Contacts of the strand formed by residues 87 - 98 (chain E) in PDB entry 1U3H
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 THR 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E TYR 3.8 0.7 - - - +
36E GLN* 3.7 1.7 - - - -
37E GLN* 2.9 38.7 + - - +
39E PRO* 5.6 0.2 - - - +
86E ALA* 1.3 79.8 - - - +
88E TYR* 1.3 65.7 + - - +
89E PHE* 3.9 31.3 + - + -
109E GLY* 4.2 4.5 - - - -
110E THR 3.4 24.9 - - - +
111E LYS* 3.4 25.9 - - + +
37F GLN* 5.4 0.7 - - - +
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Residues in contact with TYR 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLN* 2.8 22.7 + - - +
20E LEU* 3.5 32.8 - - + -
34E TRP* 4.5 9.2 - - + -
35E TYR 3.3 4.3 - - - +
36E GLN* 3.1 54.0 + - + -
38E PHE* 5.0 0.5 - - - -
46E LEU* 4.2 18.2 - - + -
62E PHE* 4.9 2.0 - + - -
75E LEU* 4.9 1.6 - - + -
77E ILE* 3.6 19.9 - - + +
84E ASP* 2.9 41.2 + - - +
86E ALA 4.2 12.7 + - - -
87E THR* 1.3 74.5 - - - +
89E PHE* 1.3 62.0 + - - +
110E THR* 3.0 17.6 + - - +
112E LEU* 3.9 10.8 - - + -
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Residues in contact with PHE 89 (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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5E GLN* 3.2 3.6 - - - +
33E PRO 4.0 0.2 - - - +
34E TRP* 3.3 8.2 - - - -
35E TYR* 2.9 40.7 + - + +
37E GLN* 3.2 26.9 - - + -
43E PRO* 4.4 14.1 - - + -
87E THR* 3.9 19.3 - - + -
88E TYR* 1.3 73.2 - - - +
90E CYS* 1.3 60.8 + - - +
91E ALA 3.9 0.9 + - - -
106E PHE* 4.2 16.8 - + + -
107E GLY 3.7 12.8 - - - +
108E THR 3.2 20.9 - - - -
109E GLY* 3.7 15.0 - - - -
37F GLN* 3.0 20.2 - - - -
42F GLY* 3.8 8.5 - - - -
43F LEU* 3.4 31.4 - - + -
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Residues in contact with CYS 90 (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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3E VAL* 3.4 11.7 - - - +
5E GLN* 2.9 16.3 - - - +
22E CYS* 2.0 48.5 - - - -
32E PHE* 5.3 0.7 - - - -
33E PRO 4.1 0.4 - - - -
34E TRP* 3.5 36.3 - - + -
73E LEU* 3.7 13.0 - - - -
89E PHE* 1.3 72.8 - - - +
91E ALA* 1.3 64.5 + - - +
92E ALA* 6.1 0.2 - - - -
106E PHE* 5.0 0.2 - - - -
107E GLY* 3.1 20.8 + - - +
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 4.7 0.4 - - - -
32E PHE* 3.2 26.3 - - - +
33E PRO* 3.0 31.9 + - + +
35E TYR* 4.3 0.4 - - + -
89E PHE 3.9 0.4 + - - -
90E CYS* 1.3 78.3 - - - +
92E ALA* 1.3 64.4 + - - +
104E GLN* 4.0 11.4 - - + +
105E ARG 3.3 13.9 - - - +
106E PHE* 3.9 25.1 - - + +
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 4.1 15.9 - - + -
24E TYR* 5.5 1.1 - - + -
29E PHE* 3.9 25.1 - - + -
31E TYR 3.1 8.7 - - - -
32E PHE* 3.7 21.1 - - + -
33E PRO* 4.3 0.6 - - - +
91E ALA* 1.3 79.0 - - - +
93E SER* 1.3 59.6 + - - +
104E GLN* 3.4 4.5 - - - -
105E ARG* 2.9 34.0 + - - +
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PHE* 3.1 7.8 - - - -
30E ASP* 2.9 27.4 + - - +
31E TYR* 3.0 28.2 + - - +
92E ALA* 1.3 76.2 - - - +
98E ALA* 1.3 64.6 + - - +
102E THR 4.1 9.0 - - - -
103E TYR 4.6 3.8 - - - -
104E GLN* 4.1 6.7 - - - -
99F GLY 3.4 24.0 - - - -
100F GLY* 3.6 10.2 - - - -
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Residues in contact with ALA 98 (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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26E ASN* 4.9 3.8 - - - +
28E ALA* 3.4 18.4 - - + +
29E PHE* 3.3 15.3 - - + -
30E ASP* 3.3 10.0 - - - +
93E SER* 1.3 74.9 + - - +
99E ASN* 1.3 57.3 + - - +
100E SER* 2.6 32.6 - - - +
101E GLY* 4.5 0.3 - - - -
102E THR* 3.2 25.2 + - - +
103E TYR 5.2 0.4 + - - -
100F GLY* 6.0 0.2 - - - -
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Residues in contact with ASN 99 (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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28E ALA* 2.9 29.8 + - - +
30E ASP* 3.3 18.3 + - + +
98E ALA* 1.3 68.4 - - - +
100E SER* 1.3 75.6 + - - +
74H GLU* 5.4 0.2 - - - +
77H THR* 3.3 32.4 + - - +
78H VAL* 4.5 3.5 - - + +
81H TYR* 3.3 31.5 - - - -
-1I GLY 3.7 4.0 - - - +
0I GLY* 3.2 18.3 + - - -
1I ALA 3.1 23.2 + - - +
3I GLN* 3.7 3.5 - - - +
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Residues in contact with SER 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ALA* 2.6 23.9 - - - +
99E ASN* 1.3 84.5 + - - +
101E GLY* 1.3 60.7 + - - +
102E THR* 3.0 31.1 + - - +
54G PHE* 3.7 26.0 - - - -
55G ASP* 4.4 8.2 - - - +
58G GLY* 4.9 0.7 - - - -
-1I GLY 3.8 9.6 - - - -
1I ALA* 3.8 11.2 - - - +
3I GLN* 3.6 1.1 - - - -
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Residues in contact with GLY 101 (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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98E ALA 4.8 0.2 - - - -
100E SER* 1.3 75.2 - - - +
102E THR* 1.3 55.9 + - - +
98F GLY 2.4 30.3 - - - +
100F GLY 5.8 0.4 - - - -
58G GLY* 3.9 18.1 - - - -
61G GLN* 3.9 12.7 - - - +
62G ASN* 4.7 2.3 - - - +
1I ALA* 4.9 1.2 - - - +
3I GLN* 3.1 33.3 + - - -
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Residues in contact with THR 102 (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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93E SER* 4.1 9.4 - - - -
98E ALA* 3.2 23.1 + - + +
100E SER* 3.0 24.9 + - - +
101E GLY* 1.3 79.5 - - - +
103E TYR* 1.3 66.5 + - + +
105E ARG* 4.2 14.2 + - - +
98F GLY 4.1 0.9 - - - -
99F GLY* 3.8 10.2 - - - -
55G ASP* 3.1 36.1 - - + +
57G GLN* 4.4 16.2 - - + -
58G GLY 4.5 2.9 - - - +
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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