Contacts of the strand formed by residues 507 - 516 (chain C) in PDB entry 3U1K
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 507 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488C ALA* 5.3 0.4 - - - -
489C CYS* 3.6 15.7 - - - +
506C VAL* 1.3 77.4 - - - +
508C GLY* 1.3 58.9 + - - +
548C ALA* 3.3 5.5 - - - -
549C GLY 3.0 29.6 + - - +
582C LYS* 3.7 19.4 - - + +
585C ILE* 3.9 17.0 - - + -
586C LEU* 3.6 26.1 - - + +
589C MET* 4.0 0.9 - - - -
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Residues in contact with GLY 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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388C ARG* 4.5 4.0 + - - -
485C MET* 3.6 29.3 + - - +
488C ALA* 4.9 1.4 - - - +
489C CYS* 3.5 13.7 - - - -
507C ALA* 1.3 76.2 - - - +
509C VAL* 1.3 64.0 + - - +
547C ILE 3.4 10.5 - - - -
548C ALA* 3.7 4.9 - - - +
582C LYS* 5.6 1.1 - - - -
585C ILE* 3.5 15.0 - - - +
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Residues in contact with VAL 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 4.3 13.2 - - + -
388C ARG* 5.3 2.9 - - - +
482C SER* 4.9 0.9 - - - -
485C MET* 3.6 10.4 - - - +
508C GLY* 1.3 76.3 - - - +
510C ALA* 1.3 71.1 + - - +
511C ILE* 4.5 4.5 - - + -
532C ASP* 4.0 28.5 - - + +
545C PHE 3.6 1.4 - - - +
546C LYS* 3.6 0.7 - - - -
547C ILE* 3.0 33.4 + - - +
578C ALA* 3.9 40.4 - - + +
581C ALA* 4.2 9.4 - - + -
582C LYS* 4.6 4.3 - - + +
585C ILE* 4.1 8.5 - - + -
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Residues in contact with ALA 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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482C SER* 4.0 23.0 + - - +
509C VAL* 1.3 76.9 - - - +
511C ILE* 1.3 62.8 + - - +
532C ASP* 2.9 28.5 + - - +
533C ILE* 3.5 13.3 + - + +
544C ASP* 3.3 25.8 - - - +
545C PHE 3.2 4.0 - - - +
546C LYS* 3.9 13.5 - - + -
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Residues in contact with ILE 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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509C VAL* 4.5 5.6 - - + -
510C ALA* 1.3 77.4 - - - +
512C GLY* 1.3 69.9 + - - +
529C LEU* 3.9 21.3 - - + -
530C LEU 3.1 20.6 - - - +
531C THR* 3.9 13.9 - - + -
533C ILE* 4.2 2.2 - - - -
543C MET* 3.6 8.2 - - + +
544C ASP 4.0 0.2 - - - -
545C PHE* 2.8 47.0 + - + +
547C ILE* 5.1 0.4 - - + -
574C ALA* 3.3 15.0 - - + +
577C GLN* 4.0 5.4 - - + +
578C ALA* 3.0 51.8 - - + +
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Residues in contact with GLY 512 (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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511C ILE* 1.3 82.6 - - - +
513C LEU* 1.3 63.7 + - - +
529C LEU* 3.6 3.8 - - - +
530C LEU* 2.8 33.3 + - - -
533C ILE* 3.5 23.0 - - - +
537C GLU 5.4 1.8 - - - -
543C MET* 3.6 15.9 - - - -
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Residues in contact with LEU 513 (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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512C GLY* 1.3 75.1 - - - +
514C VAL* 1.3 68.6 + - - +
515C THR* 3.7 17.5 - - + -
527C TYR* 3.9 24.7 - - + -
528C ARG 3.4 15.7 - - - +
529C LEU* 4.0 7.2 - - + -
530C LEU* 4.7 2.6 - - - +
537C GLU 5.1 1.6 + - - +
541C GLY* 3.6 3.1 - - - -
542C ASP* 2.8 48.3 + - + +
543C MET* 3.8 27.8 + - + +
566C ILE* 4.0 22.7 - - + -
570C ILE* 4.0 23.8 - - + -
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Residues in contact with VAL 514 (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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348C PHE* 5.4 5.4 - - + -
349C ARG* 3.6 43.3 - - + +
352C VAL* 4.5 25.1 - - + -
353C LEU* 3.8 24.3 - - + +
513C LEU* 1.3 78.3 - - - +
515C THR* 1.3 63.4 + - - +
527C TYR* 3.2 3.8 - - - -
528C ARG* 2.9 35.8 + - + +
530C LEU* 4.5 13.0 - - + -
537C GLU* 5.5 1.3 - - + +
540C ASN 5.0 0.2 - - - +
541C GLY* 4.6 8.7 - - - -
542C ASP* 3.5 2.2 - - - -
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Residues in contact with THR 515 (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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349C ARG* 3.0 25.6 + - - +
353C LEU* 4.1 9.8 - - - +
513C LEU* 3.7 18.2 - - + -
514C VAL* 1.3 75.4 - - - +
516C LYS* 1.3 59.0 + - - +
517C THR* 3.9 17.5 + - - +
524C ILE* 3.7 16.8 - - + -
526C ASP 3.5 6.3 - - - -
527C TYR* 3.9 11.0 - - + -
542C ASP* 2.8 26.3 + - - +
563C LEU* 3.5 26.7 - - + +
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Residues in contact with LYS 516 (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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353C LEU* 4.1 21.7 - - + +
515C THR* 1.3 74.1 - - - +
517C THR* 1.3 65.4 + - - +
524C ILE* 3.7 2.4 - - - -
525C GLU* 2.8 59.5 + - + +
526C ASP* 2.9 20.9 + - + +
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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