Contacts of the helix formed by residues 351 - 355 (chain D) 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 TYR 351 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D ASP* 3.7 11.1 - - + +
27D LEU* 3.4 22.7 - - + -
28D ASP* 3.1 8.7 + - - +
31D LEU* 4.1 9.4 - - + -
267D PRO* 3.3 11.1 - - + +
272D ARG* 3.4 37.5 - - - +
276D TYR* 3.7 26.2 - + - -
346D LEU* 2.7 45.4 + - - +
348D HIS 3.3 21.3 - - - -
350D ILE* 1.3 93.6 - - + +
352D LYS* 1.3 59.7 + - - +
353D GLU 3.1 2.2 - - - -
354D THR* 2.6 39.5 + - + +
355D ALA 3.3 0.9 + - - -
367D TRP* 4.5 4.3 - + - -
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Residues in contact with LYS 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLN* 4.2 16.5 - - + +
24D ASP* 3.7 20.5 - - - +
25D ALA* 3.7 20.7 - - + +
28D ASP* 2.9 24.9 + - + +
70D ASN* 6.2 0.4 - - - +
71D THR* 3.2 31.7 + - + +
74D GLU* 3.8 21.3 + - - +
351D TYR* 1.3 70.2 - - - +
353D GLU* 1.3 56.8 + - - +
355D ALA* 2.8 31.3 + - - +
356D ALA 4.4 0.3 + - - -
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Residues in contact with GLU 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 4.6 0.2 + - - -
350D ILE* 4.4 12.9 + - - +
351D TYR 3.1 0.6 - - - +
352D LYS* 1.3 81.7 - - - +
354D THR* 1.3 58.0 + - - +
355D ALA 3.3 0.4 + - - -
356D ALA* 4.1 3.6 + - - +
362D ARG* 3.2 27.3 + - - +
364D HIS* 2.7 35.2 + - - -
365D PHE* 3.4 19.7 - - + -
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Residues in contact with THR 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 4.9 0.3 + - - -
24D ASP* 3.8 0.7 - - - +
272D ARG* 3.1 28.0 - - - +
276D TYR* 3.9 3.1 - - - +
350D ILE 4.5 2.7 + - - -
351D TYR* 2.6 32.8 + - + +
353D GLU* 1.3 73.5 - - - +
355D ALA* 1.3 59.1 + - - +
356D ALA 3.3 3.8 + - - -
358D GLY 4.0 7.2 - - - +
359D HIS* 3.2 41.4 + - + +
362D ARG* 4.4 2.5 - - - +
365D PHE* 3.4 29.0 - - - -
367D TRP* 3.9 8.5 - - - -
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 2.6 38.4 + - - +
20D ASP* 3.9 9.7 - - - +
21D GLN* 3.7 35.2 - - + +
24D ASP* 4.1 11.2 - - + +
263D SER* 4.1 7.2 - - - +
352D LYS 2.8 16.6 + - - +
354D THR* 1.3 78.7 - - - +
356D ALA* 1.3 53.4 + - - +
359D HIS* 4.7 1.3 - - - -
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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