Contacts of the helix formed by residues 428 - 435 (chain E) in PDB entry 6M04
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 GLN 428 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399E LYS* 4.9 7.4 - - - +
403E GLU* 6.0 1.7 - - - +
406E PHE* 6.5 0.9 - - + -
424E ASP* 3.6 24.6 + - - +
427E ASP* 1.3 71.4 - - - +
429E LEU* 1.3 58.9 + - - +
430E TYR 3.4 0.4 - - - -
431E SER* 3.4 13.4 + - - -
432E LYS* 3.0 34.6 + - + +
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Residues in contact with LEU 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D HIS* 5.4 13.5 - - + +
293D LYS* 4.4 22.9 - - - +
297D HIS* 4.0 37.1 + - + +
204E PHE* 4.5 20.9 - - + -
427E ASP* 3.2 16.9 - - + +
428E GLN* 1.3 79.0 - - - +
430E TYR* 1.3 66.6 + - + +
432E LYS* 3.3 9.4 + - + +
433E ARG* 2.9 39.5 + - + +
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Residues in contact with TYR 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D HIS* 5.6 1.6 + - - -
19E ILE* 5.0 7.9 - - + +
200E LEU* 3.6 43.2 - - + +
204E PHE* 3.5 50.7 - + + -
420E LEU* 5.6 0.6 - - - +
423E VAL* 4.5 12.6 - - + -
426E TYR* 4.0 19.7 - + - -
427E ASP* 3.7 31.6 + - + +
428E GLN 3.4 0.4 - - - -
429E LEU* 1.3 82.8 - - + +
431E SER* 1.3 61.0 + - - +
433E ARG* 4.2 7.0 - - - +
434E PHE* 2.9 34.7 + - - +
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Residues in contact with SER 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399E LYS* 3.1 37.9 + - - +
400E VAL* 5.4 0.9 - - - +
403E GLU* 2.9 23.3 + - - +
420E LEU* 4.7 14.0 - - - +
423E VAL* 5.6 2.7 - - - +
424E ASP* 4.1 17.5 - - - -
427E ASP 4.3 3.4 + - - -
428E GLN* 3.4 19.2 + - - -
429E LEU 3.3 0.6 - - - -
430E TYR* 1.3 80.8 - - - +
432E LYS* 1.3 57.9 + - - +
433E ARG 3.5 0.2 + - - -
434E PHE* 4.7 1.7 - - - +
435E GLY* 3.6 8.0 + - - -
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Residues in contact with LYS 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E LEU* 5.7 5.8 - - + -
403E GLU* 2.4 64.4 + - + +
406E PHE* 3.3 37.3 - - - -
407E SER* 4.0 13.4 - - - +
428E GLN* 3.0 25.5 + - + +
429E LEU* 3.6 11.7 - - + +
431E SER* 1.3 76.3 - - - +
433E ARG* 1.3 62.0 + - + +
436E VAL* 4.0 12.5 - - - +
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Residues in contact with ARG 433 (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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290D LYS* 4.2 4.4 - - - +
293D LYS* 3.8 23.7 - - - +
203E CYS* 3.0 31.7 + - - -
204E PHE* 2.7 55.9 + - + +
206E SER 3.2 10.3 + - - +
209E THR* 2.5 44.8 + - - +
429E LEU* 2.9 24.6 + - + +
430E TYR* 3.7 7.0 - - - +
431E SER 3.3 0.2 - - - -
432E LYS* 1.3 78.3 - - + +
434E PHE* 1.3 58.9 + - - +
436E VAL* 4.3 13.1 - - + +
437E PHE* 4.9 0.4 - - - -
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Residues in contact with PHE 434 (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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196E PHE* 5.0 13.2 - + - -
199E ILE* 3.5 36.6 - - + -
200E LEU* 4.6 20.0 - - + -
203E CYS* 3.6 27.5 - - + -
291E VAL* 5.0 19.5 - - + -
294E PHE* 5.9 1.3 - + + -
418E PHE* 5.4 11.0 - + - -
420E LEU* 4.5 27.1 - - + -
430E TYR* 2.9 17.7 + - + +
431E SER* 4.7 2.0 - - - +
433E ARG* 1.3 77.6 - - - +
435E GLY* 1.3 58.9 + - - +
436E VAL 3.1 10.6 + - - -
437E PHE* 3.4 16.9 + + + +
438E LEU* 4.6 1.2 + - - +
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Residues in contact with GLY 435 (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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400E VAL* 4.7 15.8 - - - +
403E GLU* 3.3 28.3 + - - +
404E SER* 5.4 2.6 + - - -
409E ILE* 5.9 0.2 - - - +
412E VAL* 4.8 0.5 - - - +
420E LEU* 6.3 1.3 - - - +
431E SER 3.6 3.8 + - - -
434E PHE* 1.3 79.6 - - - +
436E VAL* 1.3 63.2 + - - +
437E PHE 3.4 0.7 - - - -
438E LEU* 3.8 15.4 + - - +
439E SER* 4.0 10.4 + - - -
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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