Contacts of the helix formed by residues 338 - 347 (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 GLN 338 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C ILE* 5.7 1.4 - - - +
337C SER* 1.3 98.7 + - - +
339C PRO* 1.4 62.9 - - + +
340C LEU 3.7 2.0 - - - -
341C PHE* 4.0 20.2 - - - +
342C LYS* 3.1 55.5 + - + +
64F LYS* 4.6 1.1 - - - -
65F PRO* 4.4 26.0 - - + -
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Residues in contact with PRO 339 (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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336C ILE 5.5 0.7 - - - +
337C SER* 3.7 16.4 - - - +
338C GLN* 1.4 89.0 - - + +
340C LEU* 1.3 61.2 + - - +
341C PHE* 5.8 0.7 - - + -
343C LEU* 3.3 22.9 + - - +
64F LYS* 3.5 34.0 - - + +
65F PRO* 6.2 0.9 - - + -
151Y ASN* 4.2 21.3 - - + +
152Y PRO* 4.3 7.6 - - + +
153Y GLY 3.7 24.2 - - - +
154Y PHE* 5.2 3.6 - - + -
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Residues in contact with LEU 340 (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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339C PRO* 1.3 77.6 - - - +
341C PHE* 1.3 70.9 + - + +
343C LEU* 3.4 25.2 + - + -
344C LEU* 3.0 35.5 + - + +
431C PRO* 3.5 38.6 - - + +
432C ILE* 4.5 9.0 - - + +
435C ALA* 3.5 16.2 - - + -
150Y ILE* 3.8 30.3 - - + +
152Y PRO* 4.0 11.6 - - + +
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Residues in contact with PHE 341 (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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336C ILE* 3.5 29.8 - - + -
337C SER 2.9 30.7 - - - -
338C GLN* 3.9 21.8 - - - +
339C PRO* 5.6 0.7 - - + -
340C LEU* 1.3 81.1 - - + +
342C LYS* 1.4 57.2 - - - +
344C LEU* 3.5 0.6 + - - -
345C LYS* 3.2 24.4 + - - +
435C ALA* 3.7 29.4 - - + -
438C TYR* 3.6 35.9 - + + -
439C MET* 3.3 36.2 - - + +
148Y LEU* 4.5 1.1 - - + -
150Y ILE* 4.0 15.5 - - + -
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Residues in contact with LYS 342 (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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338C GLN* 3.1 41.4 + - + +
341C PHE* 1.4 74.6 - - - +
343C LEU* 1.4 52.5 + - - +
345C LYS* 2.8 39.7 + - + +
346C TRP* 2.8 27.2 + - + +
64F LYS* 3.4 37.5 - - + +
65F PRO* 5.0 7.2 - - - -
66F ALA 6.2 0.2 - - - -
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Residues in contact with LEU 343 (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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339C PRO 3.3 21.0 + - - +
340C LEU* 3.4 24.7 + - + +
342C LYS* 1.4 73.1 - - - +
344C LEU* 1.3 64.0 + - + +
346C TRP* 3.3 36.5 + - + +
347C ILE* 3.6 13.6 + - + +
64F LYS* 4.2 2.9 - - - +
89F GLY 4.2 4.0 - - - +
90F SER* 3.9 13.2 - - - +
91F SER* 3.5 41.3 - - - +
152Y PRO* 4.8 9.2 - - + -
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Residues in contact with LEU 344 (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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340C LEU* 3.0 25.4 + - + +
341C PHE 3.7 8.3 - - - +
343C LEU* 1.3 77.8 - - + +
345C LYS* 1.3 55.6 + - - +
347C ILE* 3.3 28.3 - - + +
348C HIS* 2.9 25.7 + - - -
361C ILE* 3.4 12.1 - - + +
365C VAL* 5.0 7.6 - - + -
432C ILE* 4.2 26.0 - - + -
435C ALA* 3.9 22.0 - - + -
436C LEU* 4.3 5.8 - - + -
439C MET* 3.5 29.4 - - + -
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Residues in contact with LYS 345 (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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341C PHE 3.2 12.8 + - - +
342C LYS* 2.8 34.2 + - + +
344C LEU* 1.3 74.1 - - - +
346C TRP* 1.3 62.5 + - + -
348C HIS* 3.1 27.8 + - + +
349C SER* 3.1 24.6 + - - -
358C ILE* 4.4 13.5 - - - -
439C MET* 4.1 22.9 - - - +
445C GLU* 2.6 36.4 + - - +
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Residues in contact with TRP 346 (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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342C LYS* 2.8 17.7 + - + +
343C LEU* 3.3 28.2 + - + +
345C LYS* 1.3 74.6 - - + +
347C ILE* 1.4 52.0 + - - +
348C HIS 2.9 10.9 + - - -
349C SER* 3.1 20.6 + - - -
62F LEU* 3.0 44.3 - - + +
63F GLU 3.9 2.7 - - - -
64F LYS* 3.6 50.1 + - + -
66F ALA 5.6 1.0 + - - -
68F ILE* 4.2 17.1 - - + +
87F ASN* 3.6 11.8 + - - +
88F PHE 4.5 6.0 - - - +
89F GLY* 4.7 5.8 - - - -
91F SER 3.4 22.7 - - - -
92F HIS* 3.8 15.3 - - - -
93F ASP 4.1 3.8 - - - -
94F ILE* 3.5 30.6 - - + +
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Residues in contact with ILE 347 (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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343C LEU* 3.6 8.2 + - + +
344C LEU* 3.3 34.1 - - + +
346C TRP* 1.4 70.8 - - - +
348C HIS* 1.4 61.1 + - - +
361C ILE* 3.8 37.2 - - + +
365C VAL* 5.4 6.5 - - + -
87F ASN 3.7 17.3 - - - +
88F PHE* 4.3 2.2 - - + +
89F GLY* 3.2 36.8 - - - +
191F PHE* 3.8 38.3 - - + -
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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