Contacts of the strand formed by residues 55 - 63 (chain A) in PDB entry 2OZO
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 ARG 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MET* 4.3 1.3 - - - +
51A VAL* 3.7 3.2 - - - -
52A HIS 3.1 19.8 + - - +
53A ASP* 2.8 13.0 + - + +
54A VAL* 1.3 77.3 - - + +
56A PHE* 1.3 66.2 + - - +
57A HIS* 3.2 22.9 + - + -
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Residues in contact with PHE 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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21A GLU* 3.3 45.1 - - + +
24A LEU* 3.9 21.3 - - + -
25A LYS* 3.3 30.5 - - + -
29A MET* 3.3 40.4 - - + -
50A LEU 3.8 2.2 - - - -
51A VAL* 3.9 18.2 - - + -
55A ARG* 1.3 72.1 - - - +
57A HIS* 1.3 72.6 + - - +
58A HIS* 4.1 18.5 - + + +
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Residues in contact with HIS 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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48A LEU 3.6 0.7 - - - +
49A SER* 3.4 4.7 - - - -
50A LEU* 3.0 53.9 + - + +
52A HIS* 3.9 30.8 + - + +
55A ARG* 3.2 28.6 + - + -
56A PHE* 1.3 78.5 + - - +
58A HIS* 1.3 63.1 + - - +
59A PHE* 3.8 11.7 - + + -
95A PRO* 4.1 20.2 - - + +
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Residues in contact with HIS 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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17A ARG* 3.6 39.9 - - + +
20A ALA* 4.7 2.2 - - + -
21A GLU* 3.3 34.8 + - + +
24A LEU* 5.4 1.3 - - + -
37A ARG* 3.5 12.4 + - - +
47A VAL* 4.2 9.4 - - + -
48A LEU 3.5 1.3 - - - -
49A SER* 2.9 33.7 + - - -
56A PHE* 4.1 14.1 - + + +
57A HIS* 1.3 75.9 - - - +
59A PHE* 1.3 65.4 + - - +
60A PRO* 3.6 10.2 - - + +
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Residues in contact with PHE 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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47A VAL* 3.2 3.4 - - - -
48A LEU* 2.5 51.3 + - + +
50A LEU* 3.5 33.2 - - + -
57A HIS* 3.8 15.9 - + + -
58A HIS* 1.3 75.5 - - - +
60A PRO* 1.3 66.3 - - + +
61A ILE* 3.6 0.9 - - - +
71A ILE* 3.6 34.8 - - + -
93A GLY 5.7 1.1 - - - -
94A LEU* 3.8 28.7 - - + -
95A PRO* 3.9 17.7 - - + -
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Residues in contact with PRO 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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39A CYS* 5.4 7.6 - - - -
46A TYR 3.4 9.0 - - - +
47A VAL* 4.1 9.6 - - + -
58A HIS 3.6 9.0 - - - +
59A PHE* 1.3 88.6 - - + +
61A ILE* 1.3 62.5 + - - +
62A GLU 4.1 1.6 + - - -
71A ILE* 3.9 19.1 - - + +
72A ALA* 4.5 4.9 + - + +
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Residues in contact with ILE 61 (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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36A LEU* 4.1 17.9 - - + -
45A GLY* 3.2 6.2 - - - -
46A TYR* 2.7 50.8 + - + +
48A LEU* 3.7 31.0 - - + +
59A PHE 3.6 6.1 - - - +
60A PRO* 1.3 80.0 - - - +
62A GLU* 1.3 60.2 + - - +
69A TYR* 3.9 10.5 - - + -
70A ALA 3.9 19.5 - - - +
71A ILE* 3.7 11.7 - - + -
83A LEU* 3.6 37.7 - - + -
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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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42A SER* 5.5 3.8 - - - +
45A GLY* 4.7 3.1 - - - -
60A PRO 4.1 1.6 + - - -
61A ILE* 1.3 74.8 - - - +
63A ARG* 1.3 62.9 + - - +
64A GLN* 4.0 11.7 + - - +
69A TYR* 3.4 6.6 - - - +
70A ALA 3.3 33.5 + - - +
218A ALA* 5.6 7.6 - - + -
220A LYS* 4.9 8.3 - - + +
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Residues in contact with ARG 63 (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 4.8 2.0 - - - +
44A GLY* 4.2 14.8 - - - +
45A GLY* 4.9 1.2 - - - -
62A GLU* 1.3 75.1 - - - +
64A GLN* 1.3 87.2 + - - +
65A LEU* 3.5 28.7 + - - +
67A GLY* 4.1 12.6 - - - +
68A THR 3.5 7.9 - - - +
69A TYR* 3.5 37.5 - - + -
218A ALA* 5.3 0.5 - - - +
220A LYS* 3.6 26.4 + - - +
230A ASP* 2.9 45.1 + - - +
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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