Contacts of the strand formed by residues 20 - 25 (chain B) in PDB entry 2E9D
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 HIS 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS* 3.7 0.4 - - - -
19B ARG* 1.3 80.3 - - - +
21B VAL* 1.3 76.2 + - - +
64B ALA* 3.4 31.0 - - + +
66B THR* 2.8 30.5 + - - -
140B ASN* 4.4 0.9 - - - -
183B MET* 3.8 17.3 - - + -
186B LEU* 4.5 5.6 - - + +
187B ALA* 3.1 24.9 + - + +
188B PRO 3.4 16.2 - - - +
189B VAL* 3.6 27.7 - - + +
190B ASP* 2.7 32.2 + - - +
191B LEU 3.3 5.2 + - - -
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Residues in contact with VAL 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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18B CYS* 3.3 31.4 - - - -
20B HIS* 1.3 78.6 - - - +
22B ALA* 1.3 57.2 + - - +
23B ILE* 4.0 21.1 - - + -
62B ILE* 4.3 16.8 - - + -
64B ALA 3.1 4.9 + - - +
65B LEU* 3.3 18.6 - - + +
66B THR 2.8 30.0 + - - -
191B LEU* 3.3 11.7 - - + +
193B ILE* 4.1 17.9 - - + -
229B PHE* 4.2 7.4 - - + -
233B LEU* 4.2 11.7 - - + -
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Residues in contact with ALA 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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20B HIS 4.3 0.2 + - - -
21B VAL* 1.3 73.7 - - - +
23B ILE* 1.3 57.4 + - - +
66B THR* 3.4 11.4 - - - +
189B VAL* 3.9 10.5 - - + -
191B LEU 2.6 12.8 + - - +
192B VAL* 3.0 13.5 - - + +
193B ILE* 2.6 33.1 + - - +
204B PHE* 3.9 10.3 - - + -
205B LEU* 3.7 29.8 - - + -
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Residues in contact with ILE 23 (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 VAL* 4.0 10.8 - - + -
22B ALA* 1.3 78.3 - - - +
24B ILE* 1.3 67.4 + - - +
25B MET* 3.7 10.9 + - + -
53B ALA* 4.6 3.4 - - + -
65B LEU* 3.8 23.1 - - + -
66B THR 2.9 9.2 + - - +
67B LEU* 3.7 17.4 - - + -
68B TYR* 3.0 29.5 + - - +
193B ILE* 3.1 24.0 - - + +
195B THR* 5.0 0.7 - - + -
204B PHE* 4.3 1.2 - - - -
221B TRP* 3.5 37.7 - - + -
224B PHE* 4.9 2.9 - - + -
229B PHE* 4.2 20.4 - - + -
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Residues in contact with ILE 24 (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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23B ILE* 1.3 71.6 - - - +
25B MET* 1.3 61.1 + - - +
26B ASP* 3.4 0.9 + - + -
68B TYR* 3.5 17.3 - - + -
70B PHE* 3.9 22.7 - - + -
192B VAL* 4.7 10.5 - - + -
193B ILE 2.7 11.7 + - - +
194B ARG* 3.8 34.2 - - + +
195B THR* 3.3 23.6 + - - -
200B ARG 4.1 13.5 - - - +
201B ILE* 3.4 29.8 - - + +
204B PHE* 3.5 30.3 - - + -
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Residues in contact with MET 25 (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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23B ILE* 3.8 16.2 - - + +
24B ILE* 1.3 69.1 - - - +
26B ASP* 1.3 59.0 + - - +
28B ASN* 6.0 2.0 - - - +
50B VAL* 3.7 30.1 - - + -
67B LEU* 3.9 20.6 - - + -
68B TYR 3.0 16.1 + - - +
69B ALA* 3.2 40.4 - - + +
70B PHE* 3.0 30.7 + - - +
141B ILE* 6.5 0.7 - - + -
195B THR* 3.8 5.4 - - - -
221B TRP* 3.6 36.6 - - + -
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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