Contacts of the strand formed by residues 17 - 23 (chain J) in PDB entry 3T30
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 VAL 17 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15J THR* 5.2 5.6 - - - +
16J THR* 1.3 82.4 - - - +
18J LEU* 1.3 77.6 + - - +
118J GLN* 3.2 5.0 - - - -
119J GLU* 2.8 69.4 + - + +
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Residues in contact with LEU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ILE* 3.5 44.9 - - + +
65F LEU 6.2 0.4 - - - -
78F VAL* 3.7 29.4 - - + +
80F ILE* 5.7 1.8 - - + -
98F LEU* 4.1 21.1 - - + -
16J THR* 5.2 0.4 - - - +
17J VAL* 1.3 85.7 - - - +
19J TRP* 1.3 60.6 + - - +
47J HIS* 5.4 3.4 - - - +
116J SER* 5.9 0.4 - - - -
117J GLY 3.4 17.0 - - - +
118J GLN* 4.1 13.0 - - + +
119J GLU* 5.1 0.3 - - - +
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Residues in contact with TRP 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F VAL* 3.7 9.9 - - - +
17J VAL 3.3 0.2 + - - -
18J LEU* 1.3 75.6 - - - +
20J GLY* 1.3 72.2 + - - +
21J CYS* 3.9 15.7 - - + -
30J TRP* 4.2 19.7 - + - +
32J PHE* 3.7 20.1 - + + -
44J LEU* 3.4 30.5 - - + -
46J LEU* 4.0 13.7 - - + -
104J PHE* 3.7 32.3 - + - -
115J LEU* 3.9 22.0 - - + -
116J SER* 3.5 16.8 - - - -
117J GLY* 2.8 44.4 + - - +
119J GLU* 3.9 33.0 - - + +
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Residues in contact with GLY 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F PRO 5.5 0.4 - - - -
78F VAL* 3.7 20.8 - - - +
19J TRP* 1.3 88.8 + - - +
21J CYS* 1.3 63.1 + - - +
30J TRP* 6.0 1.2 - - - -
115J LEU 3.2 11.7 - - - -
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Residues in contact with CYS 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J TRP* 3.9 21.8 - - + -
20J GLY* 1.3 74.6 - - - +
22J GLU* 1.3 67.0 + - - +
23J LEU* 4.0 15.7 - - - -
27J ARG* 5.2 3.8 - - - -
30J TRP* 3.6 45.5 - - + +
104J PHE* 6.0 1.8 - - + -
113J VAL 3.8 0.7 - - - +
114J PHE* 3.4 5.4 - - - +
115J LEU* 2.8 41.4 + - + +
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Residues in contact with GLU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F GLN* 5.7 0.3 - - - +
21J CYS* 1.3 81.3 - - - +
23J LEU* 1.3 63.8 + - - +
24J SER* 4.1 7.1 + - - +
27J ARG* 4.2 16.1 - - - +
112J PRO* 3.3 32.3 - - + +
113J VAL 3.5 3.6 - - - +
114J PHE* 3.4 34.2 - - + -
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J CYS* 4.0 19.7 - - - -
22J GLU* 1.3 72.5 - - - +
24J SER* 1.3 65.1 + - - +
27J ARG* 3.3 8.7 - - + +
28J ARG 4.0 13.2 - - - +
30J TRP* 4.1 15.7 - - + -
62J VAL* 4.5 10.8 - - + -
104J PHE* 4.2 18.2 - - + +
105J GLN 4.2 5.6 - - - -
106J LEU* 3.9 35.7 - - + +
111J GLY* 4.1 0.7 - - - -
112J PRO* 3.4 2.3 - - - +
113J VAL* 2.8 37.8 + - + +
115J LEU* 3.8 25.6 - - + -
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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