Contacts of the helix formed by residues 44 - 52 (chain A) in PDB entry 4IXU
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 HIS 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLY* 2.9 14.2 + - - +
43A GLU* 1.3 102.4 + - + +
45A GLY* 1.3 62.8 + - - +
46A PRO* 3.4 1.6 - - - -
47A ALA* 3.4 13.1 + - + +
48A ALA* 3.1 22.2 + - - +
299A PRO* 3.9 14.6 - - + -
300A GLN* 3.4 31.5 + - + -
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Residues in contact with GLY 45 (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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42A VAL 3.1 5.9 + - - -
44A HIS* 1.3 78.1 - - - +
46A PRO* 1.3 69.1 - - - +
48A ALA* 3.1 4.3 + - - +
49A ILE* 2.9 29.0 + - - +
117A GLY 3.5 10.3 - - - -
297A VAL* 3.4 27.0 + - - -
299A PRO* 3.9 5.1 - - - +
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Residues in contact with PRO 46 (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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30A GLY* 4.1 4.7 - - - -
31A ALA 4.0 7.6 - - - +
32A PRO* 4.1 11.7 - - + -
43A GLU 3.4 15.0 - - - +
44A HIS 3.6 0.9 - - - -
45A GLY* 1.3 88.8 - - - +
47A ALA* 1.3 61.3 + - - +
49A ILE* 3.3 3.0 + - + +
50A ARG* 3.0 29.2 + - - +
70A ASP* 3.8 21.5 - - - +
116A LEU* 3.3 43.9 - - + +
117A GLY 3.2 13.2 - - - +
118A GLY 3.8 0.9 - - - +
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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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43A GLU 5.3 0.2 + - - -
44A HIS* 3.4 14.6 + - + +
45A GLY 3.3 0.6 - - - -
46A PRO* 1.3 79.9 - - - +
48A ALA* 1.3 57.2 + - - +
50A ARG* 3.3 10.1 + - - +
51A GLU* 2.9 50.0 + - + +
70A ASP* 4.4 9.3 + - - +
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Residues in contact with ALA 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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44A HIS 3.1 14.9 + - - +
45A GLY* 3.5 9.0 - - - +
47A ALA* 1.3 77.4 - - - +
49A ILE* 1.3 62.1 + - - +
51A GLU* 3.4 13.6 + - - +
52A ALA 3.1 16.8 + - - -
297A VAL* 4.7 4.3 - - + -
299A PRO* 4.0 23.1 - - + -
308A ALA 5.7 0.9 - - - +
312A ALA* 3.5 23.5 - - + +
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Residues in contact with ILE 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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45A GLY 2.9 23.8 + - - +
46A PRO 3.8 4.0 - - - +
48A ALA* 1.3 75.2 - - - +
50A ARG* 1.3 64.7 + - - +
52A ALA* 3.2 9.3 + - - -
53A GLY 3.7 0.9 + - - -
54A LEU* 3.7 13.5 + - + -
116A LEU* 4.1 30.3 - - + -
117A GLY 4.5 2.0 - - - +
294A LEU* 3.9 24.7 - - + +
297A VAL* 4.1 15.7 - - + -
312A ALA* 4.5 7.2 - - - +
315A ALA* 3.8 25.6 - - + -
316A VAL* 3.4 28.6 - - + +
319A ILE* 4.3 7.2 - - + -
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Residues in contact with ARG 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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28A VAL* 4.0 15.8 + - - +
30A GLY* 4.0 4.8 - - - +
46A PRO 3.0 20.5 + - - +
47A ALA* 3.7 8.1 - - - +
49A ILE* 1.3 77.5 - - - +
51A GLU* 1.3 58.1 + - + +
53A GLY* 2.9 21.0 + - - -
54A LEU* 3.7 11.3 + - + -
55A MET* 4.2 24.4 + - + +
67A ASP* 2.6 45.1 + - - -
69A GLY* 3.4 26.2 + - - -
70A ASP* 3.5 17.5 + - - -
116A LEU* 4.3 10.6 - - + +
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Residues in contact with GLU 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* 2.9 37.6 + - - +
48A ALA* 3.7 10.4 - - - +
49A ILE 3.3 0.2 - - - -
50A ARG* 1.3 77.3 - - + +
52A ALA* 1.3 60.0 + - - +
53A GLY* 3.0 4.8 + - - -
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Residues in contact with ALA 52 (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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48A ALA 3.1 12.9 + - - +
49A ILE 3.5 9.6 - - - +
50A ARG 3.1 1.4 - - - -
51A GLU* 1.3 76.3 - - - +
53A GLY* 1.3 58.4 + - - +
54A LEU 3.7 1.1 - - - -
57A ARG* 5.2 3.5 + - - +
312A ALA* 3.7 15.9 - - + +
313A ASN* 3.4 26.1 - - - +
316A VAL* 3.7 22.2 - - + +
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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
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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