Contacts of the strand formed by residues 7 - 24 (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 PHE 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C THR* 1.3 72.0 - - - +
8C ARG* 1.3 62.0 + - - +
9C LYS* 3.6 33.7 - - - -
10C LEU* 3.7 13.7 - - + -
40C ILE* 3.7 26.7 - - + -
41C GLU 4.0 2.9 - - - -
43C GLU* 4.8 0.9 - - - +
71C SER* 3.7 25.8 - - - -
74C LEU* 3.6 42.6 - - + +
75C ALA 3.8 0.2 - - - -
76C GLY* 2.9 30.0 + - - -
77C GLN 2.9 20.3 + - - +
78C PRO 4.9 0.4 - - - +
79C LEU* 3.7 34.5 - - + +
84C ILE* 4.8 7.0 - - + -
112C VAL* 4.9 2.9 - - + -
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Residues in contact with ARG 8 (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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6C THR 3.4 0.6 + - - -
7C PHE* 1.3 75.3 - - - +
9C LYS* 1.3 71.4 + - + +
41C GLU* 2.8 59.0 + - - +
42C THR 3.7 19.2 + - - -
43C GLU* 3.5 49.3 + - - +
45C GLY* 5.4 1.6 - - - +
75C ALA* 3.5 25.3 - - - +
76C GLY 4.8 0.7 - - - +
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Residues in contact with LYS 9 (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* 3.6 9.4 - - - -
8C ARG* 1.3 90.5 - - + +
10C LEU* 1.3 65.7 + - - +
11C THR* 3.8 23.1 + - - +
39C ASP 3.8 0.3 - - - +
40C ILE* 3.7 1.9 - - - -
41C GLU* 3.0 59.4 + - + +
71C SER* 3.3 12.1 - - - +
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.7 14.4 - - + -
9C LYS* 1.3 79.2 - - - +
11C THR* 1.3 75.6 + - - +
12C ALA* 4.3 2.7 - - + +
38C ILE* 3.5 25.1 - - + -
39C ASP 3.2 3.8 - - - +
40C ILE* 3.4 24.5 - - + -
67C LEU* 4.1 35.9 - - + +
68C HIS* 3.4 15.0 - - + -
70C MET* 6.4 0.2 - - + -
71C SER* 2.7 20.9 + - - +
74C LEU* 6.1 0.7 - - + -
108C VAL* 3.9 28.9 - - + -
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Residues in contact with THR 11 (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 23.9 + - - +
10C LEU* 1.3 78.0 - - - +
12C ALA* 1.3 63.5 + - - +
13C ARG* 4.6 19.4 - - + +
37C LEU 3.4 1.9 - - - +
38C ILE* 3.3 4.5 - - - -
39C ASP* 2.9 45.9 + - - +
41C GLU* 4.9 3.3 + - - +
68C HIS* 3.8 8.3 - - + +
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Residues in contact with ALA 12 (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* 4.5 2.7 - - + -
11C THR* 1.3 75.3 - - - +
13C ARG* 1.3 64.0 + - - +
14C PRO* 3.6 9.1 - - - +
36C ILE* 3.8 9.6 - - + -
37C LEU 3.3 4.3 - - - +
38C ILE* 4.6 1.6 - - + +
64C VAL* 3.9 11.8 - - + +
67C LEU* 3.5 39.3 - - + -
68C HIS* 3.1 27.2 + - + +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C THR* 4.6 15.6 + - + +
12C ALA* 1.3 75.3 - - - +
14C PRO* 1.3 67.9 - - + +
15C VAL* 3.6 9.1 + - + +
36C ILE* 3.6 2.6 - - - +
37C LEU* 2.8 43.8 + - + +
39C ASP* 3.1 28.3 + - - -
356C TRP* 3.2 14.8 - - - +
358C GLU* 2.7 43.8 + - - -
361C VAL* 3.7 15.2 - - + +
365C LEU* 4.2 20.0 - - + -
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Residues in contact with PRO 14 (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 3.6 8.7 - - - +
13C ARG* 1.3 84.0 - - + +
15C VAL* 1.3 65.2 + - - +
35C LEU 3.6 6.7 - - - +
36C ILE* 4.5 3.4 - - + -
60C MET* 3.8 30.7 - - + -
64C VAL* 4.4 13.2 - - + -
365C LEU* 3.3 17.7 - - + +
366C VAL* 3.5 31.5 + - + +
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Residues in contact with VAL 15 (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 3.8 9.0 - - - +
14C PRO* 1.3 81.0 - - - +
16C LEU* 1.3 64.3 + - - +
17C LEU* 3.5 27.8 - - + -
33C TRP 4.0 0.5 - - - +
34C PRO* 3.4 2.4 - - - +
35C LEU* 2.7 45.2 + - + +
37C LEU* 4.1 13.9 - - + -
60C MET* 4.1 5.2 - - - +
332C ILE* 4.4 10.5 - - + -
361C VAL* 4.1 28.9 - - + +
364C ASN* 3.6 16.8 - - + +
365C LEU* 4.1 7.2 - - + -
366C VAL* 4.5 0.9 - - - -
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Residues in contact with LEU 16 (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* 1.3 72.0 - - - +
