Contacts of the strand formed by residues 47 - 59 (chain C) in PDB entry 3U8M
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 GLU 47 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU 4.2 0.2 - - - +
41C VAL* 3.7 1.0 - - - -
42C ASN* 3.0 30.8 + - + +
45C THR* 3.4 32.8 + - - +
46C ASN* 1.3 82.6 - - - +
48C VAL* 1.3 67.0 + - - +
92C ILE* 3.6 28.3 - - + +
120C ARG* 6.0 0.8 - - + -
121C PHE 3.1 8.3 - - - +
122C SER* 4.8 2.9 - - - -
125C VAL* 3.7 0.4 - - - +
39D LEU* 3.7 34.1 - - + +
118D ARG* 5.4 3.1 + - - -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 5.2 1.6 - - + -
40C GLU 3.4 5.8 - - - +
41C VAL* 4.0 20.0 - - + -
47C GLU* 1.3 79.0 - - - +
49C ASP* 1.3 60.5 + - - +
50C VAL* 3.9 20.1 + - + -
119C GLN 4.0 0.2 - - - +
120C ARG* 3.2 6.8 - - - +
121C PHE* 2.9 38.0 + - + +
123C CYS* 3.7 23.8 - - - -
125C VAL* 3.5 22.0 - - + -
136C CYS* 3.8 8.1 - - + -
199C LEU* 6.3 0.4 - - + -
201C PHE* 4.1 13.5 - - + -
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 3.7 2.4 - - - +
39C LEU* 2.9 31.7 + - + +
40C GLU* 2.7 37.4 + - + +
48C VAL* 1.3 73.8 - - - +
50C VAL* 1.3 64.6 + - - +
118C ARG* 2.9 51.9 + - - +
119C GLN 3.9 2.5 - - - +
120C ARG* 3.3 29.9 + - + +
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Residues in contact with VAL 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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35C PHE* 3.5 35.2 - - + -
37C ASN 3.6 10.1 - - - +
38C ILE* 4.7 13.0 - - + -
39C LEU* 5.0 0.4 - - - +
48C VAL* 3.9 25.4 - - + -
49C ASP* 1.3 80.2 + - - +
51C VAL* 1.3 72.2 + - - +
52C PHE* 3.9 8.0 - - + -
117C ILE 3.6 0.7 - - - +
118C ARG* 3.2 4.9 - - - +
119C GLN 2.9 36.6 + - - +
121C PHE* 4.4 12.1 - - + -
136C CYS* 5.9 0.2 - - - -
138C ILE* 5.4 2.9 - - + -
199C LEU* 4.8 9.2 - - + -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR 6.0 0.7 - - - +
91B ALA 5.2 3.4 - - - +
92B ILE* 4.7 8.3 - - + -
36C ILE* 2.8 40.5 + - + -
37C ASN* 3.0 21.0 + - + +
39C LEU* 3.9 19.7 - - + +
50C VAL* 1.3 77.6 - - - +
52C PHE* 1.3 64.4 + - - +
98C LEU* 4.1 11.4 - - + -
116C SER* 3.8 19.7 - - - +
117C ILE 3.1 4.9 - - - +
118C ARG* 3.6 30.5 - - + -
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Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.6 31.2 - - + -
34C LYS 3.3 19.1 - - - +
35C PHE* 4.1 14.6 - + + -
36C ILE* 3.9 1.3 - - - -
50C VAL* 3.9 14.1 - - + -
51C VAL* 1.3 79.1 - - - +
53C TRP* 1.3 67.2 + - - +
54C GLN* 3.5 28.8 + - + -
116C SER* 4.4 0.2 - - - -
117C ILE* 2.7 68.3 + - + +
119C GLN* 3.9 17.0 - - + -
121C PHE* 3.9 26.2 - + - -
138C ILE* 5.7 0.4 - - + -
140C ILE* 5.4 2.2 - - + -
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Residues in contact with TRP 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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89B TYR* 4.0 18.7 + + - -
143B TRP* 3.4 35.9 - + - -
185B TYR* 3.8 32.3 - + + -
33C LEU* 3.6 2.9 - - - -
34C LYS* 2.8 42.1 + - + +
36C ILE* 3.5 29.9 - - + +
52C PHE* 1.3 72.7 - - - +
54C GLN* 1.3 59.5 + - - +
55C GLN 3.5 4.0 + - - -
114C MET* 3.8 39.0 - - + -
