Contacts of the strand formed by residues 29 - 42 (chain B) in PDB entry 3UGV
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 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PRO* 3.7 26.9 - - + -
23B VAL 3.3 12.6 + - - +
24B THR* 4.4 15.3 - - - +
28B ALA* 1.3 77.7 - - - +
30B ILE* 1.3 71.5 + - - +
31B PRO* 3.6 12.7 - - + +
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Residues in contact with ILE 30 (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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19B LEU* 3.9 2.4 - - - +
23B VAL* 2.8 54.6 + - + +
25B ALA* 6.1 1.3 - - + -
27B ILE* 4.8 10.8 - - + -
28B ALA* 4.3 17.9 - - + +
29B THR* 1.3 85.1 - - - +
31B PRO* 1.3 62.5 - - + +
32B ASP* 3.7 21.0 + - + +
55B TYR 5.9 2.5 - - - +
57B PRO* 6.5 2.5 - - + -
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Residues in contact with PRO 31 (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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18B LYS* 3.7 28.9 - - + +
19B LEU* 2.8 37.8 + - + +
22B PRO* 4.0 19.5 - - + -
29B THR* 3.6 13.9 - - + +
30B ILE* 1.3 86.9 - - + +
32B ASP* 1.3 64.2 + - + +
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Residues in contact with ASP 32 (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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16B LEU* 3.3 35.6 - - + +
17B LEU 3.4 1.4 - - - +
18B LYS* 3.2 39.2 + - - +
19B LEU* 4.5 1.8 - - - +
30B ILE* 3.4 20.5 - - + +
31B PRO* 1.3 86.3 - - + +
33B TRP* 1.3 68.8 + - - +
34B PRO* 4.1 5.8 - - - +
55B TYR 5.2 1.0 - - - +
57B PRO* 5.2 7.6 - - + +
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Residues in contact with TRP 33 (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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16B LEU* 4.6 0.7 - - - -
17B LEU* 3.0 35.9 + - + +
19B LEU* 3.6 26.5 - - + -
23B VAL* 5.7 2.0 - - + -
32B ASP* 1.3 81.8 - - - +
34B PRO* 1.3 72.4 - - + +
35B LEU* 3.8 16.1 + - + +
53B GLU* 2.9 45.0 + - + -
55B TYR* 3.9 51.4 - + - -
305B LEU* 4.3 7.4 - - + -
328B TRP* 3.6 61.6 + + + +
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Residues in contact with PRO 34 (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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15B VAL 3.4 7.4 - - - +
16B LEU* 4.3 4.2 - - + -
32B ASP 4.1 4.7 - - - +
33B TRP* 1.3 95.6 + - + +
35B LEU* 1.3 62.7 + - - +
53B GLU* 3.9 6.8 - - - +
54B PRO* 3.5 14.5 - - + +
55B TYR* 3.3 43.3 - - - +
56B VAL 4.1 0.9 - - - -
57B PRO* 3.8 22.9 - - + -
60B MET* 3.7 28.7 - - + -
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Residues in contact with LEU 35 (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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15B VAL* 2.9 35.4 + - + +
17B LEU* 3.7 32.1 - - + -
33B TRP* 3.8 10.9 + - + +
34B PRO* 1.3 77.4 - - - +
36B ILE* 1.3 63.9 + - - +
37B LEU* 3.7 12.3 - - + -
51B TYR* 3.9 7.9 - - + -
52B LEU 3.4 4.5 - - - +
53B GLU* 3.6 31.9 - - + +
54B PRO* 4.3 0.7 - - - -
60B MET* 3.4 5.7 - - - +
329B ALA* 3.9 20.4 - - + -
332B ILE* 3.5 32.1 - - + -
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Residues in contact with ILE 36 (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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12B ALA* 3.9 16.6 - - + -
13B ARG 3.6 6.1 - - - +
14B PRO* 4.7 0.9 - - + -
