Contacts of the strand formed by residues 382 - 388 (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 GLY 382 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C LEU* 3.0 8.8 - - - +
381C HIS* 1.3 80.3 - - - +
383C SER* 1.3 64.7 + - - -
396C THR* 3.5 2.4 - - - -
397C VAL* 2.8 30.0 + - - +
494C ALA* 4.0 2.9 - - - -
497C ASP* 3.3 12.8 - - - -
498C SER* 3.8 15.3 - - - -
601C LYS* 4.9 0.9 - - - -
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Residues in contact with SER 383 (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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374C VAL* 3.2 7.6 - - - +
375C ASP* 3.0 24.8 + - - -
376C MET* 3.3 34.2 + - - +
377C PHE 4.0 4.9 + - - -
380C LEU* 3.8 23.5 - - - +
382C GLY* 1.3 77.5 - - - -
384C ALA* 1.3 62.8 + - - +
394C LEU* 5.3 2.2 - - - -
395C CYS 3.2 11.7 - - - -
396C THR* 4.9 0.4 - - - -
494C ALA* 3.8 8.2 - - - +
497C ASP* 3.0 9.2 + - - +
601C LYS* 5.7 0.3 + - - -
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Residues in contact with ALA 384 (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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373C GLU 3.1 13.0 - - - +
374C VAL* 4.0 0.9 - - + -
376C MET* 4.0 7.2 - - - -
383C SER* 1.3 76.8 - - - +
385C LEU* 1.3 60.5 + - - +
386C PHE 4.1 0.4 - - - -
393C VAL 3.9 0.5 - - - +
394C LEU* 3.6 4.3 - - - +
395C CYS* 2.8 34.6 + - - +
490C GLY* 3.5 16.2 - - - +
493C LEU* 3.5 33.4 - - + -
494C ALA* 3.6 3.8 - - + +
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Residues in contact with LEU 385 (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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372C CYS* 3.2 8.5 - - - +
373C GLU* 2.9 57.2 + - + +
376C MET* 3.9 9.3 - - - +
384C ALA* 1.3 75.4 - - - +
386C PHE* 1.3 60.6 + - - +
387C GLN* 4.2 4.4 + - + +
392C GLN* 3.8 30.7 - - + +
393C VAL 3.6 12.8 - - - +
394C LEU* 4.0 19.7 - - + -
477C LEU* 4.7 0.9 - - + -
493C LEU* 5.2 0.2 - - - -
62D LYS* 5.0 6.7 - - + -
63D LEU* 3.8 29.4 - - + -
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Residues in contact with PHE 386 (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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370C VAL* 4.3 20.9 - - + -
371C SER 4.0 0.7 - - - -
372C CYS* 4.0 15.7 - - + -
384C ALA 4.1 0.4 - - - -
385C LEU* 1.3 75.8 - - - +
387C GLN* 1.3 62.3 + - - +
388C ARG* 3.9 31.6 - - + -
391C THR 3.8 1.2 - - - +
392C GLN* 3.6 2.9 - - - +
393C VAL* 2.9 35.7 + - - +
486C ALA* 3.6 35.7 - - + +
489C CYS* 3.6 34.8 - - + -
490C GLY* 4.0 11.7 - - - -
493C LEU* 4.1 8.1 - - + -
585C ILE* 3.9 13.0 - - + -
589C MET* 4.0 18.2 - - + -
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Residues in contact with GLN 387 (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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369C ASN 3.6 1.6 - - - +
370C VAL* 3.1 6.9 - - - +
371C SER* 2.9 52.6 + - - +
385C LEU* 5.2 5.3 - - + +
386C PHE* 1.3 76.7 - - - +
388C ARG* 1.3 61.0 + - - +
389C GLY 2.9 24.6 + - - +
390C GLN* 4.0 3.6 - - - +
391C THR 3.4 14.0 + - - -
392C GLN* 3.1 32.1 + - - +
478C GLU* 3.1 21.4 + - - -
65D ARG* 3.2 14.4 + - - +
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Residues in contact with ARG 388 (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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367C LEU* 4.4 7.9 - - - -
368C ARG* 3.1 23.0 - - + +
369C ASN 3.4 3.8 - - - -
370C VAL* 4.3 18.4 - - + +
386C PHE* 3.9 18.5 - - + -
387C GLN* 1.3 73.7 - - - +
389C GLY* 1.3 65.2 + - - +
390C GLN 3.3 0.3 + - - -
391C THR* 3.0 29.7 + - + +
481C GLY 4.1 4.2 + - - -
482C SER* 3.2 38.2 + - - -
485C MET* 3.9 5.9 - - - +
486C ALA* 3.4 23.6 - - - +
508C GLY 4.5 3.6 + - - -
509C VAL* 5.3 3.5 - - - +
532C ASP* 3.1 42.8 + - - +
585C ILE* 4.7 10.6 - - - +
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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