Contacts of the helix formed by residues 386 - 395 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332K VAL* 3.5 43.3 + - + +
381K GLY 3.6 10.1 + - - -
382K ILE* 3.3 10.3 - - + -
383K HIS* 2.8 62.2 + + - +
385K TRP* 1.3 77.0 - - - +
387K MET* 1.3 64.1 + - - +
388K PRO* 3.4 0.9 - - - -
389K ALA* 3.1 10.3 + - - +
390K LEU* 3.0 35.7 + - + +
465K ILE 4.3 9.1 + - - -
466K LYS* 5.0 6.5 - - + -
467K PHE* 4.5 4.9 - + - -
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Residues in contact with MET 387 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K LEU* 4.4 0.9 - - + -
383K HIS 3.7 2.0 + - - -
384K VAL* 3.0 18.2 + - - +
386K HIS* 1.3 77.3 - - - +
388K PRO* 1.3 67.8 - - + +
390K LEU* 3.2 4.5 + - - +
391K VAL* 3.0 30.2 + - + +
400K LEU* 3.7 28.9 - - - -
402K PHE* 3.5 33.0 - - + -
420K ASN* 3.4 31.2 - - - +
423K ALA* 3.7 15.9 - - + +
424K LEU* 3.7 31.0 - - + +
427K CYS* 3.9 7.6 - - - -
445K ILE* 4.4 0.2 - - + -
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Residues in contact with PRO 388 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K VAL 4.1 2.0 - - - +
385K TRP 3.4 16.6 - - - +
386K HIS 3.5 0.7 - - - -
387K MET* 1.3 95.2 - - + +
389K ALA* 1.3 56.6 + - - +
392K GLU* 3.0 29.9 + - - +
427K CYS* 3.7 20.6 - - + -
437K LEU* 3.8 23.1 - - + +
441K GLY* 3.6 43.5 - - - +
445K ILE* 3.9 6.3 - - + -
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Residues in contact with ALA 389 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332K VAL* 4.4 24.2 - - + -
339K ARG* 6.2 0.2 - - - +
385K TRP 5.8 0.2 - - - +
386K HIS* 3.1 11.0 + - - +
388K PRO* 1.3 80.1 - - - +
390K LEU* 1.3 58.5 + - - +
392K GLU* 3.4 8.4 + - - +
393K ILE* 2.8 42.8 + - + +
438K ALA* 6.4 1.3 - - - +
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Residues in contact with LEU 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330K THR* 3.8 27.4 - - - +
332K VAL* 4.2 8.5 - - + -
378K ALA* 4.3 12.1 - - + -
382K ILE* 3.6 24.7 - - + -
386K HIS* 3.0 31.4 + - + +
387K MET* 3.6 8.7 - - - +
389K ALA* 1.3 75.1 - - - +
391K VAL* 1.3 58.0 + - - +
393K ILE* 3.2 2.2 + - + -
394K PHE* 2.9 52.6 + - + +
400K LEU* 4.1 20.9 - - + -
402K PHE* 3.9 17.3 - - + -
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Residues in contact with VAL 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387K MET* 3.0 24.6 + - + +
390K LEU* 1.3 74.4 - - - +
392K GLU* 1.3 57.6 + - - +
394K PHE* 5.4 0.2 - - - -
395K GLY* 2.8 36.1 + - - +
396K ASP* 5.1 1.3 - - - +
400K LEU* 4.6 4.3 - - + -
424K LEU* 3.7 30.3 - - + -
427K CYS* 4.2 16.6 - - + +
428K THR* 4.8 8.1 - - - +
431K ARG* 4.0 26.7 + - - +
437K LEU* 3.6 24.7 - - + -
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Residues in contact with GLU 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K ARG* 2.8 43.3 + - - -
388K PRO 3.0 18.6 + - - +
389K ALA* 3.6 6.9 - - - +
391K VAL* 1.3 80.1 - - - +
393K ILE* 1.3 65.9 + - - +
395K GLY 4.3 1.4 + - - -
431K ARG* 6.6 0.2 - - - +
436K ASP* 5.7 0.4 - - - +
437K LEU* 4.2 14.5 - - + +
438K ALA* 4.6 25.5 - - + +
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Residues in contact with ILE 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330K THR 4.2 6.5 - - - +
331K VAL* 3.9 37.0 - - + -
332K VAL* 4.7 4.0 - - + -
339K ARG* 3.5 31.9 - - + +
342K THR* 5.2 2.5 - - + -
343K LEU* 3.5 33.5 - - + +
346K VAL* 6.0 0.5 - - - +
350K ARG* 5.3 2.4 + - - -
389K ALA* 2.8 35.6 + - + +
390K LEU* 3.8 5.2 - - + +
392K GLU* 1.3 76.4 - - - +
394K PHE* 1.3 89.1 + - + +
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Residues in contact with PHE 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K SER* 3.4 19.3 - - - -
329K GLY 3.3 24.2 - - - -
330K THR* 4.2 7.4 - - - -
342K THR* 4.5 8.5 - - + -
343K LEU* 6.3 0.2 - - + -
346K VAL* 3.9 25.8 - - + -
350K ARG* 2.8 34.4 + - - +
376K PRO* 4.5 7.0 - - + -
378K ALA* 3.7 20.9 - - + -
390K LEU* 2.9 42.5 + - + +
393K ILE* 1.3 94.1 - - + +
395K GLY* 1.3 64.1 + - - +
397K ASP 4.3 0.2 + - - -
398K ALA* 3.7 28.0 - - + -
400K LEU* 4.4 4.5 - - + -
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Residues in contact with GLY 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY* 4.8 3.6 + - - -
391K VAL* 2.8 32.1 + - - +
392K GLU 4.3 1.4 + - - -
393K ILE 3.7 0.8 - - - -
394K PHE* 1.3 82.4 - - - +
396K ASP* 1.3 66.6 + - - -
397K ASP 3.5 0.2 + - - -
398K ALA* 4.4 3.8 - - - +
400K LEU* 5.8 1.7 - - - +
431K ARG* 4.4 9.0 - - - -
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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