Contacts of the strand formed by residues 29 - 42 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C PRO* 4.1 22.7 - - + -
23C VAL 3.3 11.9 - - - +
24C THR* 4.1 20.0 - - - +
25C ALA 5.2 0.2 + - - -
28C ALA* 1.3 81.9 + - - +
30C ILE* 1.3 63.0 + - - +
31C PRO* 3.3 12.9 - - + +
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Residues in contact with ILE 30 (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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19C LEU* 3.4 8.8 - - + +
22C PRO* 4.5 1.3 - - - -
23C VAL* 3.0 57.5 + - + +
25C ALA* 5.0 5.8 - - + -
27C ILE* 6.4 1.1 - - + -
28C ALA* 4.5 9.6 - - + +
29C THR* 1.3 78.8 - - - +
31C PRO* 1.3 65.1 - - + +
32C ASP* 3.6 24.9 - - + +
33C TRP* 6.2 0.7 - - + -
55C TYR 5.7 4.3 - - - +
57C PRO* 6.3 2.2 - - + -
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Residues in contact with PRO 31 (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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18C LYS* 3.6 28.4 - - + +
19C LEU* 2.6 38.9 + - + +
22C PRO* 4.0 20.0 - - + -
29C THR* 3.3 13.2 - - + +
30C ILE* 1.3 87.3 - - + +
32C ASP* 1.3 72.3 + - + +
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Residues in contact with ASP 32 (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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16C LEU* 3.7 27.9 - - + +
17C LEU 3.3 9.6 - - - +
18C LYS* 3.1 33.6 + - - +
19C LEU* 4.5 2.5 - - - +
30C ILE* 3.4 20.7 - - + +
31C PRO* 1.3 91.8 - - + +
33C TRP* 1.3 67.8 + - - +
34C PRO* 3.9 6.8 - - - +
55C TYR 5.0 0.9 - - - +
57C PRO* 5.3 5.6 - - + +
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Residues in contact with TRP 33 (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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15C VAL 4.0 0.2 - - - +
16C LEU* 4.0 2.9 - - - -
17C LEU* 2.9 38.3 + - + +
19C LEU* 3.7 24.9 - - + -
30C ILE* 6.2 0.9 - - + -
32C ASP* 1.3 79.1 - - - +
34C PRO* 1.3 72.6 - - + +
35C LEU* 3.8 15.3 + - + +
53C GLU* 3.0 43.4 + - + -
55C TYR* 3.7 52.9 - + - -
305C LEU* 4.1 8.5 - - + -
328C TRP* 3.5 61.6 - + + +
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Residues in contact with PRO 34 (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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15C VAL 3.4 7.2 - - - +
16C LEU* 3.9 5.3 - - + -
32C ASP 3.9 4.7 - - - +
33C TRP* 1.3 96.2 + - + +
35C LEU* 1.3 69.5 + - - +
53C GLU* 3.9 3.1 - - - -
54C PRO* 3.4 14.2 - - + +
55C TYR 3.2 46.2 - - - +
56C VAL 3.9 2.2 - - - +
57C PRO* 3.9 26.5 - - + -
60C MET* 3.9 14.4 - - + -
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Residues in contact with LEU 35 (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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13C ARG 4.5 0.2 - - - -
15C VAL* 2.7 35.9 + - + +
17C LEU* 3.7 23.1 - - + -
33C TRP* 4.0 13.5 - - + +
34C PRO* 1.3 83.6 - - - +
36C ILE* 1.3 64.7 + - - +
37C LEU* 4.0 12.3 - - + -
51C TYR* 4.2 7.6 - - + -
52C LEU 3.4 5.8 - - - +
53C GLU* 3.4 36.1 - - + +
54C PRO* 4.3 0.2 - - - -
60C MET* 3.4 6.8 - - - +
328C TRP 4.7 0.2 - - - +
329C ALA* 4.2 10.1 - - + -
332C ILE* 3.6 34.5 - - + -
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Residues in contact with ILE 36 (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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12C ALA* 3.8 29.2 - - + -
