Contacts of the strand formed by residues 15 - 22 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B TRP 4.1 3.8 + - - -
13B PHE* 3.3 39.5 + - - +
14B GLY* 1.3 80.2 + - - -
16B ILE* 1.3 66.4 + - - +
17B PRO* 3.9 6.2 - - - +
38B LEU* 3.8 31.8 + - + +
39B LEU 3.2 14.1 - - - -
40B PRO* 3.9 22.4 - - - +
41B ARG* 4.4 1.9 + - - +
160B ASP* 2.9 30.9 + - - -
24C ARG* 5.1 0.6 - - - +
25C ASP* 5.2 2.6 + - - -
28C GLN* 4.1 18.0 - - - +
29C ARG* 3.6 49.2 - - + +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 1.3 78.4 - - - +
17B PRO* 1.3 80.7 - - + +
18B THR* 3.1 13.6 + - - +
38B LEU* 4.2 1.8 - - - -
39B LEU* 2.8 39.9 + - + +
41B ARG* 3.6 35.7 - - + +
83B ILE* 4.3 11.2 - - + -
84B GLY* 4.0 10.3 - - - -
87B PHE* 3.5 56.3 - - + -
98B TRP* 4.1 5.2 - - + -
28C GLN* 4.7 2.2 - - - +
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG 3.9 3.8 - - - +
16B ILE* 1.3 87.6 - - + +
18B THR* 1.3 59.2 + - - +
37B LEU 3.7 4.0 - - - +
38B LEU* 3.7 9.8 - - + -
96B LEU* 4.1 18.6 - - + -
97B PRO* 3.8 7.9 - - + -
98B TRP* 2.8 24.1 + - - +
28C GLN* 3.2 33.0 - - + +
32C PHE* 3.7 41.1 - - + -
36C ILE* 4.3 3.8 - - + -
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE 3.1 13.0 + - - -
17B PRO* 1.3 74.3 + - - +
19B CYS* 1.3 65.6 + - - +
20B PHE* 3.6 25.2 - - + -
35B TYR 3.7 1.0 - - - +
36B TYR* 3.3 7.4 - - - -
37B LEU 2.7 39.8 + - - +
39B LEU* 3.3 18.8 - - + +
97B PRO* 4.2 3.1 - - - +
98B TRP* 3.4 23.1 - - + +
100B ILE* 3.7 25.4 - - + -
36C ILE* 4.9 1.4 - - - +
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Residues in contact with CYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 1.3 72.8 - - - +
20B PHE* 1.3 61.8 + - - +
21B THR* 3.7 19.6 + - - -
34B PRO* 4.0 11.2 - - - -
35B TYR 3.8 2.7 - - - -
36B TYR* 3.5 39.3 - - + -
97B PRO* 4.1 7.9 - - + +
98B TRP 2.7 10.8 + - - +
99B ASN* 3.7 24.8 + - - +
100B ILE 3.0 25.3 + - - +
34F GLU* 6.4 0.4 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 3.6 23.1 - - + -
19B CYS* 1.3 71.8 - - - +
21B THR* 1.3 59.7 - - - +
34B PRO* 3.2 8.0 - - - +
35B TYR* 2.8 47.7 + - + +
37B LEU* 4.0 18.8 - - + -
39B LEU* 4.1 11.7 - - + -
45B LEU* 4.8 1.6 - - + -
49B THR* 3.8 21.1 - - + -
52B VAL* 3.7 26.2 - - + -
56B PHE* 3.4 13.8 - - + -
70B PHE* 3.9 18.4 - + - -
100B ILE* 3.3 29.8 - - + -
102B VAL* 3.8 24.7 - - + -
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS* 3.8 17.4 - - - -
20B PHE* 1.3 75.5 + - - +
22B LEU* 1.3 71.5 + - - +
24B GLN* 6.5 0.4 - - + -
34B PRO* 3.9 11.4 - - + +
56B PHE* 4.3 2.0 - - - -
99B ASN* 5.3 2.5 + - - -
100B ILE 3.0 9.9 + - - -
101B THR* 3.2 12.8 - - + +
102B VAL* 2.7 28.4 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B THR* 1.3 84.0 - - - +
23B TYR* 1.3 73.7 + - - +
24B GLN* 3.5 4.3 + - - +
26B GLU* 3.9 18.6 - - + -
28B THR* 3.5 33.0 - - + -
32B ALA* 3.9 18.8 + - + -
56B PHE* 3.5 32.1 - - + -
59B VAL* 4.3 5.2 - - + -
60B MET* 4.6 4.7 - - - -
102B VAL* 3.4 33.2 - - + +
104B PHE* 4.3 13.2 - - + -
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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
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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