Contacts of the helix formed by residues 386 - 395 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332E VAL* 3.6 43.1 + - + +
381E GLY 3.6 12.1 + - - -
382E ILE* 3.3 11.0 - - + -
383E HIS* 2.8 59.6 + + - +
385E TRP* 1.3 77.4 - - - +
387E MET* 1.3 63.7 + - - +
388E PRO* 3.4 1.1 - - - -
389E ALA* 3.1 9.8 + - - +
390E LEU* 3.0 35.2 + - + +
465E ILE 4.3 8.2 + - - -
466E LYS* 5.0 7.0 - - + -
467E PHE* 4.5 5.3 - + - -
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Residues in contact with MET 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E LEU* 4.4 1.3 - - + -
383E HIS 3.8 2.0 + - - -
384E VAL* 3.0 17.3 + - - +
386E HIS* 1.3 76.7 - - - +
388E PRO* 1.3 68.3 - - + +
390E LEU* 3.2 4.9 + - - +
391E VAL* 3.0 25.5 + - + +
400E LEU* 3.7 29.4 - - - -
402E PHE* 3.5 32.8 - - + -
420E ASN* 3.4 31.6 - - - +
423E ALA* 3.7 14.1 - - + +
424E LEU* 3.7 31.9 - - + +
427E CYS* 3.9 7.0 - - - -
445E ILE* 4.4 0.2 - - + -
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Residues in contact with PRO 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E VAL 4.0 2.9 - - - +
385E TRP 3.4 15.9 - - - +
386E HIS 3.5 0.9 - - - -
387E MET* 1.3 94.7 - - + +
389E ALA* 1.3 54.9 + - - +
391E VAL 3.5 0.3 + - - -
392E GLU* 3.0 29.7 + - - +
427E CYS* 3.6 20.9 - - + -
437E LEU* 3.8 23.3 - - + +
441E GLY* 3.6 42.0 - - - +
445E ILE* 3.8 7.4 - - + -
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Residues in contact with ALA 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E VAL* 4.4 23.8 - - + -
339E ARG* 6.2 0.4 - - - +
385E TRP 5.2 0.4 + - - +
386E HIS* 3.1 11.8 + - - +
388E PRO* 1.3 79.4 - - - +
390E LEU* 1.3 56.9 + - - +
392E GLU* 3.3 7.3 + - - +
393E ILE* 2.8 41.8 + - + +
437E LEU 6.2 0.4 - - - -
438E ALA* 6.4 1.3 - - - +
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E THR* 3.8 26.7 - - - +
332E VAL* 4.2 8.1 - - + -
378E ALA* 4.3 12.6 - - + -
382E ILE* 3.7 24.2 - - + -
386E HIS* 3.0 32.8 + - + +
387E MET* 3.2 7.6 + - - +
389E ALA* 1.3 73.4 - - - +
391E VAL* 1.3 59.8 + - - +
393E ILE* 4.6 1.1 - - + -
394E PHE* 2.9 54.1 + - + +
400E LEU* 4.1 21.1 - - + -
402E PHE* 3.9 17.0 - - + -
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Residues in contact with VAL 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E MET* 3.0 19.5 + - + +
390E LEU* 1.3 75.0 - - - +
392E GLU* 1.3 57.7 + - - +
395E GLY* 2.8 35.5 + - - +
396E ASP* 5.1 2.0 - - - +
400E LEU* 4.6 5.8 - - + -
424E LEU* 3.7 29.8 - - + -
427E CYS* 4.1 18.6 - - + +
428E THR* 4.8 8.1 - - - +
431E ARG* 4.0 23.9 + - - +
437E LEU* 3.6 23.8 - - + -
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Residues in contact with GLU 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E ARG* 2.8 42.6 + - - -
388E PRO 3.0 19.4 + - - +
389E ALA* 3.6 7.5 - - - +
390E LEU 3.3 0.2 - - - -
391E VAL* 1.3 78.6 - - - +
393E ILE* 1.3 65.3 + - - +
395E GLY* 4.4 1.7 + - - -
436E ASP* 5.8 0.4 - - - +
437E LEU* 4.2 14.8 - - + +
438E ALA* 4.6 26.7 - - + +
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Residues in contact with ILE 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E THR 4.2 7.0 - - - +
331E VAL* 3.9 37.2 - - + -
332E VAL* 4.7 4.3 - - + -
339E ARG* 3.5 33.2 - - + +
342E THR* 5.2 2.5 - - + -
343E LEU* 3.5 34.0 - - + +
346E VAL* 5.9 1.1 - - + +
350E ARG* 5.3 2.4 + - - -
389E ALA* 2.8 36.1 + - + +
390E LEU* 3.9 4.5 - - + +
392E GLU* 1.3 76.2 - - - +
394E PHE* 1.3 89.1 + - + +
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Residues in contact with PHE 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E SER* 3.4 18.8 - - - -
329E GLY 3.3 23.8 - - - -
330E THR* 4.2 7.0 - - - -
342E THR* 4.4 8.1 - - + -
346E VAL* 3.9 27.4 - - + -
350E ARG* 2.8 33.8 + - - +
376E PRO* 4.5 7.2 - - + -
378E ALA* 3.7 20.2 - - + -
390E LEU* 2.9 40.9 + - + +
393E ILE* 1.3 98.4 - - + +
395E GLY* 1.3 63.8 + - - +
397E ASP 4.4 0.2 + - - -
398E ALA* 3.7 27.1 - - + -
400E LEU* 4.4 4.0 - - + -
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Residues in contact with GLY 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLY* 4.9 3.3 - - - -
391E VAL* 2.8 27.5 + - - +
392E GLU 4.4 1.2 + - - -
393E ILE 3.7 1.2 - - - -
394E PHE* 1.3 87.3 - - - +
396E ASP* 1.3 68.0 + - - -
397E ASP 3.5 0.2 + - - -
398E ALA* 4.4 3.5 - - - +
400E LEU* 5.9 1.4 - - - +
431E ARG* 4.4 9.2 - - - -
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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