Contacts of the helix formed by residues 354 - 362 (chain A) in PDB entry 4UHW
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 SER 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A MET* 3.5 22.2 - - - +
308A ALA 3.5 13.7 + - - -
309A GLY* 4.4 7.0 - - - -
310A LEU 3.3 10.1 - - - -
311A SER* 4.2 0.9 - - - +
312A LEU* 3.9 3.8 - - - +
352A MET 3.6 1.5 + - - -
353A ALA* 1.3 75.3 - - - +
355A LEU* 1.3 59.1 - - - +
357A GLY* 2.9 19.8 + - - -
358A HIS* 3.0 26.2 + - - +
3006A FAD 3.0 23.9 + - - +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 4.0 23.3 - - + -
307A GLY 4.0 11.7 - - - +
308A ALA* 3.5 4.2 + - - +
310A LEU 3.0 15.2 + - - +
312A LEU* 4.0 18.5 - - + +
315A VAL* 4.3 24.9 - - + -
337A LEU* 6.6 0.2 - - + -
354A SER* 1.3 70.8 - - - +
356A GLY* 1.3 65.0 + - - +
358A HIS* 3.3 4.6 + - + +
359A ILE* 3.1 39.6 + - + +
368A LEU* 4.9 10.3 - - + -
372A LEU* 5.2 9.0 - - + -
414A VAL* 3.4 32.3 - - + -
416A ILE* 5.4 0.9 - - + -
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Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 2.8 27.8 + - - +
355A LEU* 1.3 74.6 - - - +
357A GLY* 1.3 57.5 + - - -
359A ILE* 3.4 0.9 + - - -
360A ILE* 2.9 36.7 + - - +
411A LEU* 3.9 21.8 - - - -
3006A FAD 4.0 9.4 - - - -
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Residues in contact with GLY 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A SER* 2.9 21.0 + - - -
356A GLY* 1.3 75.3 - - - +
358A HIS* 1.3 57.0 + - - +
361A SER* 2.4 39.3 + - - -
3006A FAD 3.5 37.7 - - - +
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Residues in contact with HIS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU* 4.3 7.2 - - + +
344A LEU* 4.1 1.3 - - + -
354A SER 3.0 11.7 + - - +
355A LEU* 3.4 12.6 - - + +
356A GLY 3.3 0.2 - - - -
357A GLY* 1.3 76.9 - - - +
359A ILE* 1.3 65.3 + - + +
361A SER* 3.5 13.3 - - - -
362A ARG 3.6 4.2 + - - -
363A HIS* 5.0 1.4 + - - -
366A SER* 2.6 30.7 + - - -
368A LEU* 3.6 37.1 + - + +
369A ASN* 3.5 15.0 + - - -
372A LEU* 5.6 0.2 - - + -
3006A FAD 3.3 65.1 + + - +
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Residues in contact with ILE 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU* 3.1 24.5 + - + +
356A GLY 3.9 3.4 - - - +
357A GLY 3.3 0.2 - - - -
358A HIS* 1.3 82.4 - - + +
360A ILE* 1.3 62.1 + - - +
362A ARG* 3.4 21.5 + - - +
369A ASN* 3.7 19.5 + - - +
372A LEU* 4.0 21.8 - - + -
379A LEU* 4.4 9.2 - - + -
392A LEU* 4.4 13.0 - - + -
396A PHE* 3.6 28.3 - - + -
411A LEU* 4.3 17.3 - - + -
414A VAL* 4.2 30.5 - - + -
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A GLY 2.9 20.4 + - - +
359A ILE* 1.3 74.6 - - - +
361A SER* 1.3 66.4 + - - +
362A ARG* 3.1 28.6 + - - +
396A PHE* 4.1 10.1 - - + -
399A LYS* 4.3 3.8 + - - -
405A LEU* 3.7 39.0 - - + -
411A LEU* 4.0 20.2 - - + -
3006A FAD 3.7 46.0 - - + +
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A SER* 3.4 21.8 + - - -
357A GLY 2.4 27.6 + - - -
358A HIS* 3.5 8.1 - - - -
360A ILE* 1.3 76.2 - - - +
362A ARG* 1.3 68.0 + - - +
363A HIS* 3.3 31.8 + - - -
399A LYS* 3.9 11.8 + - - -
3006A FAD 3.7 14.0 + - - -
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A HIS 3.6 6.3 + - - -
359A ILE 3.4 12.4 + - - +
360A ILE* 3.1 44.5 + - - +
361A SER* 1.3 81.3 - - - +
363A HIS* 1.3 65.0 + - - +
364A PRO* 3.6 4.9 - - - +
369A ASN* 3.9 9.2 - - - +
396A PHE* 2.7 53.7 + - - -
397A LEU* 3.7 35.5 - - + +
399A LYS* 3.6 35.5 + - + +
404A ASP* 3.1 34.2 + - - -
405A LEU* 5.2 0.2 - - - +
468A PRO 4.8 4.3 - - - +
469A ALA* 5.2 3.5 - - - +
470A THR* 5.9 0.4 - - - -
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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
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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