Contacts of the strand formed by residues 29 - 42 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D PRO* 3.8 25.8 - - + -
23D VAL 3.2 10.5 - - - +
24D THR* 4.1 20.2 + - - +
28D ALA* 1.3 72.9 - - - +
30D ILE* 1.3 69.5 + - - +
31D PRO* 3.4 14.3 - - + +
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.7 5.5 - - + +
23D VAL* 2.7 53.6 + - + +
25D ALA* 5.5 1.6 - - + -
27D ILE* 4.5 9.2 - - + -
28D ALA* 3.3 27.6 - - + +
29D THR* 1.3 82.6 - - - +
31D PRO* 1.3 63.0 - - + +
32D ASP* 3.6 22.9 - - + +
33D TRP* 5.9 3.1 - - + -
55D TYR 5.9 2.0 - - - +
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Residues in contact with PRO 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LYS* 3.8 24.2 - - - +
19D LEU* 2.9 32.9 + - - +
22D PRO* 4.3 17.3 - - + -
29D THR* 3.4 14.1 - - + +
30D ILE* 1.3 85.9 - - + +
32D ASP* 1.3 79.6 + - + +
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Residues in contact with ASP 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.7 33.4 - - + +
17D LEU 3.4 7.7 - - - +
18D LYS* 3.5 30.7 + - - +
19D LEU* 4.5 1.3 - - - +
30D ILE* 3.5 18.7 - - + +
31D PRO* 1.3 91.9 - - + +
33D TRP* 1.3 64.8 + - - +
34D PRO* 3.9 7.2 - - - +
55D TYR 5.0 1.2 - - - +
57D PRO* 5.3 5.5 - - + +
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Residues in contact with TRP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.8 3.1 - - - -
17D LEU* 2.9 44.1 + - + +
19D LEU* 3.6 35.9 - - + -
30D ILE* 5.9 2.2 - - + -
31D PRO 4.3 0.2 + - - -
32D ASP* 1.3 79.3 - - - +
34D PRO* 1.3 75.0 + - + +
35D LEU* 4.0 14.7 + - + +
53D GLU* 3.0 48.4 + - + +
55D TYR* 4.0 51.8 - + - -
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Residues in contact with PRO 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL 3.5 6.7 - - - +
16D LEU* 3.7 10.1 - - + -
32D ASP 3.9 5.6 - - - +
33D TRP* 1.3 99.3 + - + +
35D LEU* 1.3 66.9 + - - +
53D GLU* 3.9 4.0 - - - -
54D PRO* 3.5 15.0 - - + +
55D TYR* 3.2 43.7 - - - +
56D VAL 4.0 1.1 - - - +
57D PRO* 4.0 13.0 - - + -
60D MET* 3.9 25.1 - - + -
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG 3.7 1.0 - - - +
14D PRO* 3.7 2.4 - - - +
15D VAL* 2.9 49.6 + - + +
17D LEU* 3.5 33.7 - - + -
33D TRP* 4.3 9.9 - - + +
34D PRO* 1.3 76.9 - - - +
36D ILE* 1.3 63.1 + - - +
37D LEU* 3.9 11.4 - - + +
51D TYR* 3.8 19.5 - - + -
52D LEU 3.3 6.5 - - - +
53D GLU* 3.3 37.2 - - + +
54D PRO* 4.3 0.4 - - - -
60D MET* 3.7 0.7 - - - +
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.9 28.0 - - + -
13D ARG 3.6 7.0 - - - +
14D PRO* 4.6 2.9 - - + -
35D LEU* 1.3 75.2 - - - +
37D LEU* 1.3 64.2 + - - +
38D ILE* 3.7 6.9 + - + +
51D TYR* 3.3 4.9 - - - -
52D LEU* 3.0 44.7 + - + -
54D PRO* 4.2 9.0 - - + -
60D MET* 3.7 34.5 - - + -
63D LEU* 3.8 36.6 - - + -
64D VAL* 4.6 7.2 - - + -
67D LEU* 3.9 10.8 - - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D THR 3.3 1.7 - - - +
12D ALA* 3.3 5.4 - - - -
13D ARG* 2.9 67.1 + - + +
15D VAL* 4.1 23.1 - - + -
35D LEU* 3.9 25.8 - - + +
36D ILE* 1.3 77.4 - - - +
38D ILE* 1.3 60.6 + - - +
39D ASP* 4.2 3.8 + - - +
50D ALA 4.0 3.6 - - - +
51D TYR* 4.5 9.6 - - + -
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.7 31.4 - - + -
11D THR 3.3 3.6 - - - +
12D ALA* 5.0 0.7 - - + -
36D ILE* 3.8 15.7 - - + +
37D LEU* 1.3 79.1 - - - +
39D ASP* 1.3 64.9 + - - +
40D ILE* 4.5 1.6 - - + -
48D GLY 3.5 0.2 - - - +
49D ARG* 3.3 7.8 - - - +
50D ALA 2.8 40.8 + - - +
52D LEU* 4.4 10.3 - - + +
67D LEU* 4.1 22.9 - - + -
107D GLY* 3.5 35.9 - - - +
111D ALA* 3.9 17.0 - - + +
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Residues in contact with ASP 39 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D LYS 4.0 0.3 - - - +
10D LEU* 3.4 2.5 - - - -
11D THR* 2.8 48.7 + - - +
13D ARG* 3.4 28.7 + - - -
37D LEU* 4.7 2.8 - - - +
38D ILE* 1.3 79.7 + - - +
40D ILE* 1.3 63.4 + - - +
41D GLU* 4.2 4.4 + - + +
48D GLY 3.3 2.7 - - - +
49D ARG* 3.3 31.6 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 4.0 20.4 - - + -
9D LYS 3.5 7.2 - - - +
10D LEU* 4.1 20.6 - - + -
39D ASP* 1.3 76.4 - - - +
41D GLU* 1.3 76.9 + - - +
42D THR* 4.6 4.0 - - + -
47D PRO* 3.4 8.5 - - - +
48D GLY* 2.7 40.5 + - - +
79D LEU* 4.3 10.3 - - + -
108D VAL 4.3 0.4 - - - +
111D ALA* 3.7 26.0 - - + -
112D VAL* 3.2 35.9 - - + +
115D ALA* 5.0 2.7 - - + -
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ARG* 2.9 57.8 + - + +
9D LYS* 2.9 48.5 + - + +
11D THR* 5.0 3.9 + - - +
39D ASP* 5.2 4.9 - - + +
40D ILE* 1.3 83.9 - - - +
42D THR* 1.3 64.5 + - - +
46D VAL 4.5 0.9 - - - -
47D PRO* 5.0 1.3 - - - -
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Residues in contact with THR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.3 10.5 - - + -
6D THR 3.0 19.3 - - - +
8D ARG* 3.8 19.2 + - - +
40D ILE* 4.6 4.0 - - + -
41D GLU* 1.3 79.2 - - - +
43D GLU* 1.3 61.5 + - - +
44D GLU* 3.7 9.0 + - - -
45D GLY* 3.2 13.6 + - - -
46D VAL* 2.6 49.7 + - + +
79D LEU* 4.0 28.0 - - + -
115D ALA* 4.9 3.8 - - + -
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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