Contacts of the helix formed by residues 247 - 252 (chain B) in PDB entry 3Q02
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 LEU 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ALA 4.1 9.2 - - - +
239B ALA* 4.1 0.7 - - - -
240B PRO* 3.5 28.3 - - + -
246B PRO* 1.3 71.5 - - - +
248B SER* 1.3 57.9 + - - +
249B ALA 3.0 0.2 - - - -
250B LEU* 2.8 25.0 + - + -
251B THR* 2.9 18.8 + - - +
356B ARG* 3.4 11.4 - - - +
357B PRO* 3.7 15.5 - - + +
358B PHE* 3.4 42.2 - - - +
359B LEU* 3.8 21.1 - - + +
375B GLN* 4.3 11.9 - - + +
377B MET* 4.5 8.5 - - + -
382B CL 3.4 10.7 - - + +
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Residues in contact with SER 248 (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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28B LYS* 4.6 24.4 - - - +
246B PRO* 3.4 22.9 - - - +
247B LEU* 1.3 78.1 - - - +
249B ALA* 1.3 62.8 + - - +
251B THR* 3.7 10.3 - - - -
252B ASN* 3.0 43.4 + - - -
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Residues in contact with ALA 249 (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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215B THR* 4.5 16.5 - - + +
216B PRO* 5.2 0.3 - - - +
217B ASP* 6.1 0.9 - - - +
219B HIS* 5.5 5.4 - - + -
240B PRO* 5.5 1.1 - - + -
245B VAL* 4.0 18.4 - - + -
246B PRO* 2.9 20.9 + - + +
248B SER* 1.3 80.7 + - - +
250B LEU* 1.3 60.1 + - + +
252B ASN* 4.6 4.3 - - - +
253B ILE* 3.6 24.8 + - - +
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Residues in contact with LEU 250 (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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215B THR* 4.8 3.1 - - + -
221B TYR* 3.3 59.9 - - + +
238B ALA* 4.0 27.8 - - + +
239B ALA* 4.1 7.2 - - - +
240B PRO* 4.9 4.7 - - + -
246B PRO 4.3 0.2 + - - -
247B LEU* 2.8 13.9 + - + +
249B ALA* 1.3 80.1 - - - +
251B THR* 1.3 65.6 + - - +
252B ASN 3.3 0.2 - - - -
253B ILE* 3.3 27.9 - - + +
254B LEU* 3.3 11.8 - - + +
262B TRP* 4.5 5.4 - - + -
359B LEU* 3.9 19.3 - - + -
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Residues in contact with THR 251 (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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20B PHE* 4.2 14.1 - - + -
21B GLN* 2.9 27.8 + - + +
24B ALA* 3.7 29.8 - - + -
25B GLN* 5.5 1.8 - - + +
247B LEU* 2.9 22.0 + - - +
248B SER* 3.3 9.5 + - - -
250B LEU* 1.3 77.5 - - - +
252B ASN* 1.3 63.7 + - - +
253B ILE 3.0 1.6 + - - -
254B LEU* 3.1 22.6 + - + +
359B LEU* 4.2 9.9 - - - +
375B GLN* 4.3 9.3 + - - +
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Residues in contact with ASN 252 (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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21B GLN* 3.0 16.5 + - - +
25B GLN* 3.4 31.1 + - - +
248B SER* 3.0 31.6 + - - +
249B ALA* 4.6 5.6 - - - +
250B LEU 3.3 0.2 - - - -
251B THR* 1.3 79.7 - - - +
253B ILE* 1.3 60.3 + - + +
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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