Contacts of the strand formed by residues 554 - 561 (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 ILE 554 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C ALA* 3.5 7.8 - - - +
235C ASN* 3.1 17.7 + - - -
236C ILE 2.8 20.3 + - - +
238C GLN* 4.0 18.2 - - + +
241C PHE* 3.6 57.2 - - + -
547C ILE* 3.9 28.5 - - + -
548C ALA 3.7 10.3 - - - +
553C GLY* 1.3 76.2 - - - +
555C THR* 1.3 64.8 + - - +
556C ALA 4.1 7.2 - - - +
575C ILE* 4.1 12.6 - - + -
582C LYS* 4.6 7.2 - - - +
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Residues in contact with THR 555 (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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232C SER* 3.5 3.3 - - - -
233C ALA* 2.8 32.5 + - - +
235C ASN* 3.8 19.5 - - + +
456C LYS 3.5 7.0 - - - +
457C ALA* 2.9 28.9 + - - +
460C PRO* 3.6 25.4 - - + -
461C VAL* 5.3 2.0 - - + -
506C VAL* 4.5 0.3 - - - +
548C ALA 2.9 7.8 + - - -
549C GLY* 3.2 23.8 + - - -
550C THR* 4.6 7.4 - - + -
554C ILE* 1.3 78.4 - - - +
556C ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 556 (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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231C ALA* 3.3 10.5 - - - +
241C PHE* 6.1 0.2 - - - -
453C LEU* 3.9 14.4 - - + -
456C LYS* 3.9 15.7 - - + -
457C ALA* 3.8 26.2 - - + +
485C MET* 6.1 0.2 - - + -
546C LYS 4.5 0.4 - - - -
547C ILE* 3.3 8.8 - - - +
548C ALA* 2.9 30.8 + - + -
554C ILE* 3.9 4.3 - - - +
555C THR* 1.3 80.4 + - - +
557C LEU* 1.3 61.0 + - - +
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Residues in contact with LEU 557 (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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216C LEU* 5.0 1.1 - - + -
229C LEU* 4.0 33.4 - - + -
230C GLU* 3.4 5.5 - - - +
231C ALA* 2.7 42.6 + - + +
241C PHE* 3.5 40.4 - - + -
245C ILE* 4.8 0.9 - - + -
453C LEU* 4.6 2.9 - - - -
456C LYS* 4.4 0.2 + - - -
545C PHE* 3.6 36.3 - - + -
546C LYS 3.4 11.4 - - - +
547C ILE* 3.9 10.8 - - + -
556C ALA* 1.3 74.7 - - - +
558C GLN* 1.3 77.1 + - - +
559C ALA 4.2 3.6 - - - +
575C ILE* 5.0 0.2 - - + -
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Residues in contact with GLN 558 (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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1C CIT 4.1 4.9 - - - +
132C ARG* 4.9 0.7 + - - -
136C ARG* 3.5 23.0 + - - +
229C LEU 3.6 3.6 - - - -
230C GLU* 3.0 31.2 + - - +
449C GLY* 4.7 6.9 + - - -
450C HIS* 4.8 3.6 - - - -
453C LEU* 3.9 33.0 - - + +
544C ASP 3.3 5.9 - - - +
546C LYS* 2.8 60.5 + - - +
557C LEU* 1.3 73.7 - - - +
559C ALA* 1.3 58.5 + - - +
560C ASP* 3.7 19.4 - - - +
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Residues in contact with ALA 559 (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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136C ARG* 4.7 2.4 + - - -
228C MET* 4.1 11.4 - - - +
229C LEU* 2.8 43.6 + - + +
544C ASP 3.9 2.5 - - - -
545C PHE* 3.5 36.3 - - + +
557C LEU* 4.2 1.8 - - + +
558C GLN* 1.3 71.8 - - - +
560C ASP* 1.3 61.4 + - - +
561C ILE* 3.6 15.9 + - + +
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Residues in contact with ASP 560 (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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1C CIT 2.7 42.1 + - + +
136C ARG* 2.6 39.3 + - + +
543C MET* 3.1 4.6 - - - +
544C ASP* 2.8 45.5 + - + +
546C LYS* 3.0 22.5 - - - -
558C GLN* 3.7 8.9 - - - +
559C ALA* 1.3 71.1 - - - +
561C ILE* 1.3 61.6 + - - +
562C LYS* 3.9 8.2 + - + +
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Residues in contact with ILE 561 (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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136C ARG* 4.9 1.9 + - - +
140C PRO* 3.1 26.3 - - - +
226C ILE* 3.7 36.3 - - + +
227C VAL 3.4 18.7 + - - +
228C MET 4.5 0.9 - - - +
542C ASP 3.8 6.3 - - - +
543C MET* 4.1 13.7 - - + -
545C PHE* 5.3 0.2 - - + -
559C ALA* 3.6 24.0 + - + +
560C ASP* 1.3 76.9 - - - +
562C LYS* 1.3 62.3 + - - +
563C LEU 3.5 18.8 - - - +
565C GLY 4.5 0.4 - - - +
566C ILE* 3.8 37.7 - - + -
571C VAL* 5.0 2.9 - - + -
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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