Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 3OPY
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 LYS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP* 5.6 0.4 - - - +
22A PHE* 4.2 13.0 - - + -
40A TYR* 3.3 13.9 - - - +
41A VAL* 4.8 8.3 - - + -
57A SER* 4.0 0.7 - - - -
58A ILE* 1.3 80.5 - - + +
60A GLU* 1.3 62.4 + - - +
61A ILE* 6.1 0.9 - - + -
110A LEU* 2.8 54.0 + - + +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.5 0.7 - - - -
38A ARG 4.0 0.7 - - - +
39A SER* 3.3 4.3 - - - -
40A TYR* 2.8 50.7 + - + +
51A THR* 3.8 13.1 - - - +
52A GLY* 3.3 28.2 + - - -
57A SER* 3.4 14.1 - - - -
59A LYS* 1.3 82.3 - - - +
61A ILE* 1.3 63.7 + - - +
62A TRP* 3.2 26.7 + - + +
108A ILE 3.4 4.9 - - - +
109A LYS* 3.3 43.6 - - + +
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Residues in contact with ILE 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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22A PHE* 3.9 31.2 - - + -
23A GLU* 4.3 8.5 - - - +
26A PHE* 3.7 46.2 - - + -
36A ALA* 3.8 11.4 - - + -
38A ARG 3.6 2.9 - - - +
39A SER* 4.5 13.0 - - - -
40A TYR 5.8 0.7 - - - +
59A LYS* 6.1 0.7 - - + -
60A GLU* 1.3 76.9 - - - +
62A TRP* 1.3 65.0 + - - +
63A LEU* 3.7 19.3 + - + -
108A ILE* 2.9 38.2 + - + +
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Residues in contact with TRP 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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11A PHE* 6.2 2.2 - + - -
36A ALA* 3.5 1.4 - - - -
37A THR* 2.8 34.3 + - - -
38A ARG* 2.7 73.5 + - + +
50A LEU* 4.4 5.2 - - + -
51A THR* 3.4 32.3 - - - -
60A GLU* 3.2 24.0 + - - +
61A ILE* 1.3 81.5 - - - +
63A LEU* 1.3 57.4 + - - +
106A VAL 4.4 3.1 - - - -
107A VAL* 3.3 37.4 - - + +
109A LYS* 5.8 0.2 - - - -
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Residues in contact with LEU 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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26A PHE* 3.7 31.6 - - + +
29A TYR* 3.8 28.0 - - + -
30A THR* 4.5 4.7 - - - +
34A PHE* 3.6 20.9 - - + -
35A HIS 3.3 7.6 - - - +
36A ALA* 3.8 24.7 - - - +
61A ILE* 3.7 9.4 + - + +
62A TRP* 1.3 72.8 - - - +
64A GLU* 1.3 60.8 + - - +
105A GLY* 3.5 2.6 - - - -
106A VAL* 3.0 37.8 + - + +
108A ILE* 3.6 30.1 - - + -
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Residues in contact with GLU 64 (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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34A PHE* 3.7 4.5 - - - -
35A HIS* 2.8 39.5 + - - +
37A THR* 3.7 17.7 - - + +
63A LEU* 1.3 73.9 - - - +
65A SER* 1.3 76.3 + - - +
66A PHE* 3.3 41.3 + - + -
67A PRO* 3.6 11.0 - - - +
104A GLY 3.9 14.7 + - - -
105A GLY* 4.3 6.9 + - - -
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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