Contacts of the strand formed by residues 44 - 51 (chain G) in PDB entry 5U72
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 ARG 44 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35G TYR* 3.4 5.1 - - - -
36G ARG* 3.0 59.6 + - + +
38G ASP* 3.0 27.7 + - - +
41G MET* 3.6 28.2 - - + +
42G GLY 3.6 12.3 - - - +
43G LEU* 1.3 73.6 - - - +
45G LEU* 1.3 63.6 + - - +
46G ILE 3.5 0.7 + - - -
59G GLU* 4.0 29.6 - - - +
60G VAL* 4.0 31.1 - - + +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLN* 6.5 1.8 - - + -
33G TYR* 3.9 24.9 - - + -
34G TRP 3.3 17.0 - - - +
35G TYR* 3.5 29.4 - - + +
43G LEU 4.3 0.2 + - - -
44G ARG* 1.3 69.9 - - - +
46G ILE* 1.3 57.2 + - - +
47G TYR 3.4 15.7 - - - +
48G TYR* 3.9 29.8 - - + -
58G GLY* 4.0 11.2 - - - -
59G GLU* 2.7 36.8 + - + +
60G VAL* 3.0 9.8 + - - +
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Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G TRP* 2.8 19.4 + - + +
35G TYR 4.0 11.2 - - - -
36G ARG* 4.0 6.7 - - + +
44G ARG 4.1 6.1 - - - +
45G LEU* 1.3 74.6 - - - +
47G TYR* 1.3 73.7 + - + +
58G GLY* 2.9 18.8 + - - -
60G VAL* 3.5 21.1 - - + +
61G PRO* 3.6 8.8 - - - +
64G TYR* 3.5 42.6 - - + -
76G LEU* 4.0 14.4 - - + -
89G TYR* 3.6 38.8 - - + -
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Residues in contact with TYR 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G TRP* 3.0 25.8 + - + +
45G LEU* 3.4 8.0 - - - +
46G ILE* 1.3 94.7 - - + +
48G TYR* 1.3 61.4 + - - +
55G THR* 5.4 1.6 - - - -
56G ASP* 3.2 25.1 - - - +
57G LYS* 2.9 44.4 + - + -
58G GLY 3.9 2.0 - - - +
61G PRO* 3.5 22.9 + - + +
64G TYR* 3.2 33.4 + - + -
65G ASN* 3.8 8.1 - - + +
66G VAL* 3.6 46.0 - - + -
74G PHE* 4.0 2.8 - - - -
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Residues in contact with TYR 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 2.9 40.2 + - - -
64A GLN* 3.5 23.2 - - + +
96B GLN* 5.7 4.3 - - - -
32G MET 3.5 5.4 - - - -
33G TYR* 3.6 34.8 - + + -
45G LEU* 3.9 18.6 - - + -
47G TYR* 1.3 76.9 - - - +
49G SER* 1.3 63.9 + - - +
50G ALA* 3.9 26.0 - - + -
55G THR* 3.3 6.1 - - - -
56G ASP* 3.0 56.4 + - + +
57G LYS 3.6 19.5 - - - -
74G PHE* 3.7 5.9 - - - -
97G THR* 5.2 2.7 - - + -
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Residues in contact with SER 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G SER* 3.2 2.3 - - - -
32G MET 2.8 34.6 + - - -
33G TYR* 6.1 0.2 - - - -
48G TYR* 1.3 76.6 - - - +
50G ALA* 1.3 63.8 + - - +
51G SER 3.1 3.8 + - - -
54G THR 2.7 22.7 + - - -
55G THR* 3.9 2.5 - - - +
68G ARG* 2.8 37.2 + - - +
74G PHE* 3.8 21.5 - - - -
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLN* 3.7 29.9 + - + +
65A LEU* 4.9 1.3 - - + +
68A GLY* 4.9 4.8 - - - -
72A MET* 5.2 1.4 - - - +
30G ASN* 3.5 4.7 - - - +
31G SER* 2.6 21.9 + - - -
48G TYR* 3.9 18.0 - - + -
49G SER* 1.3 72.5 - - - +
51G SER* 1.3 63.5 + - - +
54G THR* 3.9 10.7 + - - +
96G TRP* 5.3 0.2 - - - -
97G THR* 3.6 28.6 + - + +
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Residues in contact with SER 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 3.9 8.0 + - - +
68A GLY* 3.6 26.3 + - - -
71A GLN* 4.7 8.7 - - - +
72A MET* 4.4 14.4 - - - -
30G ASN* 3.2 14.6 - - - -
49G SER* 3.1 15.8 + - - -
50G ALA* 1.3 79.2 - - - +
52G GLU* 1.3 71.8 + - - +
53G GLY 3.4 0.2 + - - -
54G THR* 3.2 15.0 + - - +
68G ARG* 3.4 5.6 - - - -
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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