Contacts of the strand formed by residues 281 - 286 (chain A) in PDB entry 1E1A
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 THR 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A HIS 3.9 0.2 - - - +
275A PHE* 3.2 5.7 - - - -
276A LYS* 3.0 36.1 + - + +
279A THR* 3.0 18.1 + - - +
280A LYS* 1.3 78.1 - - - +
282A ILE* 1.3 64.2 + - - +
283A PHE* 3.5 24.9 + - + -
294A LYS* 4.0 26.0 - - + +
295A PHE 3.6 2.2 - - - +
296A GLU* 2.6 28.2 + - - +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.5 26.2 - - + -
273A LEU* 3.7 32.8 - - + -
274A HIS 3.5 7.4 - - - +
275A PHE* 3.4 44.6 - - + -
280A LYS 4.0 4.0 - - - +
281A THR* 1.3 72.7 - - - +
283A PHE* 1.3 65.1 + - - +
284A VAL* 3.8 1.2 + - + -
294A LYS* 3.1 4.0 - - - -
295A PHE* 2.9 59.0 + - + +
297A TRP* 3.6 13.7 - - + -
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 28.3 - - + -
23A PRO* 4.3 4.7 - - + +
25A PHE* 3.6 26.9 - + - -
31A PHE* 3.7 34.5 - + + -
53A LEU* 3.6 38.4 - - + -
273A LEU* 3.0 7.6 - - - +
274A HIS 2.8 36.3 + - - +
276A LYS* 4.0 10.5 - - + -
281A THR* 3.5 20.2 - - + -
282A ILE* 1.3 74.8 - - - +
284A VAL* 1.3 58.3 + - - +
285A THR 4.3 0.2 - - - -
292A VAL* 4.5 2.0 - - + -
293A TRP 3.2 5.6 - - - +
294A LYS* 4.1 17.9 - - + +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.3 8.5 - - + -
242A ALA* 5.8 0.7 - - + -
249A ILE* 4.0 19.5 - - + -
267A PHE* 4.2 20.2 - - + -
270A PRO* 4.4 6.7 - - + -
272A ASN 3.4 9.4 - - - +
273A LEU* 4.3 2.7 - - + -
282A ILE* 4.0 6.1 - - + +
283A PHE* 1.3 79.2 - - - +
285A THR* 1.3 76.7 + - - +
291A ALA 4.0 0.3 - - - +
292A VAL* 3.3 3.0 - - - +
293A TRP* 2.8 43.8 + - - +
295A PHE* 3.5 37.7 - - + -
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.0 36.0 + - - +
21A GLU* 3.8 0.6 - - - +
23A PRO* 3.9 16.8 - - + -
33A ILE* 3.7 29.6 - - + -
271A SER* 2.7 29.5 + - - -
272A ASN* 2.9 29.2 + - - +
284A VAL* 1.3 81.4 - - - +
286A GLU* 1.3 56.7 + - - +
291A ALA 3.4 4.5 - - - -
292A VAL* 4.0 9.9 - - + -
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 4.3 1.4 + - - +
267A PHE* 3.4 31.4 - - + +
269A LYS 3.1 14.1 - - - +
271A SER 4.0 1.1 - - - +
285A THR* 1.3 76.8 - - - +
287A HIS* 1.3 65.9 + - - +
288A GLU* 2.9 32.1 + - - +
289A ASN* 2.9 34.5 + - - +
290A ASN* 3.1 23.6 + - - -
291A ALA* 3.0 13.9 + - - +
293A TRP* 2.8 39.3 + - + +
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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