Contacts of the strand formed by residues 391 - 400 (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 THR 391 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368C ARG* 4.1 1.0 + - - -
386C PHE 3.8 1.4 - - - +
387C GLN* 3.4 7.3 + - - -
388C ARG* 3.0 41.6 + - - +
390C GLN* 1.3 77.5 - - - +
392C GLN* 1.3 60.9 + - - +
393C VAL* 4.3 7.6 - - + -
478C GLU 3.4 8.1 - - - +
479C SER* 4.9 1.3 - - - -
480C ASN* 2.9 6.1 + - - +
481C GLY 2.4 45.6 + - - +
482C SER 4.3 4.0 - - - +
483C SER* 4.5 5.6 - - - -
486C ALA* 4.2 23.1 - - + +
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Residues in contact with GLN 392 (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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385C LEU* 3.8 21.8 - - + +
386C PHE 3.6 3.6 - - - +
387C GLN* 3.1 27.1 + - - +
391C THR* 1.3 71.4 - - - +
393C VAL* 1.3 63.7 + - - +
476C VAL* 3.5 3.1 - - - -
477C LEU* 2.7 42.7 + - + +
478C GLU* 2.8 30.8 + - + +
62D LYS 3.1 24.6 + - - -
63D LEU* 3.5 14.6 - - - +
64D ALA 3.0 26.0 + - - -
65D ARG* 3.6 7.7 - - - +
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Residues in contact with VAL 393 (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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384C ALA 3.9 0.2 - - - +
385C LEU* 3.6 6.1 - - - +
386C PHE* 2.9 35.9 + - + +
391C THR* 4.4 6.7 - - + -
392C GLN* 1.3 78.6 - - - +
394C LEU* 1.3 62.1 + - - +
395C CYS* 3.9 21.8 + - - -
475C GLU 3.4 18.8 - - - +
476C VAL* 4.0 15.7 - - + +
483C SER* 3.9 10.5 - - - +
486C ALA* 3.5 32.8 - - + +
487C SER* 3.7 19.3 - - - +
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Residues in contact with LEU 394 (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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376C MET* 4.2 22.7 - - + -
377C PHE* 5.0 8.3 - - + -
380C LEU* 6.0 1.6 - - + -
383C SER* 5.3 2.5 - - - -
384C ALA 3.6 14.8 - - - +
385C LEU* 4.0 9.6 - - + +
392C GLN 4.3 0.6 - - - -
393C VAL* 1.3 72.8 - - - +
395C CYS* 1.3 67.7 + - - +
396C THR* 4.5 8.5 + - - +
473C THR 3.6 2.1 - - - +
474C SER* 3.5 1.0 - - - -
475C GLU* 2.8 58.4 + - + +
477C LEU* 3.9 23.7 - - + +
63D LEU* 6.0 3.1 - - + -
105D LYS* 4.4 4.5 - - - +
155D ASN* 5.0 1.6 - - - +
157D LEU* 3.9 30.5 - - + +
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Residues in contact with CYS 395 (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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383C SER* 3.2 6.2 - - - -
384C ALA 2.8 37.7 + - - +
393C VAL* 3.9 15.3 - - - -
394C LEU* 1.3 79.7 - - - +
396C THR* 1.3 62.4 + - - +
472C VAL* 4.6 2.2 - - + -
473C THR 3.2 4.7 - - - +
474C SER* 3.5 22.9 - - - +
487C SER* 3.7 4.0 - - - -
490C GLY* 3.5 26.7 - - - +
491C GLY* 3.4 24.5 - - - +
494C ALA* 4.2 6.1 - - + -
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Residues in contact with THR 396 (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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380C LEU* 4.0 31.6 - - + +
382C GLY 3.5 7.6 - - - +
383C SER* 4.4 0.4 - - - +
394C LEU* 4.5 14.7 + - - +
395C CYS* 1.3 76.8 + - - +
397C VAL* 1.3 68.5 + - - +
398C THR* 3.6 20.8 + - - +
471C ARG 3.5 1.2 - - - +
472C VAL* 3.2 5.6 - - - +
473C THR* 2.8 51.3 + - + +
475C GLU* 4.9 2.4 + - - -
494C ALA* 4.8 0.4 - - - -
105D LYS* 4.9 6.5 + - + -
157D LEU 4.8 2.6 + - - +
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Residues in contact with VAL 397 (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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381C HIS* 3.3 18.9 + - - +
382C GLY 2.8 18.5 + - - +
396C THR* 1.3 78.1 - - - +
398C THR* 1.3 68.1 + - - +
399C PHE* 4.1 20.9 - - + -
470C ILE* 4.4 11.0 - - + -
471C ARG 3.4 6.3 - - - +
472C VAL* 4.2 8.1 - - + -
494C ALA* 3.4 38.8 - - + +
495C LEU* 3.7 15.5 - - + +
498C SER* 3.7 25.1 - - - +
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Residues in contact with THR 398 (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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380C LEU* 5.9 0.2 - - - +
381C HIS* 3.8 10.3 - - + +
396C THR* 3.6 14.7 + - - +
397C VAL* 1.3 78.2 + - - +
399C PHE* 1.3 72.3 + - - +
470C ILE 3.9 0.2 - - - -
471C ARG* 2.7 48.2 + - - +
473C THR* 5.1 6.4 - - - +
110D GLY 5.9 3.1 - - - +
113D PRO* 3.7 29.4 - - + -
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Residues in contact with PHE 399 (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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381C HIS* 2.9 50.8 + + + +
397C VAL* 4.1 8.7 - - + -
398C THR* 1.3 82.3 - - - +
400C ASP* 1.3 62.1 + - - +
466C PHE* 3.4 32.5 - + - -
468C PHE* 4.1 8.7 - + + -
469C THR 3.4 9.4 - - - -
470C ILE* 4.1 6.1 - - + -
498C SER* 3.6 33.2 - - - -
500C VAL* 3.7 17.3 - - + -
600C ARG* 3.8 19.3 - - + -
601C LYS 6.0 0.2 - - - -
605C PRO* 3.8 27.8 - - + -
650C PHE* 4.1 7.1 - - - -
652C PRO* 5.0 3.8 - - - +
111D ARG 5.7 0.3 - - - +
113D PRO* 4.9 1.4 - - - +
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Residues in contact with ASP 400 (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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399C PHE* 1.3 73.0 - - - +
401C SER* 1.3 68.0 + - - +
404C SER* 3.0 27.6 + - - +
468C PHE* 3.4 9.2 - - - +
469C THR* 2.8 35.1 + - + +
471C ARG* 2.7 34.7 + - - +
638C THR* 5.4 0.7 + - - -
650C PHE* 3.4 13.5 - - - -
111D ARG 4.9 2.1 - - - +
112D ILE* 5.1 6.4 - - - +
113D PRO* 3.4 30.2 - - + +
116D TYR* 4.3 2.6 + - - -
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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