Contacts of the helix formed by residues 433 - 439 (chain F) 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 ARG 433 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200F LEU* 3.7 26.3 + - - +
203F CYS* 2.7 53.9 + - - -
204F PHE* 3.3 48.1 - - + +
209F THR* 4.2 22.7 - - - +
210F THR* 6.3 0.7 - - - -
213F LEU* 4.8 18.6 - - + +
429F LEU* 2.9 24.5 + - + +
430F TYR* 3.9 11.1 + - - +
432F LYS* 1.3 76.8 - - - +
434F PHE* 1.3 80.4 + - - +
435F GLY 3.5 0.3 + - - -
436F VAL* 3.8 5.9 + - - +
437F PHE* 3.8 12.6 + - - +
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Residues in contact with PHE 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F PHE* 5.0 14.6 - + - -
199F ILE* 4.2 20.4 - - + -
200F LEU* 5.1 8.3 - - + -
203F CYS* 3.7 26.7 - - + -
291F VAL* 5.6 9.9 - - + -
294F PHE* 6.0 7.6 - + - -
400F VAL* 6.1 2.9 - - + -
415F ASP* 5.4 5.8 - - + -
420F LEU* 5.0 24.0 - - + -
430F TYR 3.6 14.8 + - - +
431F SER* 3.2 11.9 + - - +
433F ARG* 1.3 91.0 - - - +
435F GLY* 1.3 61.6 + - - +
437F PHE* 3.1 10.0 + + - +
438F LEU* 2.9 44.9 + - + -
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Residues in contact with GLY 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F VAL* 4.9 4.7 - - - -
403F GLU* 3.1 30.5 + - - -
409F ILE 4.7 3.1 - - - +
411F ASP* 3.3 27.9 + - - +
431F SER 3.7 0.4 + - - -
434F PHE* 1.3 78.4 - - - +
436F VAL* 1.3 65.2 + - - +
438F LEU* 3.5 12.2 + - - +
439F SER* 3.7 3.5 + - - -
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Residues in contact with VAL 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F THR* 5.4 0.7 - - - +
212F ALA* 4.6 12.6 - - + -
213F LEU* 3.8 38.8 - - + -
403F GLU* 4.3 1.7 + - + +
407F SER* 3.6 25.1 - - - +
409F ILE* 4.5 27.1 - - + +
432F LYS 4.5 9.2 - - - +
433F ARG 3.8 3.3 + - - +
434F PHE 3.3 0.4 - - - -
435F GLY* 1.3 75.2 - - - +
437F PHE* 1.3 63.2 + - - +
438F LEU 3.3 0.7 + - - -
439F SER* 3.5 7.6 + - - -
442F SER* 3.3 34.7 - - - +
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Residues in contact with PHE 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203F CYS* 3.6 22.2 - - - -
206F SER* 5.6 0.2 - - - -
208F TRP* 3.9 20.0 - + - -
209F THR* 3.6 28.7 - - + -
284F ALA* 4.3 6.5 - - + -
287F LEU* 3.5 45.1 - - + -
288F PHE* 3.5 41.8 - + - -
291F VAL* 3.7 23.0 - - + +
433F ARG* 3.8 7.9 + - - +
434F PHE* 3.1 14.1 + + - +
436F VAL* 1.3 79.1 - - - +
438F LEU* 1.3 62.0 + - - +
439F SER 4.2 3.7 - - - +
442F SER* 4.9 3.8 - - - -
443F GLU* 4.9 1.6 + - - +
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Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F VAL* 4.8 18.3 - - + +
295F ARG* 3.4 30.3 - - - +
400F VAL* 4.0 11.7 - - + -
411F ASP* 3.8 9.0 - - + -
412F VAL* 3.5 37.5 - - + +
413F LYS* 3.9 7.6 - - - +
414F ASN 5.3 0.7 - - - +
415F ASP* 6.0 4.3 - - + +
434F PHE* 2.9 31.9 + - + +
435F GLY* 3.6 13.2 - - - +
436F VAL 3.2 0.6 - - - -
437F PHE* 1.3 80.8 - - - +
439F SER* 1.3 63.2 + - - +
440F GLU 3.8 0.5 + - - -
443F GLU* 3.9 9.0 - - - +
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Residues in contact with SER 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F ILE* 3.7 22.2 - - - -
410F PRO 2.7 27.6 + - - -
411F ASP* 3.7 12.8 - - - +
412F VAL* 4.6 4.3 - - - -
435F GLY 3.7 1.5 + - - -
436F VAL 3.5 3.8 + - - -
437F PHE 3.4 2.0 - - - +
438F LEU* 1.3 80.8 - - - +
440F GLU* 1.3 65.3 + - - +
441F VAL* 3.3 17.4 + - - +
442F SER* 3.6 3.9 + - - -
443F GLU* 3.1 25.9 + - - +
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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