Contacts of the helix formed by residues 44 - 48 (chain A) in PDB entry 3L73
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 GLY 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 1.3 77.3 - - - +
45A SER* 1.3 66.8 + - - -
46A ARG 3.1 3.1 - - - -
47A TYR* 2.9 22.8 + - - +
48A GLU* 3.4 8.7 + - - +
56A GLY* 6.0 0.9 - - - -
90A THR* 4.5 3.4 - - - -
91A SER 3.3 10.1 - - - -
92A ARG 3.2 11.2 - - - -
95A THR* 4.4 2.7 - - - -
185A TYR* 3.5 13.4 + - - -
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY* 1.3 70.4 - - - -
46A ARG* 1.3 64.6 + - - +
48A GLU* 2.9 44.3 + - - +
53A ASN* 4.2 2.6 + - - -
90A THR* 5.3 0.6 + - - -
91A SER 3.3 4.9 + - - -
92A ARG* 3.1 28.0 + - - +
162A ALA* 4.7 5.9 + - - +
165A ARG* 4.0 12.4 + - - -
166A THR 3.8 16.8 - - - -
167A VAL* 3.8 16.5 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 1.3 81.2 + - - +
47A TYR* 1.3 61.4 + - + +
48A GLU 3.4 7.1 + - - +
92A ARG* 2.7 21.0 + - - +
93A GLU* 2.6 44.1 + - + -
162A ALA* 3.5 30.7 - - + +
163A LEU* 4.0 27.2 - - + +
231A LEU* 3.8 32.1 + - + +
232A PRO 3.1 25.4 + - - -
233A ARG* 3.9 0.8 - - - +
234A CYS* 3.8 22.2 - - - +
314A TYR* 4.8 1.2 - - - +
315A SER* 3.1 2.0 + - - -
316A ASP* 2.5 41.2 + - - +
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Residues in contact with TYR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY* 3.2 28.1 + - - -
43A ALA* 3.6 8.1 - - - -
44A GLY* 2.9 29.2 + - - +
46A ARG* 1.3 74.2 - - - +
48A GLU* 1.3 66.5 + - - +
52A ASN* 4.9 1.2 + - - -
92A ARG 4.3 1.6 - - - -
93A GLU* 4.2 22.1 + - + +
189A HIS* 3.7 33.1 + + + +
194A ARG* 3.8 18.8 - - - -
229A PRO* 5.0 14.4 + - + -
231A LEU* 3.4 42.0 - - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.5 5.2 - - - +
45A SER* 2.9 35.3 + - - +
46A ARG 3.5 8.5 - - - +
47A TYR* 1.3 84.7 - - - +
49A ASN* 1.3 61.4 + - - +
52A ASN* 3.1 16.6 - - - +
53A ASN* 2.6 37.0 + - - +
54A GLY* 2.6 25.1 + - - -
55A ALA 2.9 13.5 + - - -
56A GLY* 3.1 12.5 + - - -
57A TYR 4.6 0.3 + - - -
162A ALA* 5.0 1.4 - - - +
165A ARG* 4.3 10.0 + - - -
167A VAL 4.5 1.6 - - - +
185A TYR* 4.1 12.6 - - + -
189A HIS* 5.6 0.2 - - - -
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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
------------------------------------------------------------
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