Contacts of the strand formed by residues 7 - 24 (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 PHE 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D THR* 1.3 72.4 - - - +
8D ARG* 1.3 61.7 + - - +
9D LYS* 3.5 32.1 - - - -
10D LEU* 3.8 14.4 - - + -
40D ILE* 4.0 26.5 - - + -
41D GLU 4.2 2.5 - - - -
42D THR* 4.6 0.4 - - - -
43D GLU* 4.7 1.3 - - - +
71D SER* 3.7 27.8 - - - -
74D LEU* 3.7 40.4 - - + +
75D ALA 3.8 0.4 - - - -
76D GLY* 2.8 32.1 + - - -
77D GLN 2.8 19.6 + - - +
78D PRO 4.8 0.9 - - - +
79D LEU* 3.7 32.2 - - + +
84D ILE* 4.5 7.2 - - + -
112D VAL* 4.9 1.6 - - + -
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Residues in contact with ARG 8 (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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6D THR 3.5 1.0 + - - -
7D PHE* 1.3 79.6 - - - +
9D LYS* 1.3 71.0 + - + +
41D GLU* 2.9 47.7 + - - +
42D THR 3.8 20.2 + - - -
43D GLU* 3.1 49.3 + - - +
45D GLY* 6.0 1.0 - - - -
75D ALA* 3.9 17.5 - - - +
76D GLY 4.8 0.4 - - - +
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Residues in contact with LYS 9 (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* 3.5 8.0 - - - -
8D ARG* 1.3 89.3 - - + +
10D LEU* 1.3 67.1 + - - +
11D THR* 4.2 14.6 + - - +
39D ASP 4.0 0.2 - - - +
40D ILE* 3.5 5.0 - - - +
41D GLU* 2.9 65.8 + - + +
71D SER* 3.5 11.2 - - - +
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Residues in contact with LEU 10 (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* 3.8 13.5 - - + -
9D LYS* 1.3 80.5 - - - +
11D THR* 1.3 76.1 + - - +
12D ALA* 4.2 1.8 - - + +
38D ILE* 3.7 27.8 - - + -
39D ASP 3.4 4.9 - - - -
40D ILE* 4.1 20.6 - - + -
67D LEU* 4.1 34.3 - - + +
68D HIS* 3.5 16.3 - - + -
71D SER* 2.8 20.8 + - - +
74D LEU* 5.8 0.2 - - + -
108D VAL* 3.9 28.0 - - + -
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Residues in contact with THR 11 (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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9D LYS* 4.2 20.0 + - - +
10D LEU* 1.3 76.5 + - - +
12D ALA* 1.3 62.7 + - - +
13D ARG* 4.1 26.5 - - + +
37D LEU 3.3 1.2 - - - +
38D ILE* 3.3 7.8 - - - +
39D ASP* 2.8 45.5 + - - +
41D GLU* 5.0 3.6 + - - +
68D HIS* 4.0 7.4 - - + +
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Residues in contact with ALA 12 (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* 4.4 2.2 - - + -
11D THR* 1.3 73.4 - - - +
13D ARG* 1.3 63.4 + - - +
14D PRO* 3.7 8.0 - - - +
36D ILE* 3.9 8.5 - - + -
37D LEU 3.3 4.9 - - - -
38D ILE* 4.8 1.6 - - + +
64D VAL* 3.8 18.5 - - + +
67D LEU* 3.6 39.0 - - + -
68D HIS* 3.2 21.6 + - - +
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Residues in contact with ARG 13 (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* 4.1 20.4 + - + +
12D ALA* 1.3 76.6 - - - +
14D PRO* 1.3 68.0 - - + +
15D VAL* 3.7 7.6 + - + +
35D LEU 3.7 0.2 - - - +
36D ILE* 3.6 2.5 - - - -
37D LEU* 2.9 63.1 + - + +
39D ASP* 3.4 25.6 + - - -
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Residues in contact with PRO 14 (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 3.7 7.2 - - - +
13D ARG* 1.3 85.7 - - + +
15D VAL* 1.3 64.0 + - - +
35D LEU 3.7 5.4 - - - +
36D ILE* 4.6 2.2 - - + -
60D MET* 3.8 32.8 - - + -
64D VAL* 4.3 16.1 - - + -
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Residues in contact with VAL 15 (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* 3.9 12.6 - - + +
14D PRO* 1.3 80.2 - - - +
16D LEU* 1.3 61.3 + - - +
