Contacts of the helix formed by residues 51 - 62 (chain A) in PDB entry 1Z83
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 SER 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU* 4.1 5.0 + - - +
47A VAL 4.6 0.8 + - - -
49A SER* 3.0 19.4 + - - -
50A GLY* 1.3 82.7 - - - +
52A ALA* 1.3 58.7 + - - +
53A ARG* 3.6 9.0 + - - +
54A GLY* 2.9 20.8 + - - +
55A LYS* 2.9 27.7 + - - +
165C GLU* 3.4 18.8 - - - -
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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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50A GLY 4.0 0.2 + - - -
51A SER* 1.3 69.3 - - - +
53A ARG* 1.3 66.5 + - - +
55A LYS* 3.1 20.7 + - - +
56A LYS* 3.1 14.5 + - - +
162C ALA* 6.4 1.3 - - + -
165C GLU* 3.2 25.9 + - - +
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Residues in contact with ARG 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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46A GLU* 3.0 29.6 - - - +
51A SER* 3.6 5.8 + - - +
52A ALA* 1.3 77.5 - - - +
54A GLY* 1.3 60.7 + - - +
56A LYS* 2.7 31.7 - - + +
57A LEU* 3.1 19.6 + - + +
71A THR* 5.3 12.3 + - + +
107B ARG* 3.7 48.6 - - - +
165C GLU* 4.7 0.8 + - - -
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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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46A GLU* 4.1 9.8 - - - +
47A VAL* 3.6 27.4 - - - +
51A SER* 2.9 21.5 + - - -
53A ARG* 1.3 77.4 - - - +
55A LYS* 1.3 55.7 + - - +
57A LEU* 3.3 5.8 + - - +
58A SER* 2.9 30.2 + - - -
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Residues in contact with LYS 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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47A VAL* 5.7 0.9 - - + -
50A GLY* 4.1 10.5 - - - +
51A SER 2.9 15.4 + - - +
52A ALA* 3.1 13.0 + - - +
54A GLY* 1.3 74.5 - - - +
56A LYS* 1.3 62.7 + - - +
58A SER* 3.3 7.4 + - - -
59A GLU* 3.0 40.0 + - - +
172C LYS* 3.9 26.4 - - - +
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Residues in contact with LYS 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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52A ALA 3.1 8.9 + - - +
53A ARG* 2.7 34.8 - - + +
55A LYS* 1.3 76.7 - - - +
57A LEU* 1.3 66.4 + - + +
59A GLU* 3.5 11.7 + - - +
60A ILE* 3.4 29.0 + - + +
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Residues in contact with LEU 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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43A LEU* 4.1 18.2 - - + +
46A GLU* 4.1 35.2 - - + +
47A VAL* 4.4 6.3 - - + -
53A ARG* 3.1 20.4 + - + +
54A GLY* 3.3 6.0 + - - +
56A LYS* 1.3 78.2 - - + +
58A SER* 1.3 65.3 + - - +
60A ILE* 3.1 10.7 + - + +
61A MET* 3.0 33.2 + - - +
67A VAL* 3.6 34.3 - - + +
68A PRO* 4.9 4.9 - - + -
71A THR* 4.0 13.5 - - + +
75A MET* 4.4 2.2 - - + -
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Residues in contact with SER 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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47A VAL* 3.7 28.1 - - - +
54A GLY 2.9 17.4 + - - -
55A LYS* 3.7 7.4 - - - -
57A LEU* 1.3 76.2 - - - +
59A GLU* 1.3 58.6 + - - +
61A MET* 3.2 7.0 + - - +
62A GLU* 2.8 59.5 + - - +
139A VAL* 4.4 9.0 - - - +
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Residues in contact with GLU 59 (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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55A LYS* 3.0 32.3 + - - +
56A LYS* 3.8 9.3 - - - +
57A LEU 3.2 0.4 - - - -
58A SER* 1.3 77.8 - - - +
60A ILE* 1.3 61.1 + - + +
62A GLU* 4.0 12.1 - - - +
63A LYS* 3.5 25.1 + - - +
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Residues in contact with ILE 60 (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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56A LYS* 3.4 20.2 - - + +
57A LEU* 3.1 13.3 + - + +
59A GLU* 1.3 78.1 - - + +
61A MET* 1.3 61.0 + - - +
62A GLU 3.2 0.4 - - - -
63A LYS* 3.3 9.9 + - - +
65A GLN* 3.2 44.4 + - + +
66A LEU 3.7 18.4 - - - +
67A VAL* 3.9 7.9 - - + +
68A PRO* 4.2 24.5 - - + -
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Residues in contact with MET 61 (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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40A GLY 4.3 1.6 - - - +
43A LEU* 4.0 24.9 - - + -
44A ARG* 3.8 28.3 - - + +
47A VAL* 4.2 15.3 - - - -
57A LEU* 3.0 25.7 + - - +
58A SER* 3.2 5.8 + - - +
60A ILE* 1.3 75.4 - - - +
62A GLU* 1.3 59.6 + - + +
63A LYS 3.2 2.7 - - - -
64A GLY* 3.3 14.2 + - - -
67A VAL* 4.2 7.0 - - + -
139A VAL* 6.4 0.7 - - + -
140A ASP* 3.6 22.6 - - + +
145A THR* 4.3 0.3 - - - +
149A ARG* 5.3 0.2 - - - -
631A AP5 3.3 53.1 + - - +
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Residues in contact with GLU 62 (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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58A SER* 2.8 44.6 + - - +
59A GLU* 3.8 12.7 + - - +
60A ILE 3.2 0.2 - - - -
61A MET* 1.3 78.2 - - + +
63A LYS* 1.3 59.7 + - - +
64A GLY 3.4 0.2 - - - -
139A VAL* 3.3 43.8 - - + +
142A ASN* 5.1 0.7 - - - +
145A THR* 3.0 24.8 + - - -
148A LYS* 5.3 1.6 + - - -
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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