Contacts of the helix formed by residues 49 - 55 (chain A) in PDB entry 2CX9
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 GLU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.8 16.8 + - - +
46A LYS* 3.1 25.0 + - - +
47A LEU 3.0 0.6 + - - -
48A ALA* 1.3 76.7 - - - +
50A PHE* 1.3 65.0 + - + +
51A GLY 3.1 3.4 + - - -
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Residues in contact with PHE 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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14A VAL* 5.4 9.5 - - + +
17A PRO* 4.3 10.3 - - + -
18A PHE* 3.7 49.4 - + + -
21A PHE* 3.5 44.4 - + + -
46A LYS 3.5 18.4 - - - -
47A LEU* 2.8 12.5 + - - +
49A GLU* 1.3 81.8 - - + +
51A GLY* 1.3 60.2 + - - +
52A VAL* 3.1 7.1 + - + +
64A ALA* 4.8 4.5 - - - +
66A LEU* 5.3 5.0 - - - +
74A MET* 5.4 4.5 - - - +
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Residues in contact with GLY 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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48A ALA 3.0 15.8 + - - -
49A GLU 3.1 2.4 + - - -
50A PHE* 1.3 79.0 - - - +
52A VAL* 1.3 62.2 + - - +
53A PHE 3.1 4.0 - - - -
54A GLY* 3.1 15.8 + - - -
55A ALA* 3.2 12.6 + - - -
63A GLY 6.0 0.7 - - - -
64A ALA* 3.6 15.5 - - - +
66A LEU* 5.8 0.4 - - - -
117A ALA 5.0 4.7 - - - -
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Residues in contact with VAL 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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18A PHE* 4.2 14.8 - - + -
47A LEU* 3.7 40.0 + - + +
48A ALA 4.5 0.2 + - - -
50A PHE* 3.1 5.1 - - + +
51A GLY* 1.3 78.0 - - - +
53A PHE* 1.3 67.7 + - + +
54A GLY 3.2 2.1 + - - -
55A ALA* 3.9 9.1 + - + +
71A PHE* 4.5 1.5 - - + -
74A MET* 3.5 41.1 - - + -
75A VAL 5.8 0.2 - - - +
78A ILE* 4.5 2.7 - - + -
89A VAL* 3.7 20.1 - - + +
93A ASN* 2.8 22.7 + - - +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.7 44.2 - - + -
47A LEU* 3.9 17.0 - - + -
48A ALA* 4.0 10.5 - - + +
51A GLY* 3.1 1.6 - - - -
52A VAL* 1.3 85.7 - - + +
54A GLY* 1.3 55.7 + - - +
85A LEU* 5.7 0.4 - - + -
88A THR* 4.3 12.6 - - + -
89A VAL* 3.9 24.0 - - + -
92A HIS* 2.8 63.6 + + + +
93A ASN* 3.5 8.8 - - - +
97A THR* 4.7 1.9 + - - +
116A LEU 3.1 8.2 - - - +
117A ALA* 3.5 12.3 + - - +
119A GLY* 4.1 11.2 - - - +
122A LEU* 3.7 24.5 - - + -
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Residues in contact with GLY 54 (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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51A GLY 3.1 7.5 + - - -
53A PHE* 1.3 77.4 - - - +
55A ALA* 1.3 63.0 + - - +
56A LEU 3.4 2.7 - - - -
57A VAL* 3.2 17.7 + - - -
63A GLY* 3.4 2.9 - - - -
64A ALA 2.9 24.2 + - - -
93A ASN* 3.7 3.4 - - - -
97A THR* 5.4 0.2 - - - -
117A ALA* 3.4 25.3 + - - -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 3.2 8.2 + - - +
52A VAL 3.9 5.8 - - - +
54A GLY* 1.3 79.0 - - - +
56A LEU* 1.3 55.6 + - - +
64A ALA* 4.2 5.2 - - - -
65A GLY 3.5 2.3 + - - -
66A LEU* 2.8 37.7 + - + +
71A PHE* 3.3 36.1 - - + -
74A MET* 3.8 18.2 - - + -
93A ASN* 3.2 8.3 + - - +
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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