Contacts of the strand formed by residues 234 - 242 (chain A) in PDB entry 1ATT
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 ASN 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A PHE* 5.6 0.5 - - - +
231A SER* 2.9 27.8 + - - +
233A GLU* 1.3 83.6 - - - +
235A THR* 1.3 63.3 + - - +
236A ARG* 3.9 14.4 - - - +
253A MET* 3.9 0.7 - - - +
254A TYR* 3.3 58.8 + - + +
255A GLN* 5.6 1.2 - - - +
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Residues in contact with THR 235 (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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230A PHE* 5.7 0.2 - - - +
231A SER 3.0 19.9 + - - -
232A PRO 3.3 17.2 + - - +
233A GLU 3.1 6.9 + - - +
234A ASN* 1.3 76.7 + - - +
236A ARG* 1.3 61.3 + - - +
251A LEU* 4.4 23.4 - - + +
252A MET 3.6 11.9 - - - +
253A MET* 4.6 1.1 - - - +
323A ARG* 4.3 10.8 - - - +
378A GLU* 3.2 34.4 + - - +
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Residues in contact with ARG 236 (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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234A ASN* 4.0 13.9 - - - +
235A THR* 1.3 79.5 - - - +
237A LYS* 1.3 68.2 + - - +
238A GLU* 3.7 17.8 + - + +
251A LEU* 3.6 4.8 - - - -
252A MET* 2.8 37.7 + - - +
254A TYR* 3.1 48.3 - - - +
320A HIS* 2.9 34.1 + - - -
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Residues in contact with LYS 237 (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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236A ARG* 1.3 83.1 - - - +
238A GLU* 1.3 64.1 + - - +
249A SER* 4.3 23.5 + - - -
250A VAL* 3.1 27.4 - - - +
251A LEU* 3.6 32.1 - - + +
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Residues in contact with GLU 238 (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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236A ARG* 3.7 15.2 + - - +
237A LYS* 1.3 75.2 - - - +
239A LEU* 1.3 72.3 + - - +
249A SER* 3.6 3.3 - - - -
250A VAL* 3.0 32.9 + - - +
252A MET* 3.2 39.6 - - + +
320A HIS* 3.6 11.1 + - - -
404A LYS* 2.7 38.6 + - - -
406A ASN* 4.9 1.8 - - - +
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Residues in contact with LEU 239 (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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238A GLU* 1.3 79.2 - - - +
240A PHE* 1.3 57.9 - - - +
241A TYR* 3.6 39.4 - - + +
247A SER* 4.0 12.3 - - - +
248A CYS* 3.5 22.4 - - - +
249A SER* 3.9 11.0 - - - +
250A VAL* 4.8 0.7 - - - -
406A ASN* 2.9 33.4 + - - +
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Residues in contact with PHE 240 (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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238A GLU 3.6 1.0 + - - -
239A LEU* 1.3 71.6 - - - +
241A TYR* 1.3 63.7 + - - +
242A LYS* 3.3 10.3 + - - -
247A SER* 3.1 4.8 - - - -
248A CYS* 2.8 33.2 + - - +
250A VAL* 3.6 25.1 - - + -
322A PRO* 4.1 11.2 - - + -
406A ASN* 3.2 19.3 - - - -
407A ARG* 3.1 30.3 - - - -
408A PRO* 3.3 28.0 - - + -
409A PHE* 4.0 16.2 - + - -
427A VAL 4.4 6.3 - - - -
428A ALA 3.7 14.4 - - - -
430A PRO* 3.4 34.3 - - + -
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Residues in contact with TYR 241 (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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239A LEU* 3.6 39.9 - - + +
240A PHE* 1.3 69.7 - - - +
242A LYS* 1.3 69.5 - - - +
245A GLY* 5.4 4.5 - - - -
246A GLU 3.5 3.8 - - - -
247A SER* 3.4 16.8 - - - -
406A ASN* 2.8 38.3 + - - +
407A ARG* 3.7 11.3 - - + +
408A PRO* 3.7 14.0 - - - +
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Residues in contact with LYS 242 (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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74A ASN* 3.4 15.5 - - - +
240A PHE* 3.3 13.0 + - + -
241A TYR* 1.3 79.9 - - - +
243A ALA* 1.3 78.0 + - - +
244A ASP* 3.3 28.0 + - - +
245A GLY* 2.9 14.9 + - - -
246A GLU* 2.7 32.0 + - - +
247A SER 4.6 5.4 - - - -
248A CYS* 4.5 19.7 - - - -
408A PRO* 4.1 0.9 - - - -
428A ALA 3.9 8.7 - - - +
429A ASN* 3.2 37.6 - - + +
430A PRO* 5.3 0.4 - - + -
431A CYS* 4.9 0.2 - - - -
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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