Contacts of the strand formed by residues 46 - 55 (chain C) in PDB entry 5F0P
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 PHE 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C THR* 3.5 1.0 - - - -
39C VAL* 2.8 57.9 + - + -
40C GLY* 5.8 0.2 - - - -
44C GLY 3.6 15.9 - - - -
45C ARG* 1.3 76.3 - - - +
47C THR* 1.3 66.4 + - - +
48C THR* 3.7 19.7 - - + -
70C ARG* 3.3 50.7 - - + +
110C PHE* 4.3 8.7 - - - -
201C SO4 3.5 23.8 - - - +
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO* 4.2 6.7 - - + -
37C GLN 3.3 19.1 - - - +
38C THR* 4.6 2.4 + - - +
46C PHE* 1.3 76.4 - - - +
48C THR* 1.3 73.5 + - - +
49C TYR* 3.7 38.7 - - + +
70C ARG* 4.1 7.3 - - - -
109C ILE* 4.6 3.5 + - - +
110C PHE* 3.6 24.1 - - - -
115C ILE* 4.4 15.0 - - + +
118C ARG* 5.9 3.1 - - - -
201C SO4 3.8 17.0 + - - -
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASN 3.6 2.3 - - - +
36C PRO* 3.5 5.2 - - - +
37C GLN* 2.8 34.3 + - - +
39C VAL* 3.5 22.7 - - + +
46C PHE* 3.7 25.4 - - + -
47C THR* 1.3 78.9 - - - +
49C TYR* 1.3 64.7 + - - +
68C ARG* 3.9 25.6 + - + -
69C ARG* 3.1 24.0 - - - +
70C ARG* 4.4 1.8 - - + -
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.7 21.5 - - + -
34C SER 3.9 4.9 - - - +
35C ASN 4.1 1.6 - - - -
36C PRO* 3.9 30.3 - - + -
47C THR* 3.7 28.1 - - + +
48C THR* 1.3 75.2 - - - +
50C GLU* 1.3 63.9 + - - +
51C ILE* 3.5 7.4 + - + +
68C ARG* 3.6 3.3 - - - -
69C ARG* 3.0 34.9 + - - +
71C TYR* 5.1 10.3 - - + -
74C PHE* 5.0 3.8 - + - -
115C ILE* 4.0 12.0 - - + +
118C ARG* 3.1 34.1 - - + +
119C LYS* 4.0 31.9 - - + -
122C LEU* 3.6 20.6 - - + -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ASP 3.1 15.1 - - - +
34C SER* 2.9 33.2 + - - +
35C ASN* 2.7 33.5 + - + -
49C TYR* 1.3 68.4 - - - +
51C ILE* 1.3 62.3 + - - +
52C ARG* 3.4 5.1 + - + +
66C THR* 4.3 16.0 + - - +
67C VAL 3.4 7.4 - - - +
68C ARG* 3.5 36.4 + - + +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 3.6 27.1 - - + -
32C ASP 3.7 2.0 - - - +
33C VAL* 3.8 25.6 - - + -
49C TYR* 4.0 7.4 - - + +
50C GLU* 1.3 70.5 - - - +
52C ARG* 1.3 59.2 - - - +
53C VAL* 4.0 6.0 + - + +
65C SER 4.0 0.7 - - - +
66C THR* 3.7 2.0 - - - -
67C VAL* 2.8 42.1 + - + +
69C ARG* 3.6 28.5 - - + -
74C PHE* 3.6 30.5 - - + -
126C ILE* 4.8 3.1 - - + -
144C PHE* 4.8 6.7 - - + -
145C LEU* 4.1 18.1 - - + +
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A HIS* 4.8 3.0 - - - -
203A SER* 5.6 0.4 + - - -
512A EDO 2.8 35.6 + - - -
30C GLU* 4.1 1.4 + - - +
31C ILE* 3.5 2.0 - - - -
32C ASP* 2.9 63.1 + - + +
34C SER* 5.1 4.9 + - - +
50C GLU* 3.4 6.3 + - + +
51C ILE* 1.3 73.1 - - - +
53C VAL* 1.3 66.4 + - - +
54C LYS* 3.7 37.7 - - - +
64C GLU* 6.5 0.2 - - - -
65C SER 3.5 10.3 - - - +
66C THR* 4.3 16.2 - - - +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.4 9.4 - - + -
30C GLU 3.7 8.3 - - - +
31C ILE* 4.1 23.3 - - + -
51C ILE* 4.5 5.4 - - + +
52C ARG* 1.3 78.6 - - - +
54C LYS* 1.3 82.9 + - - +
55C THR* 4.7 6.1 - - + -
60C PHE* 5.7 3.6 - - + -
63C LYS 4.6 1.3 - - - +
64C GLU* 3.7 3.3 - - - +
65C SER* 3.0 46.7 + - - +
145C LEU* 4.1 31.9 - - + +
146C GLN* 4.6 11.4 - - - +
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 3.6 31.4 - - - +
28C PHE* 3.8 21.1 - - + -
29C LEU* 3.6 3.6 - - - +
30C GLU* 3.1 39.7 + - + +
52C ARG* 3.7 38.1 - - - +
53C VAL* 1.3 80.4 - - - +
55C THR* 1.3 65.5 + - - +
63C LYS 3.5 7.2 - - - +
64C GLU* 4.3 27.7 + - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.1 26.8 + - - -
29C LEU* 4.3 11.0 - - - +
53C VAL* 4.7 7.4 - - + -
54C LYS* 1.3 76.6 - - - +
56C ASN* 1.3 68.2 + - - +
57C LEU* 3.1 25.4 + - - +
60C PHE* 4.0 20.6 - - + -
62C LEU 3.7 17.0 - - - +
63C LYS* 2.9 37.5 + - - +
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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