Contacts of the strand formed by residues 51 - 68 (chain B) in PDB entry 1UXU
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 ILE 51 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 3.7 1.7 - - - +
45B MET* 3.9 3.8 - - - -
46B ASP* 2.9 38.3 + - + +
49B ASN* 3.5 24.7 - - + +
50B GLN* 1.3 80.8 - - - +
52B LEU* 1.3 71.0 + - - +
53B THR* 3.9 6.3 + - - +
98B ALA* 3.7 18.6 - - + -
127B LYS* 4.2 16.4 - - + -
128B SER 3.4 12.3 - - - +
129B SER* 3.4 27.8 - - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ILE* 3.7 22.9 - - + -
44B ASP 3.5 13.5 - - - +
45B MET* 4.2 4.0 - - - -
51B ILE* 1.3 73.0 - - - +
53B THR* 1.3 72.6 + - - +
54B ALA* 4.1 15.5 - - + -
126B THR* 3.5 1.8 - - - +
127B LYS* 3.3 4.3 - - - -
128B SER* 2.8 37.3 + - - +
130B CYS* 3.5 20.6 - - - -
144B CYS* 3.8 22.0 - - + -
146B LEU* 4.5 16.2 - - + -
206B LEU* 3.8 18.4 - - + -
208B LEU* 4.4 13.2 - - + -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 2.8 41.0 + - + -
44B ASP* 2.8 34.2 + - - +
51B ILE* 3.9 5.8 + - - +
52B LEU* 1.3 75.7 - - - +
54B ALA* 1.3 62.2 + - - +
125B ILE* 3.8 26.7 - - + -
126B THR 3.2 5.6 - - - +
127B LYS* 3.7 30.0 - - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.1 16.6 - - + -
41B GLN 3.6 9.4 - - - +
42B ILE* 4.7 0.7 - - - +
52B LEU* 4.0 22.6 - - + -
53B THR* 1.3 75.1 - - - +
55B TYR* 1.3 67.2 + - - +
56B LEU* 4.2 6.5 - - + -
124B ALA 3.7 0.5 - - - +
125B ILE* 3.3 6.1 - - - +
126B THR* 2.9 44.4 + - - +
146B LEU* 5.5 1.6 - - + -
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 0.3 - - - +
40B SER* 2.8 43.7 + - - -
41B GLN* 2.8 46.6 + - + +
43B LYS* 3.2 49.3 + - + +
53B THR* 4.6 0.2 - - + -
54B ALA* 1.3 79.3 - - - +
56B LEU* 1.3 59.5 + - - +
124B ALA 3.6 3.6 - - - +
125B ILE* 3.6 40.4 - - + +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.1 20.4 - - + -
38B THR 3.3 10.8 - - - +
39B LEU* 3.6 30.7 - - + -
40B SER* 4.2 1.3 - - - -
54B ALA* 4.2 7.4 - - + -
55B TYR* 1.3 75.8 - - - +
57B TRP* 1.3 72.0 + - - +
58B ILE* 4.9 3.1 - - + -
123B PRO* 3.3 5.4 - - - +
124B ALA* 2.8 37.0 + - + +
126B THR* 3.5 36.8 - - + +
146B LEU* 4.4 12.8 - - + -
148B PHE* 3.9 22.9 - - + -
183B MET* 4.9 0.2 - - + -
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN 3.6 1.2 - - - +
37B ILE* 3.6 3.8 - - - +
38B THR* 2.8 45.9 + - + +
40B SER* 3.3 26.1 + - - -
56B LEU* 1.3 74.3 + - - +
58B ILE* 1.3 63.7 + - - +
59B ARG 4.1 0.4 - - - -
108B THR* 5.7 0.7 - - + -
121B ASP* 4.1 13.2 - - + +
122B ALA* 3.4 28.9 - - - -
123B PRO* 3.4 37.2 - - + +
171B ASP* 6.3 1.3 - - + -
1216B EPE 3.4 65.5 - - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.9 24.0 - - + -
36B GLN 3.5 2.5 - - - -
37B ILE* 3.5 14.8 - - + -
56B LEU* 4.9 4.3 - - + -
57B TRP* 1.3 75.7 - - - +
59B ARG* 1.3 61.5 + - - +
60B GLN* 4.0 28.9 + - + +
92B ILE* 5.7 5.2 - - + +
120B TRP* 3.2 4.3 - - - +
121B ASP* 3.4 1.5 - - - -
122B ALA* 2.7 49.0 + - + +
124B ALA* 4.2 22.4 - - + -
126B THR* 6.0 0.4 - - + -
148B PHE* 4.1 26.5 - - + -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR 3.6 0.7 - - - +
35B LEU* 3.4 5.4 - - - +
36B GLN* 2.8 64.3 + - + +
57B TRP 4.1 0.8 + - - -
58B ILE* 1.3 72.5 - - - +
60B GLN* 1.3 62.5 + - - +