35B LEU* 1.3 77.2 - - - +
37B LEU* 1.3 63.2 + - - +
38B ILE* 3.8 8.5 + - + +
51B TYR* 3.1 7.3 - - - +
52B LEU* 2.9 46.0 + - + -
54B PRO* 4.5 5.6 - - + +
60B MET* 3.8 22.4 - - + -
63B LEU* 3.6 41.1 - - + -
64B VAL* 4.1 16.2 - - + -
67B LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 37 (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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11B THR 3.5 1.9 - - - +
12B ALA* 3.4 3.3 - - - -
13B ARG* 2.9 45.1 + - + +
15B VAL* 4.2 18.8 - - + -
35B LEU* 3.7 17.3 - - + -
36B ILE* 1.3 78.2 - - - +
38B ILE* 1.3 60.9 + - - +
39B ASP* 4.0 7.1 - - - +
50B ALA 4.2 2.7 - - - -
51B TYR* 4.2 2.9 - - + -
332B ILE* 3.5 30.7 - - + -
356B TRP* 4.0 33.9 - - + +
361B VAL* 3.7 33.0 - - + -
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Residues in contact with ILE 38 (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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10B LEU* 3.8 26.5 - - + -
11B THR 3.5 2.7 - - - -
12B ALA* 4.8 2.5 - - + -
36B ILE* 4.0 14.1 - - + +
37B LEU* 1.3 76.2 - - - +
39B ASP* 1.3 66.6 + - - +
40B ILE* 4.5 0.7 - - + -
49B ARG* 3.4 6.4 - - - -
50B ALA 2.9 38.6 + - - +
51B TYR* 4.9 0.9 - - - -
52B LEU* 4.0 18.2 - - + +
67B LEU* 4.3 17.5 - - + -
107B GLY* 3.5 37.7 - - - +
108B VAL 4.4 0.2 - - - +
111B ALA* 3.7 22.2 - - + -
356B TRP* 3.7 2.6 - - - -
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Residues in contact with ASP 39 (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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9B LYS 3.8 0.5 - - - +
10B LEU* 3.4 2.9 - - - -
11B THR* 2.9 46.8 + - - +
13B ARG* 3.4 27.7 + - - -
37B LEU 4.0 6.6 - - - +
38B ILE* 1.3 74.7 - - - +
40B ILE* 1.3 63.0 + - - +
41B GLU* 5.3 3.7 - - + +
48B GLY 3.2 4.5 - - - +
49B ARG* 3.5 11.7 + - + +
356B TRP* 2.7 31.9 + - - -
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Residues in contact with ILE 40 (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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7B PHE* 3.9 15.3 - - + -
9B LYS 3.5 4.5 - - - +
10B LEU* 3.9 23.8 - - + -
38B ILE* 4.5 0.2 - - + -
39B ASP* 1.3 76.7 - - - +
41B GLU* 1.3 77.9 + - - +
42B THR* 4.6 2.9 - - + -
47B PRO* 3.4 7.6 - - - +
48B GLY* 2.6 46.3 + - - +
79B LEU* 4.0 19.1 - - + -
108B VAL 4.2 0.7 - - - +
111B ALA* 3.8 24.0 - - + -
112B VAL* 3.4 34.1 - - + +
115B ALA* 4.8 2.7 - - + -
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Residues in contact with GLU 41 (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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8B ARG* 2.8 46.5 + - + +
9B LYS* 2.9 49.0 + - + +
11B THR* 4.8 3.1 + - - +
39B ASP* 5.3 4.5 - - + +
40B ILE* 1.3 82.1 - - - +
42B THR* 1.3 64.2 + - - +
46B VAL 4.3 1.3 - - - -
47B PRO* 5.0 1.1 - - + -
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Residues in contact with THR 42 (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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5B LEU* 4.0 16.3 - - + +
6B THR 3.0 19.7 - - - +
8B ARG* 3.9 7.3 - - - +
40B ILE* 4.6 2.5 - - + -
41B GLU* 1.3 79.8 - - - +
43B GLU* 1.3 63.4 + - - +
44B GLU* 3.6 8.9 + - - -
45B GLY* 3.0 17.0 + - - -
46B VAL* 2.9 47.4 + - + +
79B LEU* 3.8 29.4 - - + -
115B ALA* 4.9 2.0 - - + -
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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