Contacts of the strand formed by residues 391 - 400 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ARG* 4.2 0.7 + - - -
386B PHE* 3.7 1.0 - - - +
387B GLN* 3.2 7.8 + - - -
388B ARG* 2.9 42.7 + - - +
390B GLN* 1.3 77.8 - - - +
392B GLN* 1.3 62.8 + - - +
393B VAL* 4.5 3.8 - - + -
478B GLU 3.4 7.6 - - - +
479B SER* 5.0 0.2 - - - -
480B ASN 2.9 22.7 + - - +
481B GLY 2.8 29.8 + - - +
482B SER 4.3 0.4 - - - +
483B SER* 4.2 23.8 - - - -
486B ALA* 4.2 16.4 - - + -
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B LEU* 3.9 21.6 - - + +
386B PHE 3.6 3.4 - - - +
387B GLN* 3.1 22.3 + - - +
391B THR* 1.3 72.9 - - - +
393B VAL* 1.3 62.8 + - - +
476B VAL 3.6 0.2 - - - -
477B LEU* 2.7 45.8 + - + +
478B GLU* 2.8 44.2 + - + +
62C LYS 3.0 24.2 + - - -
63C LEU* 3.5 14.4 - - - +
64C ALA 2.9 25.8 + - - -
65C ARG* 3.6 2.4 - - - +
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 3.6 6.2 - - - +
386B PHE* 2.9 37.5 + - + +
391B THR* 4.5 7.2 - - + -
392B GLN* 1.3 77.9 - - - +
394B LEU* 1.3 64.3 + - - +
395B CYS* 3.7 26.9 + - - -
475B GLU 3.4 15.0 - - - +
476B VAL* 4.2 15.5 - - + +
483B SER* 3.9 11.0 - - - +
486B ALA* 3.7 29.2 - - + +
487B SER* 3.8 17.3 - - - +
490B GLY* 5.6 0.2 - - - -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B MET* 4.2 20.9 - - + -
377B PHE* 4.8 7.4 - - + -
383B SER* 5.3 2.7 - - - -
384B ALA 3.5 16.4 - - - +
385B LEU* 4.1 12.8 - - + +
393B VAL* 1.3 71.6 - - - +
395B CYS* 1.3 67.7 + - - +
396B THR* 4.7 8.6 - - + +
473B THR 3.7 0.7 - - - +
474B SER* 3.6 1.2 - - - -
475B GLU* 2.9 54.4 + - + +
477B LEU* 3.8 23.8 - - + +
63C LEU* 6.0 3.6 - - + -
105C LYS* 4.6 4.0 - - - +
155C ASN* 5.2 0.2 - - - +
157C LEU* 3.7 34.1 - - + +
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Residues in contact with CYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B SER* 3.2 5.0 - - - -
384B ALA 2.9 34.3 + - - +
393B VAL* 3.7 21.1 + - - -
394B LEU* 1.3 73.0 - - - +
396B THR* 1.3 64.6 + - - +
472B VAL* 4.7 2.2 - - + -
473B THR 3.1 5.4 - - - +
474B SER* 3.3 24.7 - - - -
487B SER 3.7 4.0 - - - -
490B GLY* 3.5 45.3 - - - +
491B GLY* 3.5 6.5 - - - +
494B ALA* 3.8 4.0 - - + +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 4.3 22.7 - - + +
382B GLY 3.4 10.3 - - - -
383B SER* 4.6 1.1 - - - -
394B LEU* 4.7 13.7 - - + +
395B CYS* 1.3 78.9 - - - +
397B VAL* 1.3 63.8 + - - +
398B THR* 3.5 17.2 + - - -
471B ARG 3.5 0.7 - - - +
472B VAL* 3.4 4.1 - - - +
473B THR* 2.8 48.1 + - - +
475B GLU* 4.7 13.0 - - - +
494B ALA* 4.6 0.4 - - - -
105C LYS* 4.7 9.0 - - + +
157C LEU 5.1 2.7 - - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 5.1 0.7 - - - +
381B HIS* 3.4 8.3 + - + +
382B GLY 2.9 27.1 + - - +
396B THR* 1.3 73.3 + - - +
398B THR* 1.3 69.6 + - - +
399B PHE* 4.0 19.7 - - + -
470B ILE* 4.6 5.8 - - + -
471B ARG 3.3 8.3 - - - +
472B VAL* 4.6 11.0 - - + -
494B ALA* 3.2 41.3 - - + +
495B LEU* 3.6 15.5 - - + +
498B SER* 3.4 26.7 - - - +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU* 6.0 1.4 - - - +
381B HIS* 3.6 12.3 + - + +
396B THR* 3.5 12.5 + - - -
397B VAL* 1.3 79.0 + - - +
399B PHE* 1.3 72.1 + - - +
400B ASP 3.8 0.5 + - - -
470B ILE 4.1 0.2 - - - -
471B ARG* 2.9 39.8 + - - +
473B THR* 5.4 2.9 + - - -
110C GLY 6.0 2.0 - - - +
111C ARG 5.9 0.2 - - - +
113C PRO* 3.7 30.3 - - + -
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B HIS* 2.8 50.3 + + + +
397B VAL* 4.0 8.1 - - + -
398B THR* 1.3 80.7 - - - +
400B ASP* 1.3 59.3 + - - +
466B PHE* 3.4 34.3 - + - -
468B PHE* 4.0 13.0 - + + -
469B THR 3.4 9.0 - - - -
470B ILE* 4.1 7.0 - - + -
498B SER* 3.6 38.6 - - - -
500B VAL* 3.6 16.2 - - + -
600B ARG* 4.1 14.8 - - + -
604B GLY* 5.9 0.7 - - - -
605B PRO* 3.7 28.7 - - + -
650B PHE* 4.2 7.8 - - - -
652B PRO* 5.2 3.6 - - - +
113C PRO* 4.9 1.4 - - - +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B THR 3.8 0.2 + - - -
399B PHE* 1.3 73.9 - - - +
401B SER* 1.3 69.4 + - - +
404B SER* 3.3 26.0 + - - +
468B PHE* 3.4 9.7 - - - +
469B THR* 2.9 32.7 + - - +
471B ARG* 2.7 34.0 + - - +
638B THR* 5.6 0.9 + - - -
650B PHE* 3.4 13.0 - - - -
111C ARG 5.1 0.9 - - - +
112C ILE* 5.4 6.3 - - - +
113C PRO* 3.2 34.5 - - + +
116C TYR* 4.5 0.5 + - - -
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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