 504 (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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487C GLN* 4.6 16.4 - - - -
488C LEU* 3.3 6.6 - - - +
489C VAL* 2.9 52.4 + - + +
503C GLY* 1.3 74.6 - - - +
505C GLU* 1.3 63.8 + - - +
506C ARG* 3.6 32.6 - - + +
522C ASN* 3.1 38.7 + - + -
523C LYS 3.3 16.2 - - - -
524C ILE* 4.1 20.9 - - + -
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Residues in contact with GLU 505 (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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486C SER* 5.5 2.5 - - - +
487C GLN 3.3 9.6 - - - +
488C LEU* 4.5 15.4 - - + +
504C TYR* 1.3 80.1 - - - +
506C ARG* 1.3 67.8 + - - +
507C LYS* 3.3 39.0 + - + +
521C ASP 3.7 0.9 - - - +
522C ASN* 3.4 4.0 - - - +
523C LYS* 2.7 58.1 + - + +
547C SER* 4.3 13.4 + - - +
548C GLY* 3.9 19.3 - - - -
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Residues in contact with ARG 506 (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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484C PRO* 4.6 16.1 - - - +
485C ALA 4.8 0.2 - - - -
486C SER* 3.5 2.4 - - - -
487C GLN* 2.9 52.4 + - - +
504C TYR* 3.6 29.5 - - + +
505C GLU* 1.3 75.1 - - - +
507C LYS* 1.3 62.2 + - - +
520C TYR* 3.3 60.4 - - + +
521C ASP 3.4 4.3 - - - +
522C ASN* 3.5 20.8 + - - +
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Residues in contact with LYS 507 (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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123C SER* 5.6 0.8 + - - -
124C THR* 4.3 14.3 - - + +
485C ALA 3.5 5.4 - - - +
486C SER* 4.4 4.9 - - - +
505C GLU* 3.3 28.8 + - + +
506C ARG* 1.3 76.7 - - - +
508C ILE* 1.3 66.2 + - - +
509C THR* 3.4 3.9 + - - -
520C TYR* 3.3 9.3 - - - -
521C ASP* 3.1 40.4 + - + +
523C LYS* 4.0 27.8 - - - +
547C SER 5.5 2.2 + - - -
548C GLY 5.7 0.4 - - - -
549C ILE* 3.6 44.6 - - + +
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Residues in contact with ILE 508 (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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124C THR* 4.6 5.2 - - - +
478C ASP* 6.1 1.3 - - + -
483C GLN* 3.3 30.3 - - + +
484C PRO 3.3 24.5 - - - +
485C ALA* 2.9 25.3 + - + +
507C LYS* 1.3 73.1 - - - +
509C THR* 1.3 62.2 + - - +
510C GLY 4.0 2.9 - - - +
518C SER* 3.9 10.3 - - - +
519C LYS 3.7 3.4 - - - -
520C TYR* 3.5 14.8 - - + +
549C ILE* 3.9 14.4 - - - +
69D ILE* 4.1 7.6 - - + -
70D PHE 4.6 0.2 - - - +
71D ARG* 3.1 30.3 - - - +
73D GLY* 3.7 21.4 - - - +
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Residues in contact with THR 509 (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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115C THR* 4.4 20.2 + - + +
124C THR* 2.9 36.5 + - - +
507C LYS* 3.4 7.8 + - - -
508C ILE* 1.3 75.3 - - - +
510C GLY* 1.3 56.6 + - - +
519C LYS* 2.7 26.1 + - + +
520C TYR 3.8 5.8 - - - +
521C ASP* 3.1 37.4 + - - +
72D ASN 4.0 7.2 - - - +
73D GLY* 4.6 2.4 - - - -
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Residues in contact with GLY 510 (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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509C THR* 1.3 81.8 - - - +
511C TRP* 1.3 61.3 + - - +
518C SER* 3.6 0.7 - - - -
519C LYS* 2.9 37.4 + - - +
71D ARG 3.6 15.4 - - - +
72D ASN 3.4 12.6 + - - +
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Residues in contact with TRP 511 (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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449C ASP* 4.3 7.4 - - + -
450C TYR* 3.0 45.2 - + + -
483C GLN* 5.3 0.2 - - - -
510C GLY* 1.3 72.8 - - - -
512C ASN* 1.3 76.8 + - - +
513C ALA* 3.5 9.9 + - + +
516C GLN* 3.1 35.3 + - + -
517C THR* 3.2 30.5 - - - -
518C SER* 3.4 24.2 - - - -
519C LYS* 3.3 19.5 + - - +
71D ARG* 3.5 42.6 - - + -
72D ASN* 3.7 17.5 + - + -
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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