Contacts of the helix formed by residues 238 - 244 (chain I) in PDB entry 5G04
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 238 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I LEU* 6.0 0.2 - - + -
210I LEU* 4.6 6.3 - - + +
214I LEU 2.1 39.9 + - - +
215I LYS 2.9 18.1 + - - +
216I SER* 3.5 0.7 + - - -
217I LEU* 4.1 26.9 - - + +
236I LEU* 3.9 1.5 + - + +
237I GLU* 1.3 74.4 - - - +
239I ASN* 1.3 62.4 + - - +
240I LEU 3.3 2.9 - - - -
241I LEU* 3.6 15.2 + - + -
242I TYR* 3.5 11.4 + - - +
548I MET* 3.7 35.9 - - + -
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Residues in contact with ASN 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LYS* 5.1 1.1 - - - +
237I GLU* 3.5 22.2 + - + +
238I THR* 1.3 75.1 - - - +
240I LEU* 1.3 78.5 + - - +
242I TYR* 3.5 8.4 + - - +
243I SER* 3.1 30.2 + - - -
547I SER* 3.7 24.3 + - - +
548I MET* 5.9 0.2 - - - +
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Residues in contact with LEU 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I THR 3.3 0.4 - - - -
239I ASN* 1.3 100.0 + - - +
241I LEU* 1.3 64.2 + - - +
243I SER* 3.4 4.8 + - - +
244I PHE* 3.2 47.1 + - + +
378I PRO* 3.3 35.2 - - + +
379I LEU* 4.7 8.4 - - + +
543I VAL* 5.0 2.2 - - + +
544I ILE* 5.1 10.3 - - + +
547I SER* 3.3 37.9 - - - +
548I MET* 6.6 0.4 - - + -
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Residues in contact with LEU 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I ILE* 3.9 27.6 - - + -
187I LEU* 4.3 9.9 - - + -
195I ILE* 4.9 10.1 - - + -
196I ALA* 5.5 0.2 - - + -
210I LEU* 4.8 3.1 - - + -
214I LEU* 4.4 24.4 - - + +
238I THR* 3.6 21.0 + - + +
239I ASN 3.4 0.6 - - - -
240I LEU* 1.3 79.9 - - - +
242I TYR* 1.3 61.4 + - - +
244I PHE 4.1 0.7 - - - +
245I LEU* 3.7 21.1 + - - +
248I VAL* 4.4 30.9 - - + +
379I LEU* 6.2 0.4 - - + -
544I ILE* 3.9 26.9 - - + -
548I MET* 4.0 18.7 - - + +
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Residues in contact with TYR 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I ASP* 3.4 31.9 - - + +
214I LEU* 4.2 3.5 + - - +
215I LYS* 3.4 49.7 + - + -
238I THR 3.5 11.7 + - - +
239I ASN* 3.7 11.0 - - - +
240I LEU 3.2 0.4 - - - -
241I LEU* 1.3 80.1 - - - +
243I SER* 1.3 72.9 + - - +
244I PHE 3.5 0.2 + - - -
245I LEU* 3.6 14.4 + - - +
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Residues in contact with SER 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I ASN* 3.1 18.0 + - - -
240I LEU* 3.4 4.2 + - - +
242I TYR* 1.3 86.4 - - - +
244I PHE* 1.3 90.1 + - - +
245I LEU 3.6 2.1 + - - -
246I PRO* 4.8 2.8 - - - +
247I GLU* 4.4 4.0 - - - +
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Residues in contact with PHE 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I LEU* 3.2 27.4 + - + +
241I LEU 4.1 4.0 - - - -
243I SER* 1.3 107.0 + - - +
245I LEU* 1.3 56.8 + - - +
247I GLU* 3.2 32.4 - - + +
248I VAL* 2.9 30.0 + - - +
374I GLN* 5.0 8.5 - - - -
375I LYS* 4.0 30.3 - - + -
378I PRO* 3.8 32.8 - - + -
379I LEU* 3.9 16.6 - - + -
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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