Contacts of the helix formed by residues 346 - 356 (chain H) in PDB entry 6KW5
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 ARG 346 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H ASP* 4.1 11.4 + - - -
237H SER* 3.8 24.2 + - - -
239H GLN* 3.9 14.5 - - - +
240H ASP* 3.8 20.7 + - - -
249H ARG* 3.5 30.4 - - - +
312H LYS* 4.4 9.6 - - - +
338H ALA* 4.3 2.2 - - - -
345H LYS* 1.3 79.8 - - - +
347H VAL* 1.3 65.2 + - - +
348H GLU* 3.3 44.2 + - + +
349H ASP* 3.3 13.6 + - + +
350H CYS* 3.1 24.4 + - - -
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Residues in contact with VAL 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334H TRP* 3.5 45.5 - - + +
335H GLU* 3.3 30.3 - - + +
338H ALA* 4.3 7.4 - - + +
346H ARG* 1.3 73.8 - - - +
348H GLU* 1.3 58.5 + - - +
349H ASP 3.1 0.9 + - - -
350H CYS* 3.2 4.0 + - - +
351H ILE* 3.0 40.4 + - + +
478I TYR* 3.6 27.1 - - + -
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Residues in contact with GLU 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H SER* 4.9 0.3 + - - -
239H GLN* 2.9 47.7 + - - +
346H ARG* 3.3 39.6 + - + +
347H VAL* 1.3 78.2 - - - +
349H ASP* 1.3 58.3 + - + +
351H ILE* 5.1 5.2 - - - -
352H GLU* 3.2 32.5 - - - +
474I ILE* 4.5 8.1 - - + +
475I SER* 3.5 25.9 + - - +
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Residues in contact with ASP 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LYS* 3.8 27.5 + - - +
315H TRP* 3.3 34.3 + - - -
345H LYS* 4.3 11.1 + - + +
346H ARG* 3.3 24.3 + - + +
347H VAL 3.1 0.8 - - - -
348H GLU* 1.3 81.4 - - + +
350H CYS* 1.3 59.8 + - - +
351H ILE 3.3 1.6 - - - -
352H GLU* 3.3 12.4 + - - +
353H LYS* 2.9 27.1 + - - +
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Residues in contact with CYS 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H TRP* 4.3 13.2 - - - -
323H LEU* 4.4 14.9 - - + +
334H TRP* 4.3 17.0 - - + -
337H ILE* 5.2 2.7 - - + -
338H ALA* 4.2 22.0 - - + -
341H VAL* 4.3 11.9 - - - -
345H LYS* 4.1 19.1 - - - -
346H ARG 3.1 21.0 + - - +
347H VAL* 3.8 4.9 - - - +
349H ASP* 1.3 76.7 - - - +
351H ILE* 1.3 59.0 + - - +
353H LYS* 3.4 2.7 + - - +
354H PHE* 2.9 30.0 + - - +
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Residues in contact with ILE 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334H TRP* 3.6 48.9 - - + +
347H VAL* 3.0 36.3 + - + +
348H GLU* 5.1 2.0 - - - +
350H CYS* 1.3 75.6 - - - +
352H GLU* 1.3 62.6 + - - +
354H PHE* 3.5 1.4 + - - +
355H LEU* 3.2 36.5 + - + +
474I ILE* 3.8 33.0 - - + -
478I TYR* 4.2 18.2 - - + -
483I LEU* 5.3 5.4 - - + +
257J ILE* 5.0 7.4 - - + -
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Residues in contact with GLU 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H ILE* 5.8 4.0 - - - +
313H LYS* 4.8 9.7 + - - -
348H GLU 3.2 22.2 + - - +
349H ASP* 3.3 20.0 + - - +
351H ILE* 1.3 77.3 - - - +
353H LYS* 1.3 49.2 + - - +
355H LEU 4.2 0.9 - - - -
356H SER* 2.7 31.9 + - - -
471I MET* 3.5 36.4 - - + +
472I GLY* 5.3 0.3 - - - -
474I ILE* 3.5 28.8 - - + +
475I SER* 5.2 2.4 + - - -
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Residues in contact with LYS 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D LYS* 4.6 19.7 - - - +
315H TRP* 3.6 64.3 - - + +
320H MET* 4.2 20.6 - - + -
323H LEU* 4.9 4.0 - - + -
349H ASP* 2.9 16.9 + - - +
350H CYS 4.0 2.9 - - - +
351H ILE 3.2 0.4 - - - -
352H GLU* 1.3 77.2 - - - +
354H PHE* 1.3 63.3 + - - +
355H LEU 3.2 2.1 + - - -
356H SER* 3.5 20.2 + - - +
357H LEU* 3.3 25.3 - - - +
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Residues in contact with PHE 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323H LEU* 3.9 24.8 - - + +
324H LEU* 4.9 4.9 - - + -
327H ILE* 4.2 15.7 - - + -
334H TRP* 4.2 16.2 - + + -
350H CYS 2.9 18.0 + - - +
351H ILE* 3.5 2.9 + - + +
353H LYS* 1.3 76.4 - - - +
355H LEU* 1.3 62.0 + - + +
357H LEU* 4.3 18.1 + - + +
359H ILE* 5.5 4.0 - - + -
250J LEU* 3.9 45.1 - - + -
253J LYS* 4.4 4.5 - - + -
254J GLN* 3.2 43.2 - - + +
257J ILE* 3.7 28.9 - - + -
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Residues in contact with LEU 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H ILE* 3.2 32.0 + - + +
354H PHE* 1.3 85.5 - - + +
356H SER* 1.3 57.5 + - - +
357H LEU 3.2 3.1 + - - -
461I TYR* 3.9 11.3 - - + -
471I MET* 4.1 21.5 - - + -
474I ILE* 4.8 7.2 - - + -
254J GLN* 4.3 7.2 - - + +
257J ILE* 3.7 31.2 - - + -
258J ARG* 3.0 55.2 + - + +
261J LEU* 4.0 26.5 - - + -
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Residues in contact with SER 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LYS* 4.7 12.9 + - - +
352H GLU 2.7 24.8 + - - -
353H LYS* 3.5 24.0 + - - +
354H PHE 3.5 0.4 - - - -
355H LEU* 1.3 77.2 - - - +
357H LEU* 1.3 61.1 + - - +
358H PRO* 3.8 8.2 - - - +
458I SER* 4.8 4.9 - - - -
461I TYR* 4.2 10.8 - - - -
462I SER* 4.1 32.8 - - - +
471I MET* 5.1 0.9 - - - -
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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