Contacts of the helix formed by residues 308 - 315 (chain A) in PDB entry 1A8H
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 PRO 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 4.1 3.1 - - - -
20A LEU* 3.7 44.8 - - + +
23A ALA* 4.2 11.7 - - + -
85A LEU* 5.8 0.9 - - + -
306A VAL* 3.5 9.8 - - + +
307A ASP* 1.3 90.7 - - - +
309A PHE* 1.3 73.9 + - + +
311A LEU* 3.3 7.1 + - + +
312A LEU* 2.7 30.2 + - - +
320A LEU* 3.1 29.0 - - + +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.1 48.7 - - + -
19A HIS 4.3 0.7 - - - -
23A ALA* 5.0 4.0 - - + -
81A ALA* 3.7 30.3 - - + -
82A TRP* 5.1 1.6 - + - -
84A LEU* 4.4 21.5 - - + -
85A LEU* 4.3 17.7 - - + -
307A ASP* 2.8 17.3 + - - +
308A PRO* 1.3 92.8 - - + +
310A ALA* 1.3 64.9 + - - +
312A LEU* 3.5 12.6 + - + +
313A GLU* 3.3 20.4 + - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ASP* 3.5 27.3 + - + +
308A PRO 3.3 0.2 - - - -
309A PHE* 1.3 77.6 - - - +
311A LEU* 1.3 67.6 + - + +
313A GLU* 3.2 16.2 + - - +
314A LYS* 3.3 15.3 + - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL* 3.5 32.1 - - + -
307A ASP 3.3 9.0 + - - +
308A PRO* 3.5 11.0 - - + +
310A ALA* 1.3 85.5 - - + +
312A LEU* 1.3 55.7 + - - +
314A LYS* 3.4 5.3 + - + -
315A TYR* 3.1 38.9 + - + +
316A GLY 4.8 0.2 - - - +
320A LEU* 4.7 9.2 - - + +
323A TYR* 6.1 1.6 - - + -
337A SER 4.8 2.7 - - - +
338A GLU* 3.8 46.4 - - + +
341A LEU* 4.4 24.8 - - + +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.5 48.9 - - + +
85A LEU* 4.0 21.3 - - + -
308A PRO 2.7 20.5 + - - +
309A PHE* 3.7 14.6 - - + +
310A ALA 3.2 0.2 - - - -
311A LEU* 1.3 75.1 - - - +
313A GLU* 1.3 71.8 + - - +
316A GLY* 2.8 33.9 + - - -
317A ARG* 3.7 24.0 - - + +
320A LEU* 3.7 9.4 - - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PHE 3.3 10.1 + - - +
310A ALA* 3.2 10.6 + - - +
312A LEU* 1.3 94.5 - - - +
314A LYS* 1.3 60.6 + - - +
316A GLY 4.6 0.2 - - - -
500A LYS* 5.2 1.7 + - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ALA 3.3 11.7 + - - +
311A LEU* 3.7 7.2 - - + +
312A LEU 3.2 0.6 - - - -
313A GLU* 1.3 81.0 - - - +
315A TYR* 1.3 77.3 + - + +
338A GLU* 3.0 30.3 - - - +
342A ARG* 4.5 15.5 - - - +
500A LYS* 2.8 35.1 + - + +
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Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU* 3.1 21.7 + - + +
314A LYS* 1.3 90.4 - - + +
316A GLY* 1.3 62.4 + - - +
319A ALA* 3.6 25.3 + - + +
320A LEU 5.4 0.4 - - - +
338A GLU* 2.9 36.6 + - + +
341A LEU* 3.3 33.2 - - + -
342A ARG* 3.2 52.8 + - + +
345A TYR* 4.0 30.3 + + + -
497A PHE* 5.9 0.5 - - - -
500A LYS* 3.9 26.8 + - + +
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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