115C PRO 3.4 4.7 - - - -
116C SER* 3.5 24.9 + - - -
164C TYR* 3.8 38.8 - + + -
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Residues in contact with GLN 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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31C VAL* 4.4 7.9 - - + -
32C SER 3.9 2.5 - - - -
33C LEU* 3.9 14.4 - - + -
52C PHE* 3.5 26.5 + - + -
53C TRP* 1.3 68.9 - - - +
55C GLN* 1.3 59.5 + - - +
56C THR* 3.3 19.1 + - - +
86C LEU* 4.3 22.4 + - - +
113C TYR 3.1 14.6 - - - +
114C MET* 4.1 2.2 - - - +
115C PRO* 2.9 24.3 + - + +
117C ILE* 3.8 22.6 - - + +
119C GLN* 5.4 1.2 - - - +
140C ILE* 4.2 14.8 - - - +
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Residues in contact with GLN 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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187B CYS* 3.7 23.3 - - - +
30C SER* 3.4 2.8 - - - +
31C VAL* 3.4 6.8 - - - +
32C SER* 2.9 47.6 + - - +
34C LYS* 3.4 26.3 + - + +
53C TRP 3.5 1.6 + - - -
54C GLN* 1.3 71.8 - - - +
56C THR* 1.3 58.5 + - - +
57C THR* 5.6 4.2 + - - +
112C LEU* 3.8 19.1 - - + -
113C TYR 3.8 0.4 - - - -
114C MET* 3.4 27.5 - - - +
155C THR* 3.6 25.3 + - - +
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Residues in contact with THR 56 (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 VAL* 3.8 19.7 - - + -
30C SER 3.3 3.1 - - - +
31C VAL* 4.8 0.3 - - - +
54C GLN* 3.3 29.1 + - - +
55C GLN* 1.3 74.5 + - - +
57C THR* 1.3 63.1 + - - +
58C TRP* 3.6 25.9 - - + -
83C VAL* 6.1 0.7 - - + -
84C PRO* 4.1 4.7 - - + -
86C LEU* 3.9 16.5 - - + +
111C VAL 3.7 0.5 - - - +
112C LEU* 3.5 6.5 - - - +
113C TYR* 2.8 45.8 + - + -
115C PRO* 5.3 0.2 - - - +
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Residues in contact with THR 57 (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 ALA 3.7 1.4 - - - +
29C VAL* 3.4 2.3 - - - +
30C SER* 2.8 54.8 + - - +
55C GLN* 5.7 4.6 + - - -
56C THR* 1.3 76.6 + - - +
58C TRP* 1.3 70.0 + - - +
110C GLU* 4.8 9.9 - - - +
111C VAL 3.3 11.3 + - - +
112C LEU* 3.9 14.4 - - - +
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Residues in contact with TRP 58 (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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20C PRO* 4.5 0.7 - - + -
27C VAL* 4.2 9.4 - - + -
28C ALA 3.8 15.0 - - - +
29C VAL* 4.4 5.8 - - + -
56C THR* 3.6 31.2 - - + -
57C THR* 1.3 86.4 - - - +
59C SER* 1.3 75.6 + - - +
60C ASP* 4.1 5.4 - - - +
81C LEU* 5.2 2.2 - - + -
82C TRP* 3.2 49.5 + + - -
83C VAL* 4.2 14.6 - - + -
84C PRO* 3.6 28.7 - - + -
103C ALA* 5.6 1.1 - - + -
110C GLU* 3.6 8.8 - - - +
111C VAL* 2.8 65.8 + - + +
113C TYR* 4.2 14.4 - - + -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 3.7 21.8 - - - +
22C GLN* 6.0 0.7 - - - +
27C VAL* 4.3 6.5 - - - +
28C ALA 4.7 2.6 + - - -
58C TRP* 1.3 78.3 - - - +
60C ASP* 1.3 60.8 + - - +
61C ARG* 3.2 31.2 + - - +
108C ASP 4.7 0.3 + - - -
109C GLY 3.5 7.3 + - - -
110C GLU* 2.9 24.5 + - - -
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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