Contacts of the helix formed by residues 343 - 348 (chain C) in PDB entry 3G4G
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 SER 343 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C ASN* 5.6 1.3 + - - -
295C ARG* 3.1 13.3 + - - +
339C HIS* 3.0 19.6 + - - -
340C VAL* 3.1 12.7 + - - -
342C LEU* 1.3 74.6 - - - +
344C THR* 1.3 69.6 + - - +
345C PRO* 3.4 7.1 - - - +
348C GLU* 5.0 5.2 - - - +
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Residues in contact with THR 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 VAL 3.6 5.1 + - - -
341C LEU* 3.2 23.7 + - - +
342C LEU 4.5 0.2 - - - +
343C SER* 1.3 79.3 - - - +
345C PRO* 1.4 66.4 - - - +
346C ALA 4.2 0.2 - - - +
347C LEU* 3.0 41.9 + - + +
348C GLU* 3.6 4.7 + - - +
550C TRP* 5.5 1.8 - - + -
554C VAL* 4.1 14.3 - - + +
557C ASP* 2.6 35.9 + - - +
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Residues in contact with PRO 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C SER 3.4 5.4 - - - +
344C THR* 1.4 76.9 - - - +
346C ALA* 1.3 62.1 + - - +
347C LEU 2.9 6.6 + - - -
348C GLU* 3.0 40.9 + - + +
463C VAL* 3.9 9.0 - - - +
557C ASP* 3.0 27.1 - - + +
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Residues in contact with ALA 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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344C THR 3.3 0.4 + - - -
345C PRO* 1.3 72.2 - - - +
347C LEU* 1.3 58.7 + - - +
348C GLU 3.5 0.2 - - - -
456C LYS* 5.3 1.8 - - - +
462C GLY 4.1 18.2 - - - +
463C VAL* 3.6 3.8 - - - +
464C LEU* 2.9 36.1 + - + +
553C LEU 4.4 4.7 - - - +
554C VAL* 3.6 40.4 - - + +
555C HIS 4.9 3.4 - - - +
557C ASP* 2.7 14.7 + - - +
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Residues in contact with LEU 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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341C LEU 3.8 3.4 - - - +
342C LEU* 4.5 11.9 - - - +
344C THR* 3.0 32.5 + - + +
345C PRO 2.9 1.6 - - - -
346C ALA* 1.3 80.9 - - - +
348C GLU* 1.3 62.2 + - - +
349C ALA 3.2 1.2 + - - -
350C VAL* 3.2 25.6 + - + +
351C PHE* 4.2 23.9 + - + -
464C LEU* 3.7 32.3 - - + -
466C LEU* 4.8 0.4 - - + -
475C VAL* 4.6 6.1 - - + -
479C MET* 3.4 33.4 - - + -
550C TRP* 4.3 11.2 - - + -
554C VAL* 4.4 6.3 - - + -
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Residues in contact with GLU 348 (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 LEU 6.0 0.2 - - - -
343C SER 5.0 4.5 - - - +
344C THR 3.6 3.3 + - - +
345C PRO* 3.0 42.0 + - + +
346C ALA 3.5 1.0 + - - -
347C LEU* 1.3 74.9 - - - +
349C ALA* 1.3 66.4 + - + +
350C VAL 3.1 4.8 + - - -
463C VAL* 3.4 26.6 - - + +
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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