Contacts of the helix formed by residues 51 - 58 (chain A) in PDB entry 4OQZ
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 THR 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.6 9.0 - - - +
49A ALA* 3.3 7.5 - - - +
50A ALA* 1.4 90.4 - - + +
52A PRO* 1.4 74.2 - - - +
53A GLU* 3.4 21.2 + - - +
54A GLN* 3.4 25.8 + - + +
55A ALA* 3.3 15.1 + - - +
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Residues in contact with PRO 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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8A ILE* 4.6 1.7 - - + +
31A TRP* 3.9 37.6 - - + -
51A THR* 1.4 83.4 - - - +
53A GLU* 1.4 70.0 + - - +
55A ALA* 3.3 9.7 + - + +
56A LEU* 2.9 37.5 + - + +
75A VAL* 3.7 41.5 - - + +
79A ALA* 4.7 2.2 - - + -
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Residues in contact with GLU 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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51A THR* 3.3 18.4 + - - +
52A PRO* 1.4 90.0 - - - +
54A GLN* 1.4 57.6 + - + +
56A LEU* 3.3 6.8 + - - +
57A SER* 2.9 36.5 + - - -
75A VAL 4.8 0.9 - - - +
78A GLY* 4.1 11.8 - - - +
79A ALA* 3.7 34.7 + - - +
82A ALA* 3.8 7.6 - - + +
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Residues in contact with GLN 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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29A THR* 4.6 1.5 - - - +
49A ALA* 4.2 11.2 - - + -
50A ALA* 4.9 4.9 - - + +
51A THR* 3.4 22.7 + - + +
53A GLU* 1.4 78.5 - - + +
55A ALA* 1.3 64.0 + - - +
57A SER* 3.8 9.6 + - - -
58A ALA* 3.4 24.6 + - - +
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Residues in contact with ALA 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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6A THR* 2.9 39.3 + - + +
8A ILE* 4.1 5.6 - - + -
29A THR* 4.1 7.2 - - - -
30A LEU 4.0 4.3 - - - +
31A TRP* 3.9 24.7 - - + -
49A ALA* 3.7 11.1 - - + +
51A THR 3.3 10.8 + - - +
52A PRO 3.3 10.2 + - - +
54A GLN* 1.3 79.3 - - - +
56A LEU* 1.4 59.6 + - - +
58A ALA* 3.6 5.2 - - - +
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Residues in contact with LEU 56 (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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8A ILE* 4.1 10.3 - - + -
52A PRO* 2.9 23.1 + - + +
53A GLU 3.5 4.3 - - - +
55A ALA* 1.4 72.2 - - - +
57A SER* 1.3 59.0 + - - +
58A ALA 3.1 6.6 + - - -
59A ASN 3.0 25.3 + - - +
62A VAL* 3.9 32.9 - - + +
64A LEU* 5.7 1.1 - - + -
75A VAL* 5.5 3.6 - - + -
76A LEU* 5.5 6.5 - - + -
79A ALA* 3.6 30.7 - - + +
82A ALA* 3.6 27.1 - - + +
83A VAL* 4.7 8.1 - - + -
86A ARG* 3.2 9.6 - - - -
88A LEU* 4.6 19.5 - - + -
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Residues in contact with SER 57 (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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53A GLU 2.9 20.3 + - - -
54A GLN* 3.8 12.6 + - - -
56A LEU* 1.3 74.4 - - - +
58A ALA* 1.3 59.5 + - - +
59A ASN 3.3 0.8 + - - -
82A ALA* 4.2 10.9 - - - +
86A ARG* 3.7 26.2 + - - +
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Residues in contact with ALA 58 (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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29A THR* 3.9 20.2 - - + +
54A GLN 3.4 17.6 + - - +
55A ALA 3.6 9.2 - - - +
56A LEU 3.1 1.6 - - - -
57A SER* 1.3 77.7 - - - +
59A ASN* 1.4 77.5 + - - +
86A ARG* 5.1 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
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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