Contacts of the strand formed by residues 283 - 289 (chain E) in PDB entry 2HOD
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 LYS 283 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279E ASN* 4.9 4.7 + - - +
280E THR* 3.8 25.7 + - + +
281E ASP 3.6 4.5 + - - -
282E GLY* 1.3 81.6 + - - +
284E ASN* 1.3 65.8 + - - +
285E TYR* 3.1 52.4 - - + +
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Residues in contact with ASN 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E SER* 2.9 24.8 - - - +
202E ASN* 3.1 29.5 + - - +
279E ASN* 4.2 3.4 + - - +
282E GLY 3.5 4.3 + - - -
283E LYS* 1.3 72.6 - - - +
285E TYR* 1.3 75.6 + - - +
201F SER* 5.7 4.6 - - - -
217F HIS* 3.7 23.1 + - - -
223F THR 4.6 5.1 - - - +
224F THR* 4.2 18.4 - - - -
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Residues in contact with TYR 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ASN* 4.7 11.9 - - - +
221E THR* 5.6 2.5 - - - -
222E SER 5.1 1.8 - - - -
223E GLU* 3.1 33.0 - - + +
279E ASN* 4.1 2.3 - - - -
280E THR* 3.7 24.4 + - - +
283E LYS* 3.1 50.3 - - + +
284E ASN* 1.3 89.0 - - - +
286E CYS* 1.3 61.8 + - - +
287E GLY* 3.3 25.4 - - - -
217F HIS* 3.6 29.6 - + + +
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Residues in contact with CYS 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E SER 3.7 8.1 - - - -
201E CYS* 2.0 58.3 - - + +
202E ASN 5.5 0.6 + - - -
223E GLU* 3.1 15.8 + - - +
224E MET* 3.2 12.7 + - + +
277E ALA* 3.3 17.8 - - + +
278E THR 3.4 9.4 - - - +
279E ASN* 3.8 23.6 - - - -
285E TYR* 1.3 75.5 - - - +
287E GLY* 1.3 58.9 + - - +
288E LEU 3.2 4.0 + - - -
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Residues in contact with GLY 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E SER 3.8 5.6 - - - +
223E GLU* 3.4 16.6 - - - -
239E TYR* 2.2 28.6 + - - -
280E THR* 3.3 10.7 + - - -
285E TYR* 3.3 19.3 - - - -
286E CYS* 1.3 73.7 - - - +
288E LEU* 1.3 60.9 + - - +
289E PRO* 3.5 1.7 - - - +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TYR* 3.6 1.8 - - - -
277E ALA* 2.9 8.5 - - - +
278E THR* 2.6 54.7 + - + +
279E ASN 3.9 17.0 - - - +
280E THR* 4.7 15.3 - - + -
286E CYS 3.2 0.6 - - - -
287E GLY* 1.3 82.5 - - - +
289E PRO* 1.3 73.1 - - + +
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Residues in contact with PRO 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TYR* 3.4 43.3 - - + +
251E VAL* 5.8 1.3 - - + -
254E ASN* 4.0 19.7 - - - +
256E GLN* 3.3 18.2 - - - +
276E VAL 3.5 9.6 - - - +
277E ALA* 4.2 1.1 - - - -
278E THR* 3.7 8.5 + - - -
287E GLY 3.5 2.5 - - - +
288E LEU* 1.3 99.6 - - + +
290E GLY* 1.3 59.6 + - - +
292E TYR* 5.1 1.8 - - + -
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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