17D LEU* 3.8 22.0 - - + -
34D PRO* 3.5 3.5 - - - +
35D LEU* 2.9 54.1 + - + +
37D LEU* 4.1 22.4 - - + -
60D MET* 3.6 8.1 - - - +
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Residues in contact with LEU 16 (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* 1.3 75.8 - - - +
17D LEU* 1.3 65.8 + - - +
18D LYS 4.1 0.7 + - - -
32D ASP* 3.7 40.6 - - + +
33D TRP 3.8 1.6 - - - +
34D PRO* 3.7 26.0 - - + -
57D PRO* 3.9 25.4 - - + -
60D MET* 5.0 4.3 - - + -
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Residues in contact with LEU 17 (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* 3.8 21.3 - - + -
16D LEU* 1.3 78.8 - - - +
18D LYS* 1.3 65.1 + - - +
19D LEU* 3.5 1.3 + - + -
32D ASP* 3.4 9.7 - - - +
33D TRP* 2.9 47.3 + - + +
35D LEU* 3.5 24.0 - - + -
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Residues in contact with LYS 18 (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 4.1 1.0 + - - -
17D LEU* 1.3 74.3 - - - +
19D LEU* 1.3 72.6 + - - +
20D GLN* 3.5 1.9 + - - -
31D PRO* 3.8 27.0 - - - +
32D ASP* 3.5 22.8 + - - +
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Residues in contact with LEU 19 (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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17D LEU* 3.5 2.9 + - + -
18D LYS* 1.3 80.0 - - - +
20D GLN* 1.3 64.2 + - - +
21D ARG* 3.9 19.0 - - - +
22D PRO* 4.4 6.6 - - + +
23D VAL* 4.0 20.4 - - + -
30D ILE* 3.7 22.2 - - + +
31D PRO* 2.9 22.2 + - - +
32D ASP 4.5 4.0 - - - +
33D TRP* 3.6 44.0 - - + -
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Residues in contact with GLN 20 (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 3.5 2.6 + - - -
19D LEU* 1.3 74.6 - - - +
21D ARG* 1.3 98.2 + - + +
22D PRO* 3.9 5.6 - - - +
141D ASN* 6.1 0.7 - - - -
161D GLU* 4.2 6.5 + - - +
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Residues in contact with ARG 21 (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* 3.9 12.3 - - - +
20D GLN* 1.3 109.8 - - + +
22D PRO* 1.3 72.2 - - + +
23D VAL* 3.5 2.6 + - - +
141D ASN* 4.0 33.2 - - - +
142D GLY* 5.2 1.1 - - - -
144D TRP* 4.7 4.2 + - + -
154D GLU* 3.8 35.4 + - - +
157D GLU* 3.1 30.3 + - - +
158D LEU* 3.4 28.3 - - - +
161D GLU* 3.2 27.9 + - - +
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Residues in contact with PRO 22 (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* 4.4 10.5 - - + +
20D GLN 3.9 6.7 - - - +
21D ARG* 1.3 87.4 - - + +
23D VAL* 1.3 60.1 + - - +
24D THR* 3.1 17.7 + - - +
29D THR* 3.8 23.6 - - + -
30D ILE 3.8 8.7 - - - +
31D PRO* 4.3 11.4 - - + -
144D TRP* 3.8 8.3 - - - +
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Residues in contact with VAL 23 (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* 4.0 18.6 - - + +
21D ARG 3.5 1.2 + - - +
22D PRO* 1.3 67.9 - - - +
24D THR* 1.3 59.8 + - - +
25D ALA* 3.5 13.9 + - + +
28D ALA 3.8 0.2 - - - +
29D THR* 3.2 4.1 - - - -
30D ILE* 2.7 57.0 + - + +
33D TRP* 6.0 5.8 - - + -
144D TRP* 3.5 50.0 - - + +
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Residues in contact with THR 24 (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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22D PRO* 3.1 16.4 + - - +
23D VAL* 1.3 71.9 - - - +
25D ALA* 1.3 62.9 + - - +
29D THR* 4.1 21.1 + - - +
144D TRP* 3.5 21.1 - - - +
145D LEU* 3.1 41.8 + - + +
146D LYS* 4.4 17.9 - - + +
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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