Contacts of the strand formed by residues 72 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LYS* 2.6 58.3 + - + +
23B PHE* 3.4 15.8 - - - -
69B PRO* 3.4 39.4 + - + -
70B GLU 4.1 5.1 + - - -
71B LEU* 1.3 79.0 - - - +
73B LEU* 1.3 60.5 + - - +
74B TYR* 3.5 17.0 - + + -
87B ALA* 4.1 16.8 - - + -
88B ILE 3.7 22.9 - - - -
89B ARG* 4.1 6.1 - - + -
90B MET* 4.1 3.6 - - - -
96B VAL* 3.5 42.6 - - + -
116B LEU* 4.1 20.9 - - + -
117B LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.5 34.5 - - + +
25B GLU* 5.3 4.9 - - + -
43B VAL* 3.8 18.4 - - + -
47B VAL* 3.9 12.8 - - + -
72B TRP* 1.3 73.3 - - - +
74B TYR* 1.3 65.0 + - - +
75B THR* 3.9 19.5 + - + -
86B LEU 3.1 3.5 - - - +
88B ILE* 2.7 55.6 + - + +
89B ARG 5.2 0.4 - - - +
90B MET* 4.1 11.1 - - + +
93B LEU* 4.4 7.2 - - + -
209B LEU* 3.8 29.2 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS 3.6 15.0 - - - -
23B PHE 3.4 13.1 + - - +
24B THR* 3.3 18.8 - - + +
25B GLU 2.9 25.3 + - - +
72B TRP* 3.5 28.4 - + + -
73B LEU* 1.3 78.2 - - - +
75B THR* 1.3 62.7 + - - +
76B GLU 4.0 0.2 - - - -
85B THR* 3.6 22.4 - - + -
86B LEU 3.3 3.8 - - - -
87B ALA* 4.2 12.7 - - + +
105B TRP* 3.4 35.3 - + - -
117B LEU* 4.9 6.4 - - - +
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU* 3.3 7.6 - - + +
39B PHE* 4.4 22.7 - - + -
43B VAL* 4.9 4.9 - - + -
73B LEU* 3.9 27.8 - - + -
74B TYR* 1.3 75.5 - - - +
76B GLU* 1.3 60.0 + - - +
77B LEU* 3.7 8.8 + - - +
84B ILE 3.8 0.5 - - - +
85B THR* 3.6 2.1 - - - -
86B LEU* 2.9 53.6 + - - +
88B ILE* 4.1 10.8 - - + +
205B VAL* 4.3 10.9 - - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.9 7.6 - - + +
25B GLU 2.9 13.6 + - - +
26B ILE* 3.5 25.8 - - + +
27B PHE 2.9 26.9 + - - -
39B PHE* 5.4 0.3 - - - -
74B TYR 4.0 1.0 + - - -
75B THR* 1.3 73.4 - - - +
77B LEU* 1.3 63.2 + - - +
78B LYS* 2.3 47.4 - - + +
83B SER* 3.2 10.0 + - - +
84B ILE 3.5 6.7 - - - +
85B THR* 3.4 24.0 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.7 19.7 - - + -
29B VAL* 3.9 7.2 - - + -
39B PHE* 5.0 4.3 - - + -
75B THR* 4.2 19.1 - - - +
76B GLU* 1.3 77.4 - - - +
78B LYS* 1.4 62.7 + - - +
83B SER* 3.1 21.7 - - - -
84B ILE* 2.9 15.7 + - + +
86B LEU* 3.9 25.8 - - + -
149B MET* 4.5 14.6 - - + -
153B VAL* 3.3 34.9 - - + +
201B LEU* 4.1 20.9 - - + -
205B VAL* 4.7 11.4 - - + -
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.3 15.3 - - + -
27B PHE 3.0 10.2 + - - +
28B PRO* 3.4 7.7 - - + +
29B VAL* 2.7 33.9 + - - -
76B GLU* 2.3 51.3 + - - +
77B LEU* 1.4 74.2 - - - +
79B THR* 1.3 64.1 + - - +
82B SER 3.7 3.4 - - - +
83B SER* 3.4 15.3 + - - -
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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