Contacts of the helix formed by residues 386 - 395 (chain O) in PDB entry 1UW9
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 HIS 386 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332O VAL* 3.5 43.3 + - + +
381O GLY 3.6 10.1 + - - -
382O ILE* 3.3 10.3 - - + -
383O HIS* 2.9 62.3 + + - +
385O TRP* 1.3 77.0 - - - +
387O MET* 1.3 64.4 + - - +
388O PRO* 3.4 0.7 - - - -
389O ALA* 3.1 10.1 + - - +
390O LEU* 3.0 35.9 + - + +
465O ILE 4.4 8.9 + - - -
466O LYS* 5.0 6.3 - - + -
467O PHE* 4.5 5.0 - + - -
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Residues in contact with MET 387 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O LEU* 4.5 1.3 - - + -
383O HIS 3.8 1.8 + - - -
384O VAL* 3.1 17.8 + - - +
386O HIS* 1.3 77.4 - - - +
388O PRO* 1.3 68.4 - - + +
390O LEU* 3.2 4.7 + - - +
391O VAL* 3.0 30.2 + - + +
400O LEU* 3.8 28.3 - - - -
402O PHE* 3.4 33.7 - - + -
420O ASN* 3.4 31.0 - - - +
423O ALA* 3.7 30.5 - - + +
424O LEU* 3.7 16.4 - - + +
427O CYS* 3.8 7.2 - - - -
445O ILE* 4.4 0.2 - - + -
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Residues in contact with PRO 388 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384O VAL 4.1 2.0 - - - +
385O TRP 3.4 16.6 - - - +
386O HIS 3.5 0.9 - - - -
387O MET* 1.3 95.4 - - + +
389O ALA* 1.3 56.9 + - - +
391O VAL 3.9 0.3 - - - -
392O GLU* 3.0 30.2 + - - +
427O CYS* 3.6 20.4 - - + -
437O LEU* 3.8 22.5 - - + +
441O GLY* 3.6 43.7 - - - +
445O ILE* 3.8 6.3 - - + -
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Residues in contact with ALA 389 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332O VAL* 4.4 23.3 - - + -
339O ARG* 6.2 0.7 - - - +
385O TRP 5.8 0.4 - - - +
386O HIS* 3.1 10.7 + - - +
388O PRO* 1.3 79.6 - - - +
390O LEU* 1.3 53.8 + - - +
392O GLU* 3.3 8.0 + - - +
393O ILE* 2.8 46.9 + - + +
437O LEU 5.9 0.4 - - - -
438O ALA* 6.3 1.6 - - - +
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Residues in contact with LEU 390 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330O THR* 3.7 27.8 - - - +
332O VAL* 4.2 9.0 - - + -
378O ALA* 4.3 11.9 - - + -
382O ILE* 3.7 24.2 - - + -
386O HIS* 3.0 32.8 + - + +
387O MET* 3.6 8.7 - - - +
389O ALA* 1.3 75.7 - - - +
391O VAL* 1.3 57.4 + - - +
393O ILE* 3.3 1.2 + - - -
394O PHE* 2.9 53.2 + - + +
400O LEU* 4.1 20.6 - - + -
402O PHE* 3.9 17.3 - - + -
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Residues in contact with VAL 391 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387O MET* 3.0 25.0 + - + +
390O LEU* 1.3 74.2 - - - +
392O GLU* 1.3 57.9 + - - +
395O GLY* 2.9 34.9 + - - +
396O ASP* 5.1 1.8 - - - +
400O LEU* 4.6 4.0 - - + -
424O LEU* 3.7 29.6 - - + -
427O CYS* 4.1 17.3 - - + +
428O THR* 4.8 8.5 - - - +
431O ARG* 4.0 24.7 + - - +
437O LEU* 3.6 24.9 - - + -
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Residues in contact with GLU 392 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339O ARG* 2.8 42.9 + - - -
388O PRO 3.0 18.2 + - - +
389O ALA* 3.6 7.5 - - - +
391O VAL* 1.3 79.4 - - - +
393O ILE* 1.3 63.7 + - - +
395O GLY* 4.5 1.4 + - - -
436O ASP* 5.8 0.4 - - - +
437O LEU* 4.2 15.0 - - + +
438O ALA* 4.6 25.9 - - + +
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Residues in contact with ILE 393 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330O THR 4.3 6.3 - - - +
331O VAL* 3.9 37.9 - - + -
332O VAL* 4.8 4.3 - - + -
339O ARG* 3.5 31.2 - - + +
342O THR* 5.2 2.5 - - + -
343O LEU* 3.5 33.6 - - + +
346O VAL* 5.9 0.9 - - - +
350O ARG* 5.2 2.8 + - - -
389O ALA* 2.8 35.2 + - + +
390O LEU* 3.3 5.1 + - + +
392O GLU* 1.3 78.9 - - - +
394O PHE* 1.3 85.8 + - + +
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Residues in contact with PHE 394 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328O SER* 3.4 18.4 - - - -
329O GLY 3.3 23.3 - - - -
330O THR* 4.2 7.0 - - - -
342O THR* 4.4 8.3 - - + -
346O VAL* 3.9 27.1 - - + -
350O ARG* 2.8 34.0 + - - +
376O PRO* 4.5 7.0 - - + -
378O ALA* 3.7 18.4 - - + -
390O LEU* 2.9 39.4 + - + +
393O ILE* 1.3 98.5 - - + +
395O GLY* 1.3 63.5 + - - +
397O ASP 4.4 0.3 + - - -
398O ALA* 3.7 27.6 - - + -
400O LEU* 4.4 4.7 - - + -
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Residues in contact with GLY 395 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O GLY* 4.9 3.1 - - - -
391O VAL* 2.9 26.5 + - - +
392O GLU 4.5 1.4 + - - -
393O ILE 3.7 0.8 - - - -
394O PHE* 1.3 87.1 - - - +
396O ASP* 1.3 67.6 + - - -
398O ALA* 4.4 3.8 - - - +
400O LEU* 5.9 1.7 - - - +
431O ARG* 4.4 8.3 - - - -
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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