Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 2PG4
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 VAL 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A SER* 3.7 29.6 - - - -
64A THR* 3.7 2.6 - - - +
65A LEU* 2.7 48.3 + - + -
66A SER* 3.1 25.8 + - - +
67A TYR 3.6 9.4 - - - +
68A ARG* 1.3 87.1 - - + +
70A LYS* 1.3 58.9 - - - +
96A EDO 3.3 8.5 - - - -
97A EDO 4.2 16.6 - - - +
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Residues in contact with LYS 70 (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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31A SER* 3.4 8.1 - - - -
32A LEU* 3.1 32.2 + - + +
62A GLU* 3.2 38.8 + - + +
63A GLU 3.3 15.4 - - - +
64A THR* 3.8 23.8 + - + +
65A LEU* 4.3 2.0 - - - -
68A ARG 5.5 1.3 - - - -
69A VAL* 1.3 77.6 - - - +
71A THR* 1.3 61.5 + - - +
96A EDO 2.9 16.5 + - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 4.1 5.7 - - + +
30A PRO* 2.4 37.1 + - - +
32A LEU* 4.0 4.7 - - - -
62A GLU* 3.3 10.6 - - - +
63A GLU* 2.8 49.5 + - + +
64A THR 5.0 0.4 - - - +
65A LEU* 3.8 26.7 - - + +
70A LYS* 1.3 74.1 - - - +
72A LEU* 1.3 77.2 + - - +
73A LYS* 5.0 7.4 - - + +
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Residues in contact with LEU 72 (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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16A ILE* 5.0 0.7 - - + -
20A LEU* 4.1 29.4 - - + +
30A PRO* 5.1 3.3 - - - +
32A LEU* 3.9 11.7 - - + -
35A ILE* 3.7 19.6 - - + +
46A PHE* 3.7 30.1 - - + -
51A LYS* 4.2 15.7 - - + -
54A LEU* 5.0 6.7 - - + -
55A ILE* 4.8 1.6 - - + -
60A VAL* 4.2 27.8 - - + -
61A LYS 3.5 1.1 - - - +
62A GLU* 4.0 24.2 - - + +
71A THR* 1.3 89.9 + - - +
73A LYS* 1.3 63.5 + - - +
74A LEU 4.3 0.5 + - - -
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Residues in contact with LYS 73 (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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24A GLU* 5.1 9.0 - - + +
29A GLU* 5.9 6.1 - - + +
60A VAL* 3.1 5.3 - - - -
61A LYS* 2.7 46.6 + - + +
63A GLU* 4.1 27.8 - - + +
71A THR* 4.2 7.3 - - + +
72A LEU* 1.3 75.3 - - - +
74A LEU* 1.3 69.4 + - - +
75A THR* 4.8 0.2 - - - +
79A ARG* 5.9 1.3 - - - +
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Residues in contact with LEU 74 (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 LEU* 4.3 13.5 - - + +
20A LEU* 3.8 31.1 - - + +
21A LEU* 3.7 34.8 - - + +
24A GLU* 3.7 29.3 + - - +
59A LEU 3.8 9.9 - - - +
60A VAL* 4.3 1.5 - - + +
72A LEU 4.2 1.0 + - - -
73A LYS* 1.3 80.3 - - - +
75A THR* 1.3 65.9 + - - +
78A GLY* 3.8 23.1 - - - +
79A ARG* 3.6 26.6 + - + +
82A ALA* 4.6 0.4 - - + -
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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