Contacts of the helix formed by residues 403 - 411 (chain C) in PDB entry 5MG3
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 403 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396C ARG* 2.9 24.2 - - - +
401C LYS* 2.8 27.0 + - + +
402C GLN* 1.3 70.6 - - - +
404C ILE* 1.4 65.5 + - - +
405C SER 3.3 2.2 - - - -
406C GLN* 3.1 24.1 + - + +
407C GLU* 2.7 40.9 + - + +
608D LYS* 4.4 22.8 - - - +
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Residues in contact with ILE 404 (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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393C MET* 4.3 19.2 - - - +
396C ARG* 3.4 37.0 - - + +
397C LEU* 4.6 8.7 - - + -
399C ASP* 5.1 0.2 - - + -
400C ASP 4.0 6.1 - - - +
401C LYS* 3.2 30.4 + - + +
402C GLN 3.4 1.6 - - - -
403C ARG* 1.4 76.6 - - + +
405C SER* 1.4 56.9 + - - +
407C GLU* 3.2 8.7 + - - +
408C MET* 3.0 29.8 + - + +
9Y PHE* 4.4 16.8 - - + -
179Y THR* 3.5 31.4 - - + +
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Residues in contact with SER 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C GLN 4.6 2.1 + - - -
403C ARG 3.3 1.0 - - - -
404C ILE* 1.4 77.1 - - - +
406C GLN* 1.3 63.1 + - - +
408C MET* 3.7 6.1 + - - +
409C MET* 3.7 8.5 + - - +
473D LYS* 2.9 22.5 + - - +
515G PHE* 3.7 22.1 - - - -
9Y PHE* 3.7 23.8 - - - -
10Y GLN 4.4 0.4 - - - -
11Y SER* 3.5 8.2 + - - -
12Y ALA* 3.2 36.1 + - - -
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Residues in contact with GLN 406 (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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402C GLN 5.6 0.4 - - - +
403C ARG* 3.1 18.4 + - + +
405C SER* 1.3 77.1 - - - +
407C GLU* 1.3 60.4 + - + +
409C MET* 3.3 7.9 + - - +
410C ALA* 3.0 27.1 + - - +
473D LYS* 2.7 49.7 + - - +
608D LYS* 4.8 17.0 - - - +
612D LYS* 5.6 6.1 - - - +
12Y ALA 4.1 3.1 - - - +
13Y LYS* 5.2 3.0 - - - +
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Residues in contact with GLU 407 (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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393C MET* 3.7 17.9 - - + +
396C ARG* 2.7 39.9 + - - +
403C ARG* 2.7 55.0 + - + +
404C ILE* 3.2 9.8 + - - +
406C GLN* 1.3 74.3 - - + +
408C MET* 1.3 65.0 + - - +
410C ALA* 3.4 9.6 - - + +
411C LEU* 3.1 24.4 + - - +
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Residues in contact with MET 408 (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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393C MET* 4.1 13.4 - - + +
404C ILE* 3.0 16.4 + - + +
405C SER 4.1 2.9 - - - +
406C GLN 3.3 0.2 - - - -
407C GLU* 1.3 76.9 - - - +
409C MET* 1.3 62.1 + - - +
411C LEU* 3.4 9.2 + - - +
509G SER* 3.1 32.8 - - - +
510G SER 3.6 17.7 - - - +
511G GLY 3.5 16.6 - - - +
512G SER 5.5 0.2 - - - +
513G GLY* 3.8 13.1 + - - -
514G ASN 3.2 28.9 - - - +
515G PHE* 3.5 25.1 - - + -
8Y ASP* 4.3 6.7 - - - -
9Y PHE* 3.5 29.4 - - + +
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Residues in contact with MET 409 (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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405C SER 3.7 3.4 + - - +
406C GLN* 3.3 9.9 + - - +
408C MET* 1.3 78.4 - - - +
410C ALA* 1.3 61.0 + - - +
411C LEU 3.6 0.2 + - - -
412C TYR 4.4 3.3 - - - +
413C LYS* 3.4 20.9 - - - +
471D PHE* 3.4 34.1 - - + +
472D TYR* 5.0 0.2 - - - -
473D LYS* 5.9 2.5 - - + -
612D LYS 6.0 0.7 - - - -
513G GLY* 3.2 38.5 + - - +
514G ASN* 3.5 12.8 - - - -
515G PHE* 3.8 34.5 - - + -
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Residues in contact with ALA 410 (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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406C GLN 3.0 15.1 + - - +
407C GLU* 3.4 15.9 - - + +
409C MET* 1.3 77.5 - - - +
411C LEU* 1.4 67.6 - - - +
413C LYS* 3.9 15.4 - - - +
611D LYS 5.2 9.2 - - - +
612D LYS 5.3 5.2 - - - -
14F ARG* 4.0 18.4 + - - +
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Residues in contact with LEU 411 (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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391C GLN 4.7 2.2 - - - +
392C ALA* 3.6 36.3 - - + -
393C MET* 4.4 17.3 - - + +
407C GLU 3.1 15.8 + - - +
408C MET* 3.4 7.2 + - - +
409C MET 3.4 0.2 - - - -
410C ALA* 1.4 81.2 - - - +
412C TYR* 1.4 78.2 + - + +
415C GLU* 5.0 0.2 - - - -
14F ARG* 3.5 23.4 + - + +
511G GLY* 3.6 14.6 - - - +
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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