61B ILE* 4.1 19.4 - - + +
119B THR* 3.8 27.7 - - + +
120B TRP 3.2 4.0 - - - +
121B ASP* 2.6 41.8 + - - +
1216B EPE 3.7 34.4 + - - -
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.1 3.6 - - + -
34B THR 3.3 7.9 - - - +
35B LEU* 4.7 3.8 - - + -
58B ILE* 4.0 24.3 + - + +
59B ARG* 1.3 75.3 - - - +
61B ILE* 1.3 64.3 + - - +
62B TRP* 3.6 17.0 - - + -
90B PRO* 3.2 33.7 + - - +
92B ILE* 3.3 33.4 + - + +
119B THR* 3.5 1.0 - - - -
120B TRP* 2.8 66.8 + - + +
122B ALA* 6.1 1.2 - - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN 3.9 0.3 - - - +
33B VAL* 3.3 2.3 - - - +
34B THR* 2.9 53.1 + - + +
36B GLN* 6.1 0.7 - - + +
59B ARG* 4.1 23.3 - - + +
60B GLN* 1.3 80.5 - - - +
62B TRP* 1.3 68.1 + - - +
117B LEU* 3.7 29.2 - - + -
118B ILE 3.3 9.0 - - - +
119B THR* 4.0 21.1 - - + +
163B ALA* 5.9 4.3 - - + -
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO* 4.6 0.6 - - - +
31B LEU* 3.9 13.2 - - + -
32B ASN 3.3 20.6 - - - +
33B VAL* 4.0 4.3 - - + -
60B GLN* 3.6 24.9 - - + -
61B ILE* 1.3 82.4 - - - +
63B HIS* 1.3 80.2 + - - +
64B ASP* 4.5 4.6 + - - +
87B VAL* 4.4 2.0 - - + -
88B TRP* 3.2 43.3 + + - -
89B ARG* 4.4 4.9 - - + -
90B PRO* 3.5 32.8 - - + -
110B VAL* 4.7 0.9 - - + -
116B GLY 3.7 0.2 - - - +
117B LEU* 3.7 3.9 - - - +
118B ILE* 2.8 70.0 + - + +
120B TRP* 3.8 23.3 - + + -
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PRO 4.4 1.4 - - - +
31B LEU* 3.8 16.5 - - - +
32B ASN 4.4 3.0 + - - -
62B TRP* 1.3 85.5 - - - +
64B ASP* 1.3 60.5 + - - +
65B ALA* 3.9 2.6 + - - +
113B ARG* 5.3 0.9 - - - -
115B ASP* 3.2 40.5 + - - -
116B GLY* 3.4 10.8 - - - -
117B LEU* 3.5 25.7 - - + +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 2.8 27.4 + - - -
23B PRO* 3.4 26.3 - - + +
62B TRP* 4.1 2.7 + - - +
63B HIS* 1.3 72.5 - - - +
65B ALA* 1.3 61.6 + - - +
66B TYR* 2.8 34.7 + - - +
67B LEU* 3.2 28.8 + - + +
68B THR* 3.9 2.3 - - - +
88B TRP* 4.7 1.4 + - - +
116B GLY* 2.8 25.3 + - - +
118B ILE* 3.7 24.0 - - + +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PRO 3.3 21.6 + - - +
25B GLU* 3.6 25.4 - - + +
63B HIS* 3.9 3.4 + - - +
64B ASP* 1.3 71.3 + - - +
66B TYR* 1.3 72.6 + - + +
68B THR* 4.2 14.0 + - - +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.3 9.0 - - - +
17B TYR* 4.2 17.7 - + + -
22B ARG 5.0 0.7 - - - -
23B PRO* 3.8 29.2 - - + -
24B VAL 3.1 30.0 + - - -
25B GLU* 3.4 16.4 + - + +
64B ASP* 2.8 7.5 + - - +
65B ALA* 1.3 85.1 - - + +
67B LEU* 1.3 67.9 + - - +
68B THR* 3.5 4.7 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.8 37.5 - - + +
14B PHE* 4.0 12.3 - - + -
17B TYR* 3.6 24.9 - - + -
64B ASP* 3.2 33.4 + - + +
66B TYR* 1.3 85.4 - - - +
68B THR* 1.3 61.3 + - - +
69B TRP* 3.8 5.1 - - - -
87B VAL* 3.7 27.4 - - + -
112B LEU* 3.4 27.1 - - + +
116B GLY* 3.3 17.8 + - - -
118B ILE* 4.1 7.0 - - + -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 10.0 - - - +
64B ASP 3.9 8.5 - - - +
65B ALA* 4.2 13.4 + - - +
66B TYR 3.5 3.7 - - - +
67B LEU* 1.3 79.8 - - - +
69B TRP* 1.3 67.2 + - - +
114B TYR 3.3 10.8 - - - -
115B ASP* 3.7 7.6 - - - +
116B GLY* 3.6 21.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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