Contacts of the helix formed by residues 387 - 402 (chain B) in PDB entry 3UO8
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 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ARG* 3.7 26.7 - - - +
385B ASP 5.4 0.4 - - - +
386B LEU* 1.3 76.0 - - - +
388B GLU* 1.3 66.6 + - - +
389B TYR* 3.7 6.4 + - - +
390B GLU* 2.9 39.7 + - - +
391B MET* 2.9 20.4 + - - +
427B PRO* 3.5 2.5 - - - -
428B VAL* 4.2 6.3 - - + -
429B ASP* 3.3 25.1 - - + +
677B LYS* 3.9 8.1 - - - +
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B THR* 1.3 74.2 - - - +
389B TYR* 1.3 64.1 + - - +
391B MET* 3.2 4.8 + - - +
392B ARG* 2.9 60.3 + - - +
427B PRO* 3.3 19.9 - - + +
429B ASP* 3.1 16.8 + - - +
437B GLU 3.1 19.3 - - - +
438B ASN* 3.6 22.9 - - - +
440B LEU* 4.1 5.4 - - + -
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B THR* 3.3 5.9 + - - +
388B GLU* 1.3 80.4 - - - +
390B GLU* 1.3 67.5 + - + +
392B ARG* 3.6 7.1 + - + +
393B ASN* 3.0 63.7 + - - +
429B ASP* 5.1 0.8 + - - +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ASP 4.0 0.5 - - - +
386B LEU* 3.5 18.4 - - + +
387B THR* 2.9 38.4 + - - +
389B TYR* 1.3 85.3 - - + +
391B MET* 1.3 59.2 + - - +
393B ASN* 3.3 9.5 + - - +
394B ALA* 2.9 29.5 + - - +
676B GLN* 3.0 41.2 + - + +
677B LYS* 3.0 29.6 + - - +
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 4.2 16.9 - - + +
350B ASN* 3.5 20.0 - - - -
386B LEU* 3.5 25.8 - - + -
387B THR 2.9 17.0 + - - +
388B GLU 3.6 4.7 - - - +
390B GLU* 1.3 74.8 - - - +
392B ARG* 1.3 64.0 + - - +
394B ALA* 3.3 3.0 + - - +
395B VAL* 3.0 27.7 + - - +
412B TYR* 4.0 15.9 - - + -
425B MET* 3.9 38.1 - - + +
426B VAL 4.6 0.4 - - - -
427B PRO* 3.9 24.7 - - - -
440B LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLU* 2.9 49.5 + - - +
389B TYR* 4.0 7.2 - - + +
391B MET* 1.3 73.9 - - - +
393B ASN* 1.3 67.5 + - - +
395B VAL* 3.3 3.6 + - - +
396B ASP* 2.9 33.5 + - - +
436B SER 4.8 0.6 + - - -
437B GLU* 4.1 6.1 + - - +
439B CYS 2.9 25.0 + - - -
440B LEU* 3.8 28.0 - - + +
441B CYS 5.4 0.8 - - - +
444B ASN* 6.0 2.0 - - - +
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Residues in contact with ASN 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 3.0 64.7 + - - +
390B GLU* 3.5 9.8 - - - +
391B MET 3.3 0.2 - - - -
392B ARG* 1.3 75.6 - - - +
394B ALA* 1.3 58.3 + - - +
396B ASP* 3.2 14.5 + - - +
397B GLU* 3.0 33.8 + - + +
715B LEU* 5.6 8.3 - - + +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.9 17.4 - - + +
348B ILE* 4.6 0.9 - - + -
381B VAL* 5.8 0.2 - - + -
383B LEU* 3.7 29.6 - - + -
386B LEU* 4.2 7.0 - - + -
390B GLU 2.9 17.3 + - - +
391B MET 3.6 4.3 - - - +
392B ARG 3.2 0.2 - - - -
393B ASN* 1.3 75.1 - - - +
395B VAL* 1.3 60.4 + - - +
397B GLU* 3.2 9.3 + - - +
398B PHE* 2.9 28.1 + - - +
712B ILE* 6.6 0.2 - - - -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.8 20.4 - - + -
348B ILE* 5.0 4.5 - - + -
391B MET 3.0 20.5 + - - +
392B ARG* 3.9 6.3 - - - +
394B ALA* 1.3 75.0 - - - +
396B ASP* 1.3 59.3 + - - +
398B PHE* 3.1 5.7 + - + +
399B LEU* 2.8 47.4 + - + +
410B LEU* 5.1 2.5 - - + -
425B MET* 5.6 1.1 - - + -
440B LEU* 4.0 10.1 - - + -
