Contacts of the helix formed by residues 433 - 439 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C LEU* 3.7 27.1 + - - +
203C CYS* 2.7 54.5 + - - +
204C PHE* 3.3 46.6 - - + +
209C THR* 4.2 22.1 - - - +
210C THR* 6.3 0.2 - - - -
213C LEU* 4.8 16.8 - - + +
429C LEU* 2.9 24.1 + - + +
430C TYR* 3.9 10.5 + - - +
432C LYS* 1.3 76.9 - - - +
434C PHE* 1.3 80.7 + - - +
435C GLY 3.4 0.7 + - - -
436C VAL* 3.8 6.1 + - - +
437C PHE* 3.8 12.9 + - - +
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Residues in contact with PHE 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C PHE* 5.0 14.8 - + - -
199C ILE* 4.2 21.1 - - + -
200C LEU* 5.1 8.1 - - + -
203C CYS* 3.7 28.0 - - + -
291C VAL* 5.6 9.6 - - + -
294C PHE* 6.0 7.0 - + - -
400C VAL* 6.1 2.2 - - + -
415C ASP* 5.4 5.8 - - + -
420C LEU* 5.0 24.2 - - + -
430C TYR 3.6 13.9 - - - +
431C SER* 3.2 11.7 + - - +
433C ARG* 1.3 91.4 - - - +
435C GLY* 1.3 59.8 + - - +
437C PHE* 3.1 9.6 + + - +
438C LEU* 2.9 45.5 + - + -
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Residues in contact with GLY 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C VAL* 4.9 3.8 - - - -
403C GLU* 3.1 30.7 + - - -
409C ILE 4.7 2.9 - - - +
411C ASP* 3.3 28.4 + - - +
431C SER 3.7 0.8 + - - -
434C PHE* 1.3 79.5 - - - +
436C VAL* 1.3 64.8 + - - +
438C LEU* 3.5 12.4 + - - +
439C SER* 3.7 3.5 + - - -
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Residues in contact with VAL 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C THR* 6.4 0.7 - - - -
212C ALA* 4.6 12.6 - - + -
213C LEU* 3.8 38.4 - - + -
403C GLU* 4.3 1.5 + - + +
407C SER* 3.6 25.4 - - - +
409C ILE* 4.4 27.4 - - + +
432C LYS 4.5 9.2 - - - +
433C ARG 3.8 3.7 + - - +
434C PHE 3.3 0.4 - - - -
435C GLY* 1.3 76.0 - - - +
437C PHE* 1.3 63.3 + - - +
438C LEU 3.3 0.5 + - - -
439C SER* 3.5 7.6 + - - -
442C SER* 3.3 34.2 - - - +
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Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C CYS* 3.6 21.8 - - - -
206C SER* 5.6 0.4 - - - -
208C TRP* 3.9 19.5 - + - -
209C THR* 3.6 28.5 - - + -
284C ALA* 4.3 6.5 - - + -
287C LEU* 3.5 45.5 - - + -
288C PHE* 3.5 40.1 - + - -
291C VAL* 3.7 23.6 - - + +
433C ARG* 3.8 8.3 + - - +
434C PHE* 3.1 13.7 + + - +
436C VAL* 1.3 79.3 - - - +
438C LEU* 1.3 63.6 + - - +
439C SER 4.2 3.7 - - - +
442C SER* 4.9 3.8 - - - -
443C GLU* 4.9 2.3 + - - +
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Residues in contact with LEU 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C VAL* 4.8 18.6 - - + +
295C ARG* 3.4 28.5 - - - +
400C VAL* 4.0 11.9 - - + -
411C ASP* 3.8 8.5 - - + -
412C VAL* 3.5 38.9 - - + +
413C LYS 3.9 7.0 - - - +
414C ASN 5.3 0.9 - - - +
415C ASP* 6.0 4.5 - - + +
434C PHE* 2.9 31.1 + - + +
435C GLY* 3.6 12.6 - - - +
436C VAL 3.2 0.8 - - - -
437C PHE* 1.3 80.8 - - - +
439C SER* 1.3 64.3 + - - +
440C GLU 3.8 0.5 + - - -
443C GLU* 3.9 9.5 - - - +
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Residues in contact with SER 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ILE* 3.7 21.8 - - - -
410C PRO 2.7 28.4 + - - -
411C ASP* 3.7 12.6 - - - +
412C VAL* 4.6 3.8 - - - -
435C GLY 3.7 1.9 + - - -
436C VAL 3.5 3.6 + - - -
437C PHE 3.4 2.8 - - - +
438C LEU* 1.3 81.4 - - - +
440C GLU* 1.3 63.7 + - - +
441C VAL* 3.3 17.6 + - - +
442C SER* 3.6 3.9 + - - -
443C 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