17C LEU* 1.3 63.1 + - - +
32C ASP* 3.7 37.2 - - + +
33C TRP 4.0 0.7 - - - -
34C PRO* 3.9 18.8 - - + -
57C PRO* 3.7 31.9 - - + -
60C MET* 5.1 2.5 - - + -
364C ASN* 3.0 29.7 + - - +
365C LEU 5.7 0.2 - - - +
366C VAL* 4.4 15.8 - - + +
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Residues in contact with LEU 17 (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* 3.5 25.5 - - + -
16C LEU* 1.3 75.0 - - - +
18C LYS* 1.3 64.9 + - - +
32C ASP* 3.3 10.2 - - - +
33C TRP* 2.9 41.6 + - + +
35C LEU* 3.7 22.4 - - + -
328C TRP 3.5 23.8 - - - +
329C ALA* 4.8 0.2 - - - -
331C PRO* 4.0 26.7 - - + -
332C ILE* 4.3 11.0 - - + +
360C VAL* 4.6 1.6 - - + -
364C ASN* 3.6 24.7 - - + +
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Residues in contact with LYS 18 (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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17C LEU* 1.3 78.3 - - - +
19C LEU* 1.3 72.5 + - - +
20C GLN 3.6 1.6 + - - -
31C PRO* 3.6 27.2 - - + +
32C ASP* 3.1 28.8 + - - +
331C PRO* 5.9 2.4 - - - +
364C ASN* 4.9 3.8 + - - +
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Residues in contact with LEU 19 (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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17C LEU 4.0 0.4 + - - -
18C LYS* 1.3 78.6 - - - +
20C GLN* 1.3 66.5 + - - +
21C ARG 3.5 14.1 + - - +
22C PRO* 4.2 7.0 - - + +
23C VAL* 3.9 23.6 - - + +
30C ILE* 3.4 25.8 - - + +
31C PRO* 2.6 22.7 + - - +
32C ASP 4.5 5.4 - - - +
33C TRP* 3.7 28.3 - - + -
328C TRP* 3.5 47.1 - - + +
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Residues in contact with GLN 20 (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 3.4 + - - -
19C LEU* 1.3 74.0 - - - +
21C ARG* 1.3 94.6 + - + +
22C PRO* 3.8 6.1 - - - +
161C GLU* 4.9 3.7 + - - +
327C SER* 5.0 7.1 + - - -
328C TRP* 5.9 2.0 - - - -
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Residues in contact with ARG 21 (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* 3.9 12.3 - - - +
20C GLN* 1.3 109.3 + - + +
22C PRO* 1.3 70.3 - - + +
23C VAL* 3.8 1.2 + - - +
141C ASN* 3.9 34.5 + - - +
142C GLY* 5.1 2.2 - - - -
144C TRP* 4.6 6.0 + - + -
154C GLU* 3.1 37.7 + - - +
157C GLU* 4.3 23.2 + - - +
158C LEU* 3.7 23.8 - - - +
161C GLU* 3.4 29.3 + - - +
327C SER* 5.6 0.2 + - - -
328C TRP* 5.1 4.7 + - - +
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Residues in contact with PRO 22 (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* 4.2 11.6 - - + +
20C GLN 3.8 8.5 - - - +
21C ARG* 1.3 87.4 - - + +
23C VAL* 1.3 59.0 + - - +
24C THR* 3.0 18.6 + - - +
29C THR* 4.1 17.0 - - + -
30C ILE 3.9 4.5 - - - +
31C PRO* 4.0 22.2 - - + -
144C TRP* 3.8 7.4 - - - -
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Residues in contact with VAL 23 (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* 3.9 18.8 - - + +
21C ARG 3.8 0.2 + - - -
22C PRO* 1.3 67.5 - - - +
24C THR* 1.3 59.2 + - - +
25C ALA* 3.4 9.0 + - + +
29C THR* 3.3 6.6 - - - -
30C ILE* 3.0 56.6 + - + +
33C TRP* 5.9 4.3 - - + -
144C TRP* 3.6 52.0 - - + +
328C TRP* 4.8 9.4 - - + -
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Residues in contact with THR 24 (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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22C PRO* 3.0 17.2 + - - +
23C VAL* 1.3 68.5 - - - +
25C ALA* 1.3 63.8 + - - +
29C THR* 4.1 20.2 - - - +
144C TRP* 3.4 21.8 - - - +
145C LEU* 2.9 42.9 + - - +
146C LYS* 4.2 20.2 - - + +
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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
------------------------------------------------------------
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