Contacts of the helix formed by residues 428 - 435 (chain B) in PDB entry 5MQF
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 THR 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B THR* 3.7 26.7 + - - +
317B CYS* 5.1 3.2 + - - +
322B SER* 3.7 24.0 - - - -
325B LYS* 5.8 1.8 - - - -
426B GLU* 3.4 8.9 + - - -
427B PHE* 1.3 75.3 - - - +
429B GLY* 1.3 62.5 + - - +
430B PHE* 3.1 3.8 + - - +
431B VAL* 3.5 2.3 + - - +
432B ASP* 2.9 33.9 + - - +
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Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B CYS* 4.9 6.7 - - - +
317B CYS 5.4 2.8 + - - -
318B PHE 5.2 2.3 - - - -
319B THR* 3.8 28.0 - - - -
322B SER* 3.9 8.7 - - - -
428B THR* 1.3 79.0 - - - +
430B PHE* 1.3 56.1 + - - +
432B ASP* 4.4 2.5 - - - -
433B MET* 2.6 39.7 + - - +
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B CYS* 5.5 4.2 - - - +
317B CYS* 5.6 11.0 - - + +
427B PHE* 5.0 15.3 - - + -
428B THR 3.1 1.6 - - - +
429B GLY* 1.3 77.2 - - - +
431B VAL* 1.3 51.7 + - - +
433B MET 3.9 0.2 - - - -
434B CYS* 2.6 37.6 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 4.3 16.6 - - + +
191B PRO 3.3 27.4 - - - +
192B ASP* 3.7 15.4 - - + +
198B TYR* 5.4 6.7 - - + -
427B PHE* 5.6 2.2 - - + +
428B THR 3.5 3.0 + - - +
430B PHE* 1.3 76.3 - - - +
432B ASP* 1.3 62.0 + - - +
434B CYS* 3.7 5.6 - - - -
435B VAL* 2.9 33.6 + - - +
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Residues in contact with ASP 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ASP* 4.1 6.4 - - + +
193B THR* 4.1 20.2 - - - +
194B LYS* 5.1 3.6 - - + +
321B GLY* 6.5 0.9 - - - -
428B THR 2.9 22.6 + - - +
429B GLY* 4.4 2.2 - - - -
431B VAL* 1.3 78.3 - - - +
433B MET* 1.3 60.1 + - - +
435B VAL* 4.4 1.9 - - - +
436B GLN* 3.3 25.6 + - - +
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Residues in contact with MET 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B THR* 5.4 2.3 - - - -
305B GLY* 3.3 30.6 - - - +
306B ASN 5.9 0.2 - - - -
307B VAL 5.4 2.5 - - - +
308B CYS* 5.4 3.8 - - + -
319B THR* 5.1 7.2 - - - -
429B GLY* 2.6 26.3 + - - +
430B PHE 4.6 0.2 - - - +
432B ASP* 1.3 75.9 - - - +
434B CYS* 1.3 58.2 + - - +
436B GLN* 4.1 6.8 - - - +
437B HIS* 3.2 26.9 + - - +
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Residues in contact with CYS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PHE 2.6 24.8 + - - +
431B VAL* 3.1 9.1 + - - +
433B MET* 1.3 74.5 - - - +
435B VAL* 1.3 57.8 - - - +
436B GLN 3.1 0.9 - - - -
437B HIS* 2.8 4.8 + - - -
438B ILE* 2.5 42.3 + - + +
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Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU 6.1 1.6 - - - +
198B TYR* 5.8 8.1 - - + -
431B VAL 2.9 17.7 + - - +
432B ASP* 4.6 1.6 - - - +
434B CYS* 1.3 73.2 - - - +
436B GLN* 1.3 61.5 + - - +
438B ILE* 3.1 19.9 - - - +
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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