Contacts of the strand formed by residues 15 - 22 (chain E) in PDB entry 4GDK
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 ARG 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E TRP 3.9 4.6 + - - -
13E PHE* 3.4 40.0 + - - +
14E GLY* 1.3 81.5 + - - -
16E ILE* 1.3 68.7 + - - +
17E PRO* 3.8 6.5 - - - +
38E LEU* 3.7 39.6 + - + +
39E LEU 3.3 5.4 - - - -
40E PRO* 3.8 23.8 - - - +
41E ARG* 4.5 1.4 + - - +
160E ASP* 2.6 34.4 + - - -
24F ARG* 5.6 0.6 + - - +
25F ASP* 5.3 0.8 + - - -
28F GLN* 4.1 16.8 - - - +
29F ARG* 3.6 49.4 + - + +
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Residues in contact with ILE 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 1.3 79.8 - - - +
17E PRO* 1.3 70.9 - - + +
18E THR* 2.9 22.2 + - - +
38E LEU* 4.2 0.9 - - - -
39E LEU* 2.7 34.0 + - + +
41E ARG* 3.6 34.1 - - + +
83E ILE* 3.9 12.6 - - + +
84E GLY* 3.8 11.0 - - - -
87E PHE* 3.5 58.1 - - + -
96E LEU* 4.8 0.4 - - + -
98E TRP* 4.1 5.2 - - + -
28F GLN* 4.7 2.7 - - - +
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Residues in contact with PRO 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG 3.8 5.4 - - - +
16E ILE* 1.3 87.0 - - + +
18E THR* 1.3 53.1 + - - +
37E LEU 3.9 1.1 - - - +
38E LEU* 3.6 18.1 - - + -
96E LEU* 3.7 17.1 - - + +
97E PRO* 3.3 10.0 - - + +
98E TRP* 2.8 29.5 + - - +
28F GLN* 3.4 32.1 - - + +
32F PHE* 3.6 36.3 - - + -
36F ILE* 4.2 3.8 - - + -
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Residues in contact with THR 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE 2.9 15.4 + - - -
17E PRO* 1.3 73.5 + - - +
19E CYS* 1.3 63.1 + - - +
20E PHE* 3.6 23.7 - - + -
35E TYR 3.8 0.9 - - - +
36E TYR* 3.3 8.0 - - - +
37E LEU 2.9 38.2 + - - -
39E LEU* 3.2 17.7 - - + +
97E PRO* 4.0 4.0 - - - +
98E TRP* 3.2 22.2 - - + +
100E ILE* 3.7 28.9 - - + -
36F ILE* 4.7 1.6 - - - +
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Residues in contact with CYS 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E THR* 1.3 72.3 - - - +
20E PHE* 1.3 62.0 + - - +
21E THR* 3.6 18.6 + - - -
34E PRO* 3.9 13.0 - - - -
35E TYR 3.8 2.2 - - - -
36E TYR* 3.6 38.4 - - + -
97E PRO* 4.1 7.8 - - + +
98E TRP 2.6 9.8 + - - +
99E ASN* 3.6 24.9 + - - +
100E ILE 3.1 23.9 + - - +
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Residues in contact with PHE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E THR* 3.6 23.3 - - + -
19E CYS* 1.3 71.3 - - - +
21E THR* 1.3 60.3 + - - +
34E PRO* 3.3 3.5 - - - +
35E TYR* 2.8 49.0 + - + +
37E LEU* 4.0 17.5 - - + -
39E LEU* 3.9 14.4 - - + -
45E LEU* 4.9 1.8 - - + -
49E THR* 3.8 21.3 - - + -
52E VAL* 3.8 24.2 - - + -
56E PHE* 3.2 16.3 - - + -
70E PHE* 3.8 23.6 - + - -
100E ILE* 3.3 25.1 - - + -
102E VAL* 3.7 27.1 - - + -
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Residues in contact with THR 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E CYS* 3.6 18.6 + - - -
20E PHE* 1.3 75.8 + - - +
22E LEU* 1.3 69.3 + - - +
34E PRO* 4.0 13.6 - - + +
56E PHE* 4.3 2.2 - - - -
99E ASN* 5.1 3.1 + - - -
100E ILE 3.1 9.0 + - - -
101E THR* 3.3 11.7 - - + +
102E VAL* 2.8 30.8 + - - -
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E THR* 1.3 85.7 - - - +
23E TYR* 1.3 73.3 + - - +
24E GLN* 3.4 4.0 + - - +
26E GLU* 4.0 15.7 - - + +
28E THR* 3.7 30.7 - - + -
32E ALA* 4.2 15.9 - - + +
34E PRO* 5.7 0.2 - - - +
56E PHE* 3.5 40.0 - - + +
59E VAL* 4.4 3.6 - - + -
60E MET* 5.0 0.7 - - - -
101E THR* 4.5 0.8 - - - +
102E VAL* 3.5 21.8 - - + +
104E PHE* 4.0 22.4 - - + -
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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