Contacts of the helix formed by residues 247 - 252 (chain I) in PDB entry 3PB1
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I ALA 4.2 2.5 - - - +
240I PRO* 4.2 8.5 - - + -
245I VAL 3.8 1.2 + - - -
246I PRO* 1.3 72.2 - - - +
248I SER* 1.3 54.0 + - - +
250I LEU* 2.8 44.2 + - + +
251I THR* 3.2 16.1 + - + +
356I ARG* 4.2 4.6 - - - +
357I PRO* 3.5 32.1 - - + +
358I PHE 3.8 11.0 - - - -
359I LEU* 4.0 28.0 - - + +
375I GLN* 3.8 20.6 - - + +
377I MET* 3.3 32.5 - - + -
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Residues in contact with SER 248 (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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28I LYS* 3.1 36.9 + - - -
246I PRO* 3.4 16.2 - - - +
247I LEU* 1.3 78.2 - - - +
249I ALA* 1.3 57.4 + - - +
251I THR* 3.8 12.3 - - - +
252I ASN* 2.9 49.7 + - - -
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Residues in contact with ALA 249 (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 THR* 4.1 15.8 - - + +
217I ASP* 5.2 8.1 - - - +
219I HIS* 5.4 3.6 - - - +
245I VAL* 3.7 20.2 - - + -
246I PRO* 3.1 19.7 + - + +
247I LEU 3.0 0.6 - - - -
248I SER* 1.3 80.6 + - - +
250I LEU* 1.3 64.1 + - + +
252I ASN* 4.2 5.6 + - - +
253I ILE* 3.7 22.9 - - - +
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Residues in contact with LEU 250 (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 THR* 4.1 8.7 - - + -
221I TYR* 3.6 54.7 - - + -
238I ALA* 3.8 14.6 - - + +
239I ALA* 3.7 29.2 - - - +
240I PRO* 3.9 15.7 - - + -
245I VAL* 5.6 0.2 - - + -
247I LEU* 2.8 16.9 + - + +
249I ALA* 1.3 83.5 - - + +
251I THR* 1.3 64.2 + - - +
253I ILE* 3.0 24.2 + - - +
254I LEU* 3.3 13.2 + - + +
262I TRP* 5.5 1.6 - - + -
359I LEU* 3.8 11.7 - - + -
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Residues in contact with THR 251 (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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20I PHE* 5.0 1.8 - - - -
21I GLN* 3.0 25.8 + - - +
24I ALA* 3.9 21.6 - - - +
25I GLN* 4.6 8.1 - - - +
247I LEU* 3.2 22.0 + - + +
248I SER* 3.8 11.7 - - - +
250I LEU* 1.3 74.9 - - - +
252I ASN* 1.3 61.7 + - - +
253I ILE 3.3 1.0 + - - -
254I LEU* 3.5 26.8 + - - +
359I LEU* 4.3 10.5 - - + +
375I GLN* 4.0 20.0 - - - +
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Residues in contact with ASN 252 (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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21I GLN* 3.9 7.8 + - - -
25I GLN* 3.0 33.9 + - - +
248I SER* 2.9 36.4 + - - +
249I ALA* 4.4 6.7 - - - +
251I THR* 1.3 78.2 + - - +
253I ILE* 1.3 61.5 + - + +
254I LEU 3.6 0.2 - - - -
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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