Contacts of the strand formed by residues 246 - 251 (chain E) in PDB entry 1PQ3
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 ILE 246 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E HIS* 4.6 1.8 - - - -
138E CYS* 3.6 16.8 - - - +
140E VAL* 4.2 20.2 - - + -
235E PHE* 4.4 13.7 - - + -
238E LEU* 6.1 0.9 - - + -
239E ILE* 4.3 11.4 - - + -
244E ARG 3.6 11.9 - - - +
245E PRO* 1.3 72.8 - - - +
247E HIS* 1.3 70.2 + - - +
248E LEU 4.5 0.7 - - - +
283E ILE* 4.6 11.9 - - + +
286E THR* 3.6 26.9 - - - +
288E LEU* 2.9 31.9 + - + +
289E LEU* 3.6 12.9 - - + +
290E SER* 2.9 24.3 + - - -
291E ALA 3.5 4.9 + - - -
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Residues in contact with HIS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E THR* 3.8 18.2 - - - -
127E ILE* 3.4 35.2 - - + +
130E HIS* 3.1 28.3 + - + +
137E LEU* 4.3 4.5 - - + +
138E CYS 2.9 16.7 + - - +
139E VAL* 3.4 10.5 - - + +
140E VAL 2.9 27.5 + - - +
246E ILE* 1.3 76.0 - - - +
248E LEU* 1.3 64.4 + - - +
249E SER* 4.1 3.6 - - - -
291E ALA* 3.3 22.7 - - + +
293E ASP* 2.6 35.8 + - - -
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Residues in contact with LEU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 3.5 25.6 - - + +
142E VAL* 3.7 17.5 - - + -
246E ILE* 4.1 1.4 - - + -
247E HIS* 1.3 73.4 - - - +
249E SER* 1.3 53.6 + - - +
250E PHE* 3.7 21.2 + - + -
279E ILE* 5.2 0.7 - - + -
280E ALA* 5.2 4.0 - - - -
283E ILE* 3.3 38.1 - - + -
289E LEU* 4.1 14.3 - - + +
291E ALA 2.9 9.8 + - - +
292E LEU* 3.1 15.8 - - + +
293E ASP 2.7 31.7 + - - +
318E VAL* 5.4 0.4 - - + -
322E SER* 3.8 22.7 - - - +
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Residues in contact with SER 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E HIS* 2.6 30.5 + - - -
123E ALA* 4.0 1.2 - - - +
139E VAL* 4.9 0.4 - - - -
140E VAL 3.0 9.4 + - - +
141E TRP* 3.6 31.8 - - - -
142E VAL* 3.0 26.5 + - - +
247E HIS* 3.7 8.3 + - - -
248E LEU* 1.3 71.0 - - - +
250E PHE* 1.3 58.9 + - - +
251E ASP 4.0 0.2 - - - -
293E ASP* 3.0 24.6 + - - +
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Residues in contact with PHE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL* 3.5 38.1 - - + -
248E LEU* 3.7 18.1 + - + -
249E SER* 1.3 73.5 + - - +
251E ASP* 1.3 78.2 + - - +
252E ILE* 3.7 2.9 + - + -
254E ALA* 4.3 1.8 - - + -
255E PHE* 3.5 41.3 - + - -
271E LEU* 4.6 7.0 - - + -
276E GLY* 4.6 11.7 - - - -
279E ILE* 5.0 6.7 - - + -
280E ALA* 5.7 2.0 - - + -
292E LEU* 5.3 1.3 - - + -
293E ASP 2.7 18.6 + - - +
294E LEU* 3.4 18.2 - - + +
295E VAL* 3.1 27.0 + - - +
318E VAL* 3.7 22.7 - - + -
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Residues in contact with ASP 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E HIS* 3.5 6.2 + - - +
142E VAL 2.8 9.6 + - - +
143E ASP* 3.2 22.2 - - - +
249E SER 4.0 0.6 + - - -
250E PHE* 1.3 75.8 - - - +
252E ILE* 1.3 59.4 + - - +
253E ASP* 2.7 33.3 + - - +
254E ALA* 2.8 30.0 + - - +
295E VAL* 3.9 5.2 - - - -
296E GLU* 3.4 18.2 - - - +
508E MN 2.2 32.8 + - - +
509E MN 2.6 8.5 + - - -
555E S2C 2.8 6.2 + - - -
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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