Contacts of the helix formed by residues 386 - 395 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332V VAL* 3.5 44.1 + - + +
381V GLY 3.6 10.3 + - - -
382V ILE* 3.4 9.9 - - + -
383V HIS* 2.8 63.3 + + - +
385V TRP* 1.3 78.1 - - - +
387V MET* 1.3 64.0 + - - +
388V PRO 3.4 0.9 - - - -
389V ALA* 3.1 10.2 + - - +
390V LEU* 3.0 34.8 + - + +
465V ILE 4.3 8.8 + - - -
466V LYS* 5.0 6.1 - - + -
467V PHE* 4.5 5.3 - + - -
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Residues in contact with MET 387 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170V LEU* 4.5 1.1 - - + -
383V HIS 3.7 2.2 + - - -
384V VAL* 3.1 17.3 + - - +
386V HIS* 1.3 77.2 - - - +
388V PRO* 1.3 68.2 - - + +
390V LEU* 3.1 5.9 + - - +
391V VAL* 3.0 29.4 + - + +
400V LEU* 3.7 28.7 - - - -
402V PHE* 3.5 32.3 - - + -
420V ASN* 3.3 33.0 - - - +
423V ALA* 3.7 15.0 - - + +
424V LEU* 3.7 31.0 - - + +
427V CYS* 3.9 5.8 - - - -
445V ILE* 4.5 0.2 - - + -
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Residues in contact with PRO 388 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384V VAL 4.0 1.8 - - - +
385V TRP 3.4 17.7 - - - +
386V HIS 3.5 0.9 - - - -
387V MET* 1.3 93.9 - - + +
389V ALA* 1.3 56.7 + - - +
391V VAL 3.6 0.2 + - - -
392V GLU* 3.0 29.7 + - - +
427V CYS* 3.6 21.5 - - + -
437V LEU* 3.8 23.6 - - + +
441V GLY* 3.6 42.6 - - - +
445V ILE* 3.9 7.4 - - + -
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Residues in contact with ALA 389 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332V VAL* 4.4 23.8 - - + -
385V TRP 5.8 0.2 - - - +
386V HIS* 3.1 12.7 + - - +
388V PRO* 1.3 78.8 - - - +
390V LEU* 1.3 59.4 + - - +
392V GLU* 3.4 7.7 + - - +
393V ILE* 2.8 41.5 + - + +
437V LEU 6.2 0.4 - - - -
438V ALA* 6.3 1.1 - - - +
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Residues in contact with LEU 390 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330V THR* 3.8 28.3 - - - +
332V VAL* 4.2 9.4 - - + -
378V ALA* 4.3 11.0 - - + -
382V ILE* 3.7 25.4 - - + -
386V HIS* 3.0 32.1 + - + +
387V MET* 3.1 7.8 + - - +
389V ALA* 1.3 73.8 - - - +
391V VAL* 1.3 61.7 + - - +
393V ILE* 3.2 1.9 + - + -
394V PHE* 2.8 52.8 + - + +
400V LEU* 4.1 20.6 - - + -
402V PHE* 4.0 16.4 - - + -
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Residues in contact with VAL 391 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387V MET* 3.0 24.0 + - + +
390V LEU* 1.3 73.9 - - - +
392V GLU* 1.3 58.5 + - - +
395V GLY* 2.8 34.8 + - - +
396V ASP* 5.1 2.0 - - - +
400V LEU* 4.6 4.5 - - + -
424V LEU* 3.7 29.6 - - + -
427V CYS* 4.1 17.0 - - + +
428V THR* 4.7 9.2 - - - +
431V ARG* 4.0 24.3 + - - +
437V LEU* 3.6 24.7 - - + -
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Residues in contact with GLU 392 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339V ARG* 2.8 44.4 + - - -
388V PRO 3.0 19.6 + - - +
389V ALA* 3.6 7.6 - - - +
390V LEU 3.2 0.2 - - - -
391V VAL* 1.3 78.9 - - - +
393V ILE* 1.3 64.5 + - - +
395V GLY* 4.4 1.4 + - - -
436V ASP* 5.8 0.4 - - - +
437V LEU* 4.2 14.1 - - + +
438V ALA* 4.6 25.6 - - + +
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Residues in contact with ILE 393 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330V THR 4.3 7.0 - - - +
331V VAL* 4.0 37.9 - - + -
332V VAL* 4.8 4.0 - - + -
339V ARG* 3.4 33.2 - - + +
342V THR* 5.2 2.0 - - + -
343V LEU* 3.4 34.3 - - + +
346V VAL* 5.9 0.9 - - + +
350V ARG* 5.3 2.3 + - - -
389V ALA* 2.8 35.0 + - + +
390V LEU* 3.8 4.9 - - + +
392V GLU* 1.3 77.6 - - - +
394V PHE* 1.3 88.1 + - + +
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Residues in contact with PHE 394 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328V SER* 3.4 19.3 - - - -
329V GLY 3.3 23.8 - - - -
330V THR* 4.2 7.4 - - - -
342V THR* 4.4 8.3 - - + -
343V LEU* 6.3 0.2 - - + -
346V VAL* 3.9 26.0 - - + -
350V ARG* 2.8 33.8 + - - +
376V PRO* 4.5 7.0 - - + -
378V ALA* 3.7 20.0 - - + -
390V LEU* 2.8 42.7 + - + +
393V ILE* 1.3 96.1 - - + +
395V GLY* 1.3 63.5 + - - +
397V ASP 4.4 0.2 + - - -
398V ALA* 3.6 27.8 - - + -
400V LEU* 4.4 4.3 - - + -
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Residues in contact with GLY 395 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168V GLY* 4.9 3.5 - - - -
391V VAL* 2.8 27.2 + - - +
392V GLU 4.4 1.4 + - - -
393V ILE 3.7 1.2 - - - -
394V PHE* 1.3 86.7 - - - +
396V ASP* 1.3 67.2 + - - -
397V ASP 3.5 0.2 + - - -
398V ALA* 4.3 3.5 - - - +
400V LEU* 5.9 1.6 - - - +
431V ARG* 4.4 8.7 - - - -
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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