Contacts of the strand formed by residues 45 - 52 (chain E) in PDB entry 5ISO
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 SER 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A TYR 3.6 3.7 + - - +
342A LEU* 3.9 5.2 - - - -
214B ILE* 4.3 3.1 - - - +
227B LEU* 3.6 5.5 - - - +
228B LEU* 3.0 38.8 + - - +
229B PRO 2.8 31.4 + - - -
231B PRO* 3.9 14.9 - - - +
254B THR* 5.7 0.5 - - - +
261B TYR* 3.3 8.0 - - - +
263B THR* 5.2 1.7 + - - -
43E PRO* 3.8 5.5 - - - +
44E THR* 1.3 82.2 - - - +
46E SER* 1.3 64.8 + - - +
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Residues in contact with SER 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ALA* 3.2 16.8 - - - -
228B LEU* 3.8 6.7 - - - +
261B TYR 3.2 10.2 + - - +
262B VAL* 3.5 6.2 - - - +
263B THR* 2.8 26.2 + - - -
42E ILE* 4.9 1.9 - - - +
43E PRO* 3.9 30.0 + - - +
45E SER* 1.3 79.1 + - - +
47E LYS* 1.3 65.1 + - - +
164E LEU 4.5 8.8 + - - -
165E TYR* 4.3 11.7 - - - -
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Residues in contact with LYS 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LEU* 4.1 22.2 - - + +
225B PRO 3.7 19.0 + - - -
226B ALA* 2.9 30.3 + - - +
228B LEU* 3.6 26.2 - - + +
263B THR* 3.2 10.5 - - - +
265B LEU* 4.4 9.6 - - + -
46E SER* 1.3 76.0 - - - +
48E LEU* 1.3 64.3 + - - +
49E VAL* 5.1 1.6 - - + -
67E ASN* 2.9 41.1 + - + +
69E VAL* 4.7 10.9 - - + +
165E TYR* 6.1 0.3 - - - -
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B VAL* 4.4 9.6 - - + -
263B THR 2.8 10.8 + - - +
264B THR* 3.3 14.7 - - + +
265B LEU* 2.8 32.6 + - - +
47E LYS* 1.3 77.4 - - - +
49E VAL* 1.3 60.4 + - - +
50E VAL* 4.5 10.3 - - + -
69E VAL* 6.0 0.9 - - - -
71E ALA 5.7 0.9 - - - +
73E PRO* 3.8 15.3 - - + -
163E THR* 3.5 43.5 - - + +
164E LEU 4.4 6.3 - - - +
165E TYR* 4.8 3.1 - - - -
166E ILE* 3.7 41.3 - - + +
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 3.8 14.4 - - + -
267B TYR* 4.1 16.2 - - + -
47E LYS* 5.1 2.9 - - + -
48E LEU* 1.3 78.9 - - - +
50E VAL* 1.3 63.6 + - - +
51E PHE* 3.6 34.8 - - + -
63E ALA 5.2 0.4 - - - +
64E LEU* 5.4 0.2 - - + -
67E ASN* 3.9 24.9 - - + +
69E VAL* 3.8 32.7 - - + +
71E ALA 5.1 1.6 + - - +
72E ALA* 3.1 13.6 - - + +
73E PRO* 3.0 24.1 - - - +
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Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A MET* 4.1 9.0 - - + -
264B THR* 4.0 17.5 - - + -
265B LEU 2.7 19.2 + - - +
266B LEU* 3.5 19.8 - - + -
267B TYR* 3.0 26.9 + - - +
48E LEU* 4.5 11.2 - - + -
49E VAL* 1.3 77.3 - - - +
51E PHE* 1.3 70.1 + - - +
73E PRO* 3.4 23.6 - - + +
75E TRP* 3.7 22.2 - - + -
82E PHE* 4.1 13.5 - - + -
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Residues in contact with PHE 51 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267B TYR* 3.7 12.1 - + + -
49E VAL* 3.6 21.1 - - + -
50E VAL* 1.3 80.6 - - - +
52E ASP* 1.3 61.1 + - - +
55E LEU* 3.6 20.0 - - + -
60E ALA* 3.3 38.4 - - + -
63E ALA* 3.6 23.8 - - + -
64E LEU* 3.9 13.7 - - + -
72E ALA* 3.5 25.1 - - + -
73E PRO 3.0 6.3 + - - -
74E LEU* 3.4 11.8 - - + +
75E TRP 2.8 25.7 + - - -
86E LEU* 3.9 15.5 - - + -
114E ILE* 3.8 18.4 - - + -
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Residues in contact with ASP 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A GLU* 4.6 0.9 - - - +
266B LEU* 4.1 8.5 - - + +
267B TYR 3.2 21.7 + - - +
268B LYS* 4.4 15.0 - - + +
269B PRO* 4.3 9.6 - - + -
51E PHE* 1.3 73.7 - - - +
53E THR* 1.3 68.9 + - - +
54E SER* 2.8 38.4 + - - -
55E LEU* 3.0 21.1 + - - +
75E TRP* 3.2 16.4 - - + +
77E SER* 3.0 35.0 + - - -
114E ILE* 4.0 3.3 - - - +
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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