Contacts of the strand formed by residues 13 - 24 (chain D) in PDB entry 4CDC
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 GLY 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LEU 3.6 0.2 + - - -
12D LEU* 1.3 74.9 - - - +
14D THR* 1.3 63.4 + - - -
15D TRP* 4.0 4.8 + - - -
42D VAL 3.9 0.7 - - - +
43D TYR* 3.5 3.3 - - - -
44D LEU* 2.9 37.9 + - - +
117D LYS* 4.1 3.8 - - - -
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Residues in contact with THR 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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13D GLY* 1.3 72.9 - - - -
15D TRP* 1.3 63.9 + - - +
41D VAL* 3.7 18.4 - - + -
42D VAL 3.6 3.4 - - - +
43D TYR* 3.2 37.8 - - + -
117D LYS* 3.3 10.1 - - - +
118D VAL* 2.9 51.5 + - + -
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Residues in contact with TRP 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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10D ASP 4.2 8.3 - - - -
11D LEU* 2.8 46.7 + - + +
13D GLY 4.1 6.1 - - - -
14D THR* 1.3 79.4 - - - +
16D VAL* 1.3 62.2 + - - +
17D PHE* 3.9 29.5 + + + -
40D VAL 4.0 0.5 - - - +
41D VAL* 3.5 5.0 - - - +
42D VAL* 2.8 36.8 + - + +
44D LEU* 3.8 17.7 - - + -
68D PHE* 4.8 2.5 - + - -
81D PHE* 4.5 7.2 - + - -
94D CYS 3.6 24.9 - - - -
95D ASN 3.6 14.6 - - - -
96D GLU* 4.0 1.3 - - - -
97D THR* 3.9 23.3 - - + -
115D GLY 3.9 4.9 - - - -
116D LYS 3.5 12.8 - - - -
117D LYS* 3.4 37.5 - - + +
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Residues in contact with VAL 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 TRP* 1.3 74.6 - - - +
17D PHE* 1.3 63.6 + - - +
18D GLN* 4.1 15.2 + - + +
39D LYS* 3.7 42.8 - - + -
40D VAL 3.8 3.4 - - - +
41D VAL* 4.5 11.7 - - + +
114D THR 3.8 0.5 - - - +
115D GLY* 3.4 3.1 - - - -
116D LYS* 2.8 40.5 + - + +
118D VAL* 3.8 30.7 - - + -
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Residues in contact with PHE 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 TRP* 3.9 25.4 - + + -
16D VAL* 1.3 80.4 - - - +
18D GLN* 1.3 63.4 + - - +
19D VAL* 3.9 2.0 + - - +
38D LYS 3.8 0.9 - - - +
39D LYS* 3.7 4.0 - - - -
40D VAL 2.8 38.3 + - - +
42D VAL* 4.2 23.1 - - + -
68D PHE* 3.7 20.0 - + - -
70D ILE* 3.7 32.1 - - + -
77D TRP* 3.6 48.5 - + + -
113D PHE* 3.6 18.6 - + + -
114D THR 3.5 1.6 - - - -
115D GLY* 3.6 17.3 - - - -
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Residues in contact with GLN 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 VAL* 4.1 12.1 - - + +
17D PHE* 1.3 74.9 - - - +
19D VAL* 1.3 60.7 + - - +
20D GLY 4.0 0.3 + - - -
33D MET* 4.3 2.3 - - - +
36D GLN* 3.3 52.2 - - - +
38D LYS 3.5 12.5 - - - +
39D LYS* 3.9 25.9 - - - +
113D PHE* 3.0 24.4 - - - -
114D THR* 2.8 24.6 + - - +
116D LYS* 6.2 5.6 - - + +
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Residues in contact with VAL 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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439C LEU* 3.9 18.8 - - + -
17D PHE 4.2 6.5 - - - +
18D GLN* 1.3 75.3 - - - +
20D GLY* 1.3 58.4 + - - +
22D SER* 5.1 8.3 - - - -
33D MET* 4.8 0.2 - - - -
36D GLN* 3.7 2.4 - - - -
37D GLU* 2.7 33.4 + - + +
38D LYS* 3.0 28.5 + - + +
40D VAL* 4.3 11.0 - - + -
77D TRP* 3.8 30.5 - - + -
102D VAL* 4.3 2.2 - - + -
111D ALA* 3.8 19.7 - - + -
112D CYS 3.6 11.2 - - - +
113D PHE* 4.2 0.4 - - + -
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Residues in contact with GLY 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 GLN 4.0 1.0 + - - -
19D VAL* 1.3 74.5 - - - +
21D SER* 1.3 75.8 + - - -
22D SER* 3.0 4.1 + - - -
33D MET* 4.1 10.0 - - - -
34D GLY 5.4 0.2 - - - -
35D PRO 3.4 19.7 - - - -
37D GLU* 4.1 4.9 - - - -
111D ALA* 3.2 16.5 - - - +
112D CYS* 3.0 12.6 + - - +
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Residues in contact with SER 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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20D GLY* 1.3 73.0 - - - +
22D SER* 1.3 62.5 + - - +
24D SER* 2.6 33.5 + - - -
28D VAL* 4.4 8.1 - - - -
29D ASN 5.5 0.7 + - - -
32D VAL 5.3 0.9 + - - -
34D GLY* 4.5 16.5 + - - -
35D PRO* 4.4 2.8 + - - +
37D GLU* 4.4 5.5 - - - +
110D TRP 3.4 5.9 - - - +
111D ALA* 3.7 1.2 - - - -
112D CYS* 4.2 23.7 - - - +
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Residues in contact with SER 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 VAL* 5.1 7.0 - - - -
20D GLY 3.0 6.2 + - - -
21D SER* 1.3 80.2 - - - +
23D GLY* 1.3 62.7 + - - +
24D SER* 3.1 2.6 + - - -
37D GLU* 4.2 22.9 + - - +
38D LYS* 6.6 0.2 - - - -
111D ALA* 4.1 9.6 - - - -
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Residues in contact with GLY 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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314B PHE* 3.8 34.7 - - - -
22D SER* 1.3 75.0 - - - +
24D SER* 1.3 65.2 + - - +
25D GLN* 3.5 11.1 + - - +
109D ASN* 4.9 6.2 - - - +
110D TRP 3.8 4.4 + - - +
111D ALA* 5.1 0.2 - - - +
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Residues in contact with SER 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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21D SER* 2.6 29.4 + - - -
22D SER 3.1 2.3 + - - -
23D GLY* 1.3 80.7 - - - +
25D GLN* 1.3 69.0 + - - +
28D VAL* 3.5 28.0 - - - +
109D ASN* 3.6 3.5 - - - -
110D TRP 2.8 27.7 + - - -
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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