Contacts of the strand formed by residues 279 - 284 (chain A) in PDB entry 3ATB
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 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 5.5 2.0 - - - +
225A ARG* 3.4 3.0 - - - +
226A VAL* 3.0 34.6 + - + +
273A LEU* 4.4 22.0 - - + -
274A PHE 4.0 24.0 - - - +
275A LEU* 3.6 21.5 - - + -
277A SER* 3.4 21.3 - - - +
278A PRO* 1.3 77.0 - - - +
280A ILE* 1.3 66.5 + - - +
281A ILE* 3.6 12.1 + - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ARG* 3.9 31.5 + - - +
223A MET* 3.7 20.4 - - + -
224A PHE 3.8 6.3 - - - +
225A ARG* 4.0 24.0 - - - +
279A LEU* 1.3 76.0 - - - +
281A ILE* 1.3 77.5 + - - +
282A SER* 4.1 2.6 + - - -
338A PHE* 3.5 38.8 - - + +
339A THR 5.4 0.2 - - - +
340A PRO* 6.4 0.4 - - + -
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET* 3.2 28.8 - - - +
224A PHE* 2.9 51.2 + - + +
226A VAL* 4.1 24.5 - - + -
239A ILE* 4.3 13.5 - - + -
264A VAL* 3.9 26.7 - - + +
273A LEU* 4.0 26.5 - - + -
279A LEU* 4.2 9.6 - - + -
280A ILE* 1.3 79.0 - - - +
282A SER* 1.3 64.2 + - - +
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Residues in contact with SER 282 (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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216A ARG* 3.9 19.5 + - - -
221A CYS* 3.9 24.8 - - - +
222A LEU 3.5 4.3 - - - -
223A MET* 3.7 10.0 - - - +
264A VAL* 4.3 16.4 - - - -
280A ILE 4.1 1.8 + - - -
281A ILE* 1.3 80.2 - - - +
283A HIS* 1.3 61.1 + - - +
284A GLU 4.0 1.6 + - - -
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Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A CYS* 3.6 0.7 - - - -
222A LEU* 3.0 49.4 + - + +
224A PHE* 6.2 1.1 - - + -
262A ILE* 3.4 17.6 - - + +
263A ASN* 2.7 48.0 + - + +
264A VAL* 3.7 11.6 - - + +
282A SER* 1.3 74.7 + - - +
284A GLU* 1.3 69.9 + - - +
285A ILE* 3.4 12.6 + - + +
286A ASN* 5.2 0.9 - - - -
289A SER* 2.5 44.5 + - - -
290A PRO* 4.3 2.4 - - + +
291A PHE* 4.2 6.1 - + - -
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Residues in contact with GLU 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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219A LYS* 3.5 46.6 - - + +
220A LEU 4.0 4.0 - - - +
221A CYS* 4.0 8.7 - - - -
263A ASN* 4.6 1.8 + - - +
282A SER* 4.0 3.6 + - - +
283A HIS* 1.3 85.2 + - - +
285A ILE* 1.3 65.2 + - - +
286A ASN* 3.0 38.6 + - + +
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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