Contacts of the helix formed by residues 49 - 55 (chain A) in PDB entry 2CUY
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 PRO 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.4 1.1 - - - +
44A LEU* 5.3 0.7 - - + -
47A GLU 3.7 3.3 - - - +
48A GLY* 1.3 81.5 - - - +
50A GLU* 1.3 66.6 + - - +
51A GLU* 3.1 3.4 - - + +
52A ALA* 2.9 22.7 + - + +
53A LEU 2.9 19.2 + - - -
133B LEU* 6.1 3.1 - - + -
160B GLN* 3.2 47.1 - - + +
276B GLY* 5.2 8.3 - - - +
277B LEU* 5.2 3.4 - - + -
280B ARG* 4.4 23.1 - - + +
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Residues in contact with GLU 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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12A HIS* 4.7 7.6 + - - +
13A ARG* 4.1 11.8 - - - +
14A VAL* 2.8 47.4 + - + +
48A GLY* 3.5 3.4 - - - -
49A PRO* 1.3 73.4 - - - +
51A GLU* 1.3 54.3 + - - +
53A LEU* 3.3 5.6 + - + +
54A THR* 2.7 43.9 + - - +
10B GLY 4.4 10.0 - - - +
11B SER* 5.8 0.2 - - - -
271B GLY* 6.0 0.3 - - - -
272B GLU 5.2 1.2 + - - -
273B VAL* 4.0 39.3 + - + +
276B GLY* 5.8 1.8 - - - -
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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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49A PRO* 4.2 0.4 - - - +
50A GLU* 1.3 81.6 - - - +
52A ALA* 1.3 61.7 + - - +
54A THR* 3.2 17.8 + - - +
55A LEU* 3.3 10.0 + - - +
131B ALA* 3.5 24.2 - - + +
133B LEU* 3.5 28.0 - - + -
160B GLN* 4.2 14.6 + - - +
185B VAL* 3.5 39.2 - - + +
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Residues in contact with ALA 52 (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 LEU* 3.8 18.6 - - + -
49A PRO* 2.9 29.0 + - + +
51A GLU* 1.3 78.2 - - - +
53A LEU* 1.3 58.9 + - - +
55A LEU* 3.2 23.0 + - + +
58A ASN* 2.8 28.6 + - - +
133B LEU* 4.4 10.0 - - + +
134B LYS* 4.8 7.4 - - - +
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Residues in contact with LEU 53 (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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12A HIS* 3.7 15.7 - - + -
13A ARG* 3.7 33.0 - - - +
14A VAL* 3.8 9.9 - - + +
16A MET* 4.1 6.3 - - - -
41A LEU* 6.1 0.4 - - + -
44A LEU* 3.6 39.4 - - + +
45A MET* 4.0 4.7 - - + +
49A PRO 2.9 11.9 + - - +
50A GLU* 3.6 9.6 - - - +
52A ALA* 1.3 77.4 - - - +
54A THR* 1.3 59.7 + - - +
55A LEU 3.2 0.3 + - - -
58A ASN* 4.3 7.9 - - + +
59A GLN* 3.1 33.9 + - - +
62A ALA* 3.9 28.5 - - + -
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Residues in contact with THR 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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12A HIS* 2.8 29.2 + - + +
50A GLU* 2.7 30.8 + - - +
51A GLU* 3.4 15.0 + - - +
52A ALA 3.2 0.4 - - - -
53A LEU* 1.3 74.7 - - - +
55A LEU* 1.3 64.6 + - - +
56A THR* 3.1 2.8 + - - -
59A GLN* 3.0 16.9 + - - +
188A PRO 6.0 1.1 - - - +
185B VAL* 4.4 21.1 - - + -
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Residues in contact with LEU 55 (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 GLU 3.3 7.6 + - - +
52A ALA* 3.3 21.3 - - + +
53A LEU 3.1 1.2 - - - +
54A THR* 1.3 74.3 - - - +
56A THR* 1.3 67.0 + - - +
57A GLU* 3.1 7.2 - - + +
58A ASN* 2.7 28.6 + - - +
59A GLN 2.8 11.6 + - - -
119A GLN* 6.6 0.2 - - + -
133B LEU* 3.8 16.2 - - + -
134B LYS* 4.9 4.3 - - - +
183B ARG* 3.6 49.4 - - + +
184B VAL 4.4 10.5 - - - +
185B VAL* 4.1 20.2 - - + -
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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