Contacts of the strand formed by residues 72 - 78 (chain A) in PDB entry 2PQG
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 TRP 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.8 51.9 + - + +
23A PHE* 3.2 17.1 + - - -
68A VAL* 6.4 0.2 - - + -
69A PRO* 3.2 48.1 + - + -
70A GLU 4.8 0.9 - - - -
71A LEU* 1.3 79.0 - - - +
73A LEU* 1.3 59.2 + - - +
74A TYR* 3.6 15.7 - + + -
87A ALA* 3.9 19.5 - - + -
88A ILE 3.6 22.7 - - - -
89A ARG 4.0 3.4 - - - -
90A MET* 4.2 0.2 - - - -
96A VAL* 3.4 42.6 - - + -
116A LEU* 4.4 17.7 - - + -
117A LEU* 4.0 12.1 - - + -
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Residues in contact with LEU 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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23A PHE* 3.5 30.1 - - + +
25A GLU* 3.4 30.3 - - + -
43A VAL* 3.8 22.2 - - + -
47A VAL* 4.1 11.2 - - + -
72A TRP* 1.3 72.8 - - - +
74A TYR* 1.3 64.6 + - - +
75A THR* 3.7 13.6 + - + -
86A LEU 3.4 1.2 - - - +
88A ILE* 2.8 52.3 + - + +
90A MET* 4.1 8.9 - - + +
93A LEU* 4.6 6.1 - - + -
209A LEU* 4.0 18.6 - - + -
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Residues in contact with TYR 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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22A LYS 3.6 16.8 - - - -
23A PHE 2.9 15.0 + - - +
24A THR* 3.1 15.4 - - - +
25A GLU 2.6 33.8 + - - +
72A TRP* 3.6 32.9 - + + -
73A LEU* 1.3 78.2 - - - +
75A THR* 1.3 56.7 + - - +
76A GLU 4.0 0.2 - - - -
85A THR* 3.6 22.9 - - + -
86A LEU 3.4 6.1 - - - -
87A ALA* 4.6 6.5 - - + +
105A TRP* 3.5 33.9 - + - -
117A LEU* 5.4 4.3 - - - +
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Residues in contact with THR 75 (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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25A GLU* 3.3 15.5 - - + -
39A PHE* 4.3 18.6 - - + -
43A VAL* 4.8 2.7 - - + -
73A LEU* 3.7 30.3 + - + -
74A TYR* 1.3 76.3 - - - +
76A GLU* 1.3 59.8 + - - +
77A LEU* 3.7 6.6 + - - +
85A THR* 3.5 2.3 - - - -
86A LEU* 2.8 63.6 + - - +
88A ILE* 4.0 9.6 - - + +
205A VAL* 4.3 6.4 - - + +
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Residues in contact with GLU 76 (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 THR* 4.8 6.3 - - + +
25A GLU 2.7 14.8 + - - +
26A ILE* 3.4 21.3 - - + +
27A PHE 2.9 26.3 + - - +
74A TYR 4.0 1.2 + - - -
75A THR* 1.3 71.8 - - - +
77A LEU* 1.3 62.1 + - - +
78A LYS* 3.1 37.6 + - + +
83A SER* 3.9 12.5 + - - +
84A ILE 3.4 12.3 - - - +
85A THR* 3.8 18.6 + - + +
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Residues in contact with LEU 77 (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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27A PHE* 3.6 32.8 - - + -
29A VAL* 4.1 5.6 - - + -
39A PHE* 4.8 9.6 - - + -
75A THR* 4.4 11.9 - - - +
76A GLU* 1.3 74.4 - - - +
78A LYS* 1.3 60.3 + - - +
83A SER* 3.2 4.0 - - - -
84A ILE* 2.9 35.4 + - + +
86A LEU* 3.8 28.5 - - + -
149A MET* 4.5 8.7 - - - -
153A VAL* 3.4 25.2 - - + +
201A LEU* 3.9 27.8 - - + -
205A VAL* 4.6 8.5 - - + -
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Residues in contact with LYS 78 (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 ILE* 3.4 31.6 - - + -
27A PHE 3.0 9.6 + - - +
28A PRO* 3.5 8.9 - - + +
29A VAL* 2.8 36.9 + - - +
76A GLU* 3.1 35.7 - - - +
77A LEU* 1.3 77.3 - - - +
79A THR* 1.3 68.1 + - - +
82A SER 3.6 4.0 - - - +
83A SER* 3.8 8.3 - - - -
33B ASN* 5.5 4.2 + - - -
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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