Contacts of the strand formed by residues 46 - 52 (chain B) in PDB entry 2PJ7
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 ASN 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 5.9 5.8 - - - -
128A LYS* 5.8 0.5 + - - -
137A THR 5.1 0.2 - - - -
138A CYS* 3.6 36.8 - - - +
139A ILE 4.7 3.1 + - - +
161A CYS* 3.4 13.5 - - - +
15B TRP* 3.4 12.5 - - - +
19B GLU* 4.1 5.7 + - - +
37B ALA* 4.5 1.6 - - + -
39B GLY 4.0 2.8 + - - -
40B THR* 3.9 15.2 - - - +
44B GLY 4.5 4.4 + - - -
45B ASN* 1.3 72.7 - - - +
47B ILE* 1.3 60.2 + - - +
48B TYR* 3.1 44.6 + - + +
113B ILE* 3.3 13.1 - - - +
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 3.2 3.3 - - - +
38B ILE* 3.0 46.0 + - + +
39B GLY 3.1 20.8 + - - +
40B THR 3.9 17.5 - - - +
41B THR* 3.8 18.8 - - + +
46B ASN* 1.3 68.0 - - - +
48B TYR* 1.3 60.9 + - - +
108B LEU* 4.0 25.1 - - + -
110B VAL 4.4 4.9 - - - +
111B LEU* 4.5 7.6 - - + +
113B ILE* 3.9 6.3 - - + -
175B GLU* 3.9 36.1 - - + +
178B ALA* 4.1 11.2 - - + -
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A CYS* 3.4 28.7 + - + +
162A ASP* 5.1 0.3 + - - -
15B TRP* 3.8 18.7 - + + -
19B GLU* 2.6 44.1 + - + +
22B THR* 3.9 23.8 - - + -
35B ARG* 3.6 38.2 + - + -
36B THR 3.4 9.6 - - - +
37B ALA* 4.4 4.0 - - + -
46B ASN* 3.1 46.9 + - + -
47B ILE* 1.3 75.3 - - - +
49B LEU* 1.3 60.1 + - - +
50B LEU* 5.5 0.7 - - + -
108B LEU* 3.6 13.7 - - - +
109B PRO* 3.3 23.4 - - + +
110B VAL 5.2 1.4 + - - +
113B ILE* 4.9 1.2 - - - +
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Residues in contact with LEU 49 (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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34B SER 3.8 0.7 - - - +
35B ARG* 3.6 3.3 - - - -
36B THR* 2.8 41.5 + - - +
38B ILE* 3.8 22.2 - - + -
47B ILE 3.8 0.2 + - - -
48B TYR* 1.3 73.9 - - - +
50B LEU* 1.3 63.4 + - - +
51B LYS 4.0 0.2 + - - -
63B PHE* 3.8 18.4 - - + -
106B TYR* 3.6 14.6 - - + -
107B VAL 3.6 16.6 - - - +
108B LEU* 3.7 29.4 - - + -
182B PHE* 3.2 45.8 - - + -
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Residues in contact with LEU 50 (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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21B TRP* 4.0 33.9 - - + -
22B THR* 4.4 7.2 - - + +
25B VAL* 4.5 9.0 - - + -
26B THR* 3.6 24.0 - - - +
33B ILE* 4.0 11.4 - - + -
34B SER 3.6 1.1 - - - -
35B ARG* 3.7 27.1 - - + -
48B TYR* 5.5 1.6 - - + -
49B LEU* 1.3 77.0 - - - +
51B LYS* 1.3 59.8 + - - +
52B VAL* 3.7 7.8 + - + -
83B VAL* 4.1 15.3 - - + -
105B PHE 3.3 3.1 - - - +
106B TYR* 3.4 2.5 - - - +
107B VAL* 2.6 48.2 + - + +
109B PRO* 4.2 13.2 - - + -
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Residues in contact with LYS 51 (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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32B LEU 3.4 1.9 - - - +
33B ILE* 3.4 4.2 - - - -
34B SER* 2.9 49.5 + - - +
49B LEU* 4.0 1.0 + - + -
50B LEU* 1.3 71.2 - - - +
52B VAL* 1.3 60.1 + - - +
53B GLY 3.9 1.2 + - - +
55B PRO* 6.5 0.9 - - - -
104B ASP* 3.3 37.8 + - + +
105B PHE 3.5 2.7 - - - -
106B TYR* 3.7 41.5 + - + +
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Residues in contact with VAL 52 (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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32B LEU* 3.3 8.1 - - + +
33B ILE* 4.5 15.3 - - + -
50B LEU* 4.2 17.3 - - + +
51B LYS* 1.3 75.3 - - - +
53B GLY* 1.3 60.7 + - - +
82B PHE* 5.1 1.6 - - + -
83B VAL* 4.4 13.9 - - + +
86B ALA* 3.9 27.6 - - + -
87B VAL* 4.7 5.2 - - + -
100B LEU* 3.8 14.2 - - + +
104B ASP* 3.5 3.9 - - - -
105B PHE* 2.6 53.4 + - + +
107B VAL* 4.2 14.8 - - + -
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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