445B ILE* 3.9 45.8 - - + -
448B LEU* 5.5 2.7 - - + -
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Residues in contact with ASP 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ARG* 2.9 24.0 + - - +
393B ASN* 3.3 16.3 - - - +
395B VAL* 1.3 78.1 - - - +
397B GLU* 1.3 62.0 + - + +
399B LEU* 3.4 16.0 + - - +
400B LEU* 3.1 26.5 + - - +
448B LEU* 5.6 2.9 - - - +
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Residues in contact with GLU 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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381B VAL* 6.6 0.9 - - + -
393B ASN* 3.0 20.3 + - + +
394B ALA* 3.5 10.8 - - - +
395B VAL 3.2 0.2 - - - -
396B ASP* 1.3 73.7 - - + +
398B PHE* 1.3 67.6 + - - +
400B LEU* 3.3 33.7 + - - +
401B LEU* 3.4 17.6 + - + +
712B ILE* 6.0 8.5 - - + -
715B LEU* 3.8 25.0 - - - +
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Residues in contact with PHE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL* 3.7 32.1 - - + -
345B ALA 4.2 0.4 - - - -
346B LEU* 3.6 45.3 - - + -
394B ALA 2.9 14.4 + - - +
395B VAL* 3.2 15.5 - - + +
397B GLU* 1.3 76.9 - - - +
399B LEU* 1.3 68.1 + - + +
401B LEU* 2.9 26.8 + - + +
402B LEU* 3.4 35.5 + - + +
408B GLY* 4.1 2.2 - - - -
409B LEU 3.8 26.9 - - - -
410B LEU* 5.0 7.2 - - + -
445B ILE* 5.0 2.9 - - + -
449B MET* 4.0 18.2 - - + -
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B VAL* 2.8 43.3 + - + +
396B ASP* 3.8 14.1 - - - +
398B PHE* 1.3 77.3 - - + +
400B LEU* 1.3 64.4 + - + +
402B LEU* 3.1 14.1 + - + -
445B ILE* 4.5 1.3 - - + +
448B LEU* 3.7 33.9 - - + +
449B MET* 3.5 44.9 - - + +
452B LYS* 3.1 33.8 + - + +
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Residues in contact with LEU 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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396B ASP 3.1 19.1 + - - +
397B GLU* 3.3 29.4 - - - +
398B PHE 3.2 0.4 - - - -
399B LEU* 1.3 78.3 - - - +
401B LEU* 1.3 65.8 + - + +
402B LEU 3.2 6.6 + - - +
452B LYS* 4.5 10.3 + - - +
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Residues in contact with LEU 401 (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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342B ASP* 5.4 2.3 - - - +
344B VAL* 3.9 39.9 - - + +
379B LYS* 5.5 9.4 - - + +
381B VAL* 5.2 13.0 - - + -
397B GLU* 3.4 16.8 + - + +
398B PHE* 2.9 14.3 + - - +
400B LEU* 1.3 83.6 - - + +
402B LEU* 1.3 60.2 + - - +
403B ASP* 3.9 2.3 + - - +
406B VAL* 4.3 6.6 - - - +
580B TRP* 5.1 22.2 - - - +
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Residues in contact with LEU 402 (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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344B VAL* 3.9 20.6 - - + -
398B PHE* 3.5 31.4 - - + +
399B LEU* 3.1 24.0 + - + +
400B LEU 3.8 4.2 - - - +
401B LEU* 1.3 78.7 - - - +
403B ASP* 1.3 64.0 + - - +
406B VAL* 3.7 20.6 - - + -
408B GLY* 4.0 12.3 - - - +
449B MET* 3.7 34.3 - - + -
452B LYS* 3.7 27.5 + - + +
454B THR* 4.0 14.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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