Contacts of the strand formed by residues 117 - 122 (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 LEU 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D ILE 4.0 2.6 + - - -
14D ILE* 3.1 18.5 - - + +
15D PHE 3.1 21.8 + - - +
115D PRO* 3.4 0.5 - - - +
116D GLN* 1.3 82.0 - - + +
118D VAL* 1.3 64.5 - - - +
119D ILE* 3.7 7.6 + - + +
171D THR* 5.3 0.4 - - - -
172D GLN* 3.7 8.1 - - + +
174D HIS* 6.4 2.2 - - + +
192D ALA* 5.1 4.5 - - + +
193D ILE* 6.0 2.7 - - + -
196D ILE* 3.7 26.0 - - + -
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Residues in contact with VAL 118 (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* 3.5 15.5 - - + -
17D ILE* 3.7 30.3 - - + -
115D PRO* 3.9 17.0 - - + -
117D LEU* 1.3 74.7 - - - +
119D ILE* 1.3 64.4 + - - +
120D CYS* 3.7 3.4 + - + +
164D ILE* 6.5 0.9 - - - -
167D TYR* 3.9 36.1 - - + -
171D THR* 4.1 6.0 - - + +
172D GLN 3.1 7.3 + - - -
173D LEU* 3.3 20.3 - - + +
174D HIS* 3.2 23.8 + - - +
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Residues in contact with ILE 119 (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* 4.9 6.3 - - + -
15D PHE 2.7 18.2 + - - +
16D ILE* 4.1 15.7 - - + -
17D ILE* 3.1 20.5 + - - +
31D LEU* 4.7 7.9 - - + -
94D LEU* 4.8 12.3 - - + -
117D LEU* 5.0 10.5 - - + +
118D VAL* 1.3 78.6 - - - +
120D CYS* 1.3 67.3 + - - +
121D MET* 4.8 1.3 - - - -
174D HIS* 3.8 6.3 - - + +
176D ILE* 4.1 9.0 - - + -
189D LEU* 3.4 34.8 - - + +
192D ALA* 5.1 11.4 - - + -
193D ILE* 3.9 33.4 - - + -
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Residues in contact with CYS 120 (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* 3.4 17.5 - - + -
118D VAL* 4.3 8.7 - - + +
119D ILE* 1.3 82.1 - - - +
121D MET* 1.3 66.5 - - - +
122D ASP* 3.2 5.5 + - - -
156D TYR* 5.2 4.7 - - - -
164D ILE* 5.3 13.5 - - - -
173D LEU* 5.6 4.0 - - + -
174D HIS 3.2 12.4 + - - +
175D LYS* 3.5 21.3 - - + -
176D ILE 2.7 31.5 + - - -
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Residues in contact with MET 121 (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 ILE* 4.1 16.6 - - + -
17D ILE 2.7 21.6 + - - +
18D GLY* 3.8 20.1 - - - -
19D GLY 4.7 2.9 + - - -
22D SER* 3.9 19.7 - - - +
23D GLY 4.0 2.7 - - - +
24D LYS* 3.7 30.7 - - + +
27D GLN* 3.7 27.6 - - + -
119D ILE* 4.8 0.7 - - - -
120D CYS* 1.3 72.4 - - - +
122D ASP* 1.3 61.0 + - - +
123D CYS* 3.4 6.6 + - - +
156D TYR* 4.5 6.2 + - - -
176D ILE* 3.7 23.8 - - - -
178D ALA* 4.3 9.4 - - + -
185D VAL* 4.8 2.5 - - + -
189D LEU* 4.2 13.7 - - + -
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Residues in contact with ASP 122 (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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120D CYS* 3.2 5.3 + - - +
121D MET* 1.3 67.3 - - - +
123D CYS* 1.3 64.8 + - - +
124D SER 5.1 0.2 + - - -
175D LYS* 3.9 35.1 + - + +
176D ILE 2.7 20.1 + - - +
177D ASN* 3.2 21.1 - - - +
178D ALA 3.0 20.9 + - - -
179D GLU* 3.8 0.5 - - - +
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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