Contacts of the helix formed by residues 46 - 51 (chain A) in PDB entry 5E2Q
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 LEU 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TRP 3.7 7.4 + - - +
43A TYR 3.3 15.9 - - - +
44A GLY 3.0 0.6 - - - -
45A GLY* 1.3 72.4 - - - +
47A ALA* 1.3 63.3 + - - +
48A VAL 3.1 2.7 - - - -
49A LEU* 3.2 28.0 + - + +
50A LEU 4.1 0.7 + - - -
60A TYR* 3.6 39.0 - - + +
103A MET* 4.0 15.5 - - + -
254A ILE* 4.5 6.1 - - + -
700A PHE* 6.0 0.7 - - + -
704A PHE* 4.2 12.3 - - + -
711A LEU* 3.7 44.2 - - + -
715A LEU* 3.6 24.1 - - + +
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Residues in contact with ALA 47 (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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44A GLY* 3.0 17.2 + - - +
46A LEU* 1.3 76.9 - - - +
48A VAL* 1.3 63.4 + - - +
50A LEU* 3.0 19.0 + - - +
51A GLN* 3.0 18.7 + - - +
251A TYR* 4.2 31.4 - - + -
254A ILE* 4.3 13.9 - - + +
255A LEU* 6.2 2.0 - - + -
328A PHE* 4.4 13.9 - - + -
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Residues in contact with VAL 48 (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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45A GLY 3.2 20.2 - - - +
46A LEU 3.1 0.6 - - - -
47A ALA* 1.3 75.5 - - - +
49A LEU* 1.3 60.6 + - - +
51A GLN* 3.0 10.5 + - - +
52A THR* 2.6 36.4 + - - +
102A ASN 4.2 0.2 - - - +
103A MET* 3.6 22.0 - - + +
327A GLU* 3.4 30.7 - - + +
328A PHE* 3.2 30.3 - - + +
383A GLY* 3.9 12.3 - - - -
384A SER* 3.9 10.8 - - - -
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Residues in contact with LEU 49 (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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46A LEU* 3.2 24.9 + - + +
48A VAL* 1.3 78.3 - - - +
50A LEU* 1.3 58.7 + - - +
52A THR 3.3 7.6 + - - -
53A SER 3.5 5.5 - - - +
56A ALA* 3.3 35.7 - - - +
57A PRO* 3.6 16.7 - - + +
60A TYR* 3.6 36.6 - - + -
99A VAL* 4.8 4.3 - - + -
103A MET* 3.5 40.6 + - + +
104A GLY* 3.8 6.5 - - - +
715A LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 50 (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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47A ALA* 3.0 10.3 + - - +
49A LEU* 1.3 80.6 - - - +
51A GLN* 1.3 57.5 + - - +
52A THR 3.2 1.1 - - - -
53A SER 4.7 1.3 - - - +
57A PRO* 3.6 25.6 - - + -
170A THR* 2.9 24.1 + - - +
199A ARG* 3.3 16.0 + - - +
251A TYR* 3.6 33.9 - - + -
254A ILE* 4.0 13.0 - - + -
715A LEU* 4.4 8.3 - - + +
718A LEU* 3.7 45.1 - - + +
719A ALA* 4.1 11.2 - - - +
722A ASP* 5.5 2.2 - - - +
726A TRP* 5.2 0.9 - - - -
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Residues in contact with GLN 51 (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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47A ALA* 3.0 15.9 + - - +
48A VAL* 3.0 13.7 + - - +
50A LEU* 1.3 75.0 - - - +
52A THR* 1.3 57.5 + - - +
161A LEU* 6.1 0.5 - - - +
170A THR* 3.0 13.3 + - - -
171A TYR* 3.4 43.6 + - + +
198A THR 5.9 0.4 + - - -
199A ARG* 4.9 3.9 - - - +
251A TYR* 3.3 28.6 + - + +
314A PHE* 3.7 13.9 - - - -
319A ARG* 6.2 0.2 - - - -
326A GLY 3.1 24.2 + - - -
327A GLU* 3.6 12.8 - - + +
328A PHE* 3.0 30.9 + - - +
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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