13C ARG 3.6 6.1 - - - +
14C PRO* 4.5 4.3 - - + -
35C LEU* 1.3 79.4 - - - +
37C LEU* 1.3 63.6 + - - +
38C ILE* 3.5 7.3 + - + +
51C TYR* 3.4 4.7 - - - -
52C LEU* 3.0 41.6 + - + -
54C PRO* 4.2 7.2 - - + -
60C MET* 3.7 32.3 - - + -
63C LEU* 3.9 35.9 - - + -
64C VAL* 4.6 6.3 - - + -
67C LEU* 3.9 10.5 - - + -
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Residues in contact with LEU 37 (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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11C THR 3.4 1.6 - - - +
12C ALA* 3.3 4.5 - - - -
13C ARG* 2.8 50.1 + - + +
15C VAL* 4.1 22.4 - - + -
35C LEU* 4.2 16.4 - - + -
36C ILE* 1.3 73.9 - - - +
38C ILE* 1.3 60.0 + - - +
39C ASP* 4.6 1.9 - - - +
50C ALA 4.1 3.8 - - - -
51C TYR* 4.5 3.4 - - + -
332C ILE* 4.5 15.0 - - + -
356C TRP* 3.4 54.1 - - + +
361C VAL* 3.8 26.9 - - + -
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Residues in contact with ILE 38 (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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10C LEU* 3.5 33.4 - - + -
11C THR 3.3 2.7 - - - -
12C ALA* 4.7 1.6 - - + -
36C ILE* 3.8 16.6 - - + +
37C LEU* 1.3 78.0 - - - +
39C ASP* 1.3 68.3 + - - +
48C GLY 3.6 0.5 - - - +
49C ARG* 3.5 7.6 - - - -
50C ALA 2.9 36.5 + - - +
52C LEU* 4.1 18.8 - - + +
67C LEU* 4.3 13.0 - - + -
107C GLY* 3.5 36.8 - - - +
108C VAL 4.2 1.1 - - - +
111C ALA* 3.8 16.4 - - + -
356C TRP* 4.0 2.3 - - - -
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Residues in contact with ASP 39 (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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9C LYS 3.8 0.5 - - - +
10C LEU* 3.2 5.9 - - - -
11C THR* 2.9 48.9 + - - +
13C ARG* 3.1 31.2 + - - -
37C LEU 4.6 0.5 - - - -
38C ILE* 1.3 77.1 + - - +
40C ILE* 1.3 65.6 + - - +
41C GLU* 5.4 3.3 - - + +
48C GLY 3.5 1.7 - - - +
49C ARG* 3.2 27.4 + - - +
356C TRP* 3.2 15.1 + - - -
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Residues in contact with ILE 40 (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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7C PHE* 3.7 20.6 - - + -
9C LYS 3.7 0.9 - - - -
10C LEU* 3.4 33.9 - - + -
39C ASP* 1.3 75.1 - - - +
41C GLU* 1.3 78.2 + - - +
42C THR* 4.3 4.9 - - + -
47C PRO* 3.4 10.8 - - - +
48C GLY* 2.8 35.8 + - - +
79C LEU* 3.9 24.2 - - + -
111C ALA* 3.4 35.0 - - + -
112C VAL* 4.2 9.6 - - + +
115C ALA* 4.6 3.1 - - + -
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Residues in contact with GLU 41 (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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8C ARG* 2.8 61.9 + - + +
9C LYS* 3.0 50.0 + - + +
11C THR* 4.9 3.5 + - - +
39C ASP* 5.4 3.1 - - + +
40C ILE* 1.3 81.5 - - - +
42C THR* 1.3 65.0 + - - +
46C VAL 4.4 1.1 - - - -
47C PRO* 5.3 0.2 - - - -
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Residues in contact with THR 42 (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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5C LEU* 3.6 27.6 - - + +
6C THR 3.0 15.0 - - - +
8C ARG* 3.7 12.8 + - - -
40C ILE* 4.3 4.3 - - + -
41C GLU* 1.3 79.2 - - - +
43C GLU* 1.3 57.0 + - - +
44C GLU 2.9 3.0 + - - -
45C GLY* 2.8 23.6 + - - -
46C VAL* 2.6 49.6 + - + +
79C LEU* 4.1 23.1 - - + -
115C 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