Contacts of the helix formed by residues 245 - 250 (chain B) in PDB entry 1P7L
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 LYS 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A GLY* 5.3 0.6 + - - -
8B GLU* 5.2 2.5 - - - -
10B VAL* 3.8 39.5 - - + -
14B HIS* 3.9 4.9 - - + -
16B ASP* 3.6 20.0 - - + +
17B LYS* 3.8 20.6 - - + -
20B ASP* 4.5 4.0 - - - +
165B LYS* 5.4 0.4 - - - +
243B GLY* 3.5 1.2 - - - -
244B ARG* 1.3 82.6 + - - +
246B ILE* 1.3 66.4 + - - +
247B ILE 3.0 3.7 + - - -
248B VAL* 3.3 26.0 + - + -
249B ASP* 2.9 29.1 + - - +
484B ANP 2.8 56.4 + - - -
487B MG 3.4 4.7 - - - -
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Residues in contact with ILE 246 (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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244A ARG* 6.0 3.4 - - - +
246A ILE* 4.8 28.9 - - + -
259A GLY* 5.7 1.2 - - - -
243B GLY* 4.6 12.2 - - - +
244B ARG* 3.4 2.9 - - - +
245B LYS* 1.3 77.8 - - - +
247B ILE* 1.3 75.7 + - + +
249B ASP* 3.3 16.2 + - - +
250B THR* 3.0 14.9 + - - +
257B HIS* 3.2 36.9 - - + +
259B GLY* 3.4 42.6 - - - +
260B GLY 3.9 11.0 - - - +
261B ALA* 4.4 8.7 - - + +
262B PHE* 5.6 0.2 - - - -
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Residues in contact with ILE 247 (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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121A LEU* 5.9 1.8 - - + -
257A HIS* 3.2 28.7 - - + +
258A GLY* 3.5 28.9 - - - +
259A GLY* 3.6 7.7 - - - +
8B GLU* 6.5 1.1 - - + -
245B LYS 3.0 1.2 + - - -
246B ILE* 1.3 93.4 - - + +
248B VAL* 1.3 67.8 + - + +
249B ASP 3.0 1.8 - - - -
250B THR* 3.0 18.5 + - - +
252B GLY* 3.1 17.0 + - - -
253B GLY* 3.2 31.4 - - - +
255B ALA 5.6 2.7 - - - +
256B ARG 5.8 0.2 - - - -
257B HIS* 3.8 22.4 - - + +
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Residues in contact with VAL 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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258A GLY 5.6 0.7 - - - +
8B GLU* 3.5 41.5 - - + +
9B SER* 4.1 8.7 - - - +
10B VAL* 4.3 12.1 - - + -
17B LYS* 4.5 7.6 - - - +
138B ILE* 3.8 12.4 - - - +
142B HIS* 3.1 39.4 + - + -
245B LYS* 3.3 39.2 + - + +
247B ILE* 1.3 78.6 - - + +
249B ASP* 1.3 64.2 + - - +
250B THR 3.3 0.2 + - - -
252B GLY* 4.9 0.2 - - - -
357B TYR 6.1 0.2 - - - +
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Residues in contact with ASP 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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17B LYS* 2.6 31.3 + - - -
20B ASP* 3.7 15.8 - - - +
243B GLY* 5.7 2.4 - - - -
245B LYS 2.9 24.3 + - - +
246B ILE* 3.3 11.2 + - - +
247B ILE 3.0 0.2 - - - -
248B VAL* 1.3 79.7 - - - +
250B THR* 1.3 58.5 + - + +
262B PHE* 4.5 14.4 + - + +
263B SER* 5.1 1.0 + - - -
358B GLY* 3.7 4.0 + - - -
359B HIS* 2.9 62.5 + - + +
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Residues in contact with THR 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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123B PHE 5.7 1.6 - - - +
134B MET* 3.3 21.7 - - - +
138B ILE* 4.5 4.3 - - - +
142B HIS* 5.4 1.0 + - - -
246B ILE 3.0 15.4 + - - +
247B ILE* 3.0 16.3 + - - +
248B VAL 3.1 1.7 - - - +
249B ASP* 1.3 78.3 - - - +
251B TYR* 1.3 81.6 + - + -
252B GLY 3.8 0.4 - - - -
256B ARG 5.6 0.6 + - - -
257B HIS* 3.7 17.2 + - + +
262B PHE* 3.7 33.4 - - + -
358B GLY* 5.6 0.7 - - - -
359B HIS 5.4 0.2 + - - -
360B PHE* 3.7 18.5 + - + +
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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