Contacts of the strand formed by residues 13 - 18 (chain D) in PDB entry 2BWJ
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 ILE 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU 5.3 4.3 - - - +
11D CYS* 3.3 19.0 + - - +
12D LYS* 1.3 79.7 - - - +
14D ILE* 1.3 58.8 + - - +
15D PHE* 4.5 5.4 - - + -
37D PHE* 5.9 0.2 - - - -
83D MET* 4.2 8.5 - - + -
93D PHE* 3.4 28.9 - - + -
95D ILE* 5.4 1.3 - - + -
108D PHE* 3.6 33.2 - - + -
112D ILE* 5.3 2.2 - - + -
113D GLY* 3.6 9.4 - - - +
114D ASP 3.6 20.0 - - - +
115D PRO* 3.6 15.9 - - + +
116D GLN* 3.1 25.3 + - - +
117D LEU 4.0 1.2 + - - -
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Residues in contact with ILE 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 ILE* 1.3 74.4 - - - +
15D PHE* 1.3 65.3 + - - +
37D PHE* 5.3 8.2 - - + -
93D PHE 2.8 14.0 + - - +
94D LEU* 3.4 15.2 - - + +
95D ILE* 3.0 24.0 + - - +
117D LEU* 3.1 26.5 - - + +
119D ILE* 4.9 10.1 - - + -
193D ILE* 5.9 3.6 - - + -
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Residues in contact with PHE 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 ILE* 4.5 4.3 - - + -
14D ILE* 1.3 78.4 - - - +
16D ILE* 1.3 56.6 + - - +
17D ILE* 4.8 1.8 - - + -
94D LEU* 5.2 0.2 - - - -
95D ILE* 3.6 29.2 - - + -
98D TYR* 3.4 31.2 - + - +
99D PRO* 3.6 16.2 - - + -
105D GLY* 5.5 0.2 - - - -
108D PHE* 3.6 40.6 - + - -
115D PRO* 3.8 28.0 - - + +
117D LEU 3.1 5.3 + - - +
118D VAL* 4.2 17.7 - - + -
119D ILE* 2.7 36.6 + - - +
167D TYR* 3.5 27.4 - + - -
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Residues in contact with ILE 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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14D ILE 4.1 0.2 + - - -
15D PHE* 1.3 76.2 - - - +
17D ILE* 1.3 65.9 + - - +
24D LYS* 3.9 17.9 + - + +
28D CYS* 3.8 29.6 - - - +
31D LEU* 4.6 15.9 - - + -
94D LEU* 4.0 20.6 - - + -
95D ILE 3.1 5.0 + - - +
96D ASP* 3.6 22.9 - - + +
97D GLY* 2.8 31.9 + - - -
119D ILE* 3.4 24.2 - - + -
121D MET* 4.1 18.6 - - + -
189D LEU* 4.8 0.4 - - + -
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Residues in contact with ILE 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 PHE* 4.8 1.1 - - + -
16D ILE* 1.3 82.0 - - - +
18D GLY* 1.3 53.8 + - - +
24D LYS* 4.0 4.3 - - - +
97D GLY* 4.9 5.4 - - - +
98D TYR 4.1 20.6 - - - +
99D PRO* 5.1 4.0 - - + +
118D VAL* 3.7 26.5 - - + -
119D ILE 3.1 10.2 + - - +
120D CYS* 3.4 10.8 - - + +
121D MET* 2.7 33.8 + - - +
156D TYR* 3.3 26.3 + - + +
160D SER* 4.6 10.8 - - - -
163D VAL* 4.2 25.6 - - + -
164D ILE* 5.6 5.8 - - + +
167D TYR* 5.3 0.7 - - + -
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Residues in contact with GLY 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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17D ILE* 1.3 75.7 - - - +
19D GLY* 1.3 68.4 + - - +
20D PRO* 4.6 0.3 - - - +
22D SER* 3.4 10.5 - - - -
24D LYS* 3.5 24.7 - - - +
97D GLY* 5.6 0.4 - - - -
121D MET* 3.8 11.0 - - - -
156D TYR* 3.2 20.4 + - - -
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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