Contacts of the helix formed by residues 304 - 308 (chain A) in PDB entry 1E1A
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 GLN 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 5.5 0.2 - - - +
77A GLN* 3.0 41.7 + - - +
78A CYS 5.4 2.6 - - - +
126A TYR* 4.2 1.3 - - - -
232A ASP* 3.6 18.3 + - - +
274A HIS* 3.2 33.4 - - + +
275A PHE 5.9 0.7 - - - +
302A LYS 3.3 8.1 + - - +
303A LYS* 1.3 78.1 - - - +
305A TYR* 1.3 65.4 + - - +
306A CYS* 3.1 18.1 - - - +
307A GLU* 2.9 34.0 + - - +
308A THR* 3.7 6.8 + - - +
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Residues in contact with TYR 305 (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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77A GLN* 5.5 1.0 - - - +
78A CYS 4.2 0.7 - - - +
79A ASP* 3.6 11.5 + - - -
80A ARG* 3.4 72.1 + - + +
81A ASP* 4.5 4.3 + - - -
124A PHE* 3.4 57.3 + + + +
125A ASP 3.4 15.0 - - - +
126A TYR* 4.0 20.0 - - + -
127A GLU 4.5 0.6 - - - -
128A GLY* 3.5 28.4 + - - -
160A THR* 5.8 0.2 - - - +
303A LYS 4.1 0.2 + - - -
304A GLN* 1.3 75.0 - - - +
306A CYS* 1.3 62.0 + - - +
308A THR* 2.7 30.8 + - - -
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Residues in contact with CYS 306 (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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25A PHE 4.0 11.2 - - - -
26A ASP 4.9 5.6 - - - -
27A LYS* 4.1 22.8 + - + +
78A CYS* 3.5 33.9 + - + +
79A ASP 3.4 20.0 - - - +
80A ARG* 4.0 11.2 - - - +
274A HIS* 6.1 0.7 - - - -
277A PRO* 6.0 2.5 - - - -
304A GLN* 3.1 18.4 - - - +
305A TYR* 1.3 79.2 - - - +
307A GLU* 1.3 68.0 + - - +
308A THR 3.4 5.1 + - - +
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Residues in contact with GLU 307 (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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275A PHE 5.6 0.7 - - - +
277A PRO* 3.4 41.7 - - + +
278A GLN* 4.4 8.0 + - - +
302A LYS 4.4 1.6 - - - +
303A LYS* 3.7 37.8 + - + +
304A GLN* 2.9 42.6 + - - +
306A CYS* 1.3 87.9 - - - +
308A THR* 1.3 62.5 + - - +
309A LEU* 4.9 5.6 - - - +
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Residues in contact with THR 308 (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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27A LYS* 5.7 0.9 + - - -
80A ARG* 3.3 30.4 + - - +
126A TYR* 3.9 32.5 + - + -
303A LYS* 4.9 9.6 - - + -
304A GLN 3.8 13.2 - - - +
305A TYR* 2.7 23.4 + - - +
306A CYS 4.0 2.4 - - - +
307A GLU* 1.3 83.0 - - - +
309A LEU* 1.3 68.0 + - - +
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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