Contacts of the strand formed by residues 235 - 242 (chain A) in PDB entry 4TZ1
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLN 3.3 4.2 + - - -
218A GLN* 3.2 10.9 - - + +
219A TRP 2.9 23.2 + - - +
234A TRP* 1.3 84.3 - - + +
236A MET* 1.3 64.1 + - - +
237A THR* 2.8 22.3 + - - -
249A PHE* 5.6 1.8 - - + -
253A PRO* 3.7 5.0 - - - +
255A THR* 4.3 4.0 + - - -
498A PHE* 3.5 18.8 - - - -
499A TYR 3.8 8.7 + - - -
537A GLY* 2.9 35.5 + - - -
538A MET* 3.9 1.8 - - - +
539A GLY* 4.4 2.6 - - - +
541A TYR* 4.9 3.0 + - - +
570A LEU* 3.9 14.8 - - + -
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Residues in contact with MET 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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213A PRO* 4.1 16.6 - - + -
216A GLN* 3.3 28.5 - - + +
217A GLN 3.8 1.3 - - - +
218A GLN* 3.4 27.4 - - - +
219A TRP* 3.6 9.9 - - + +
229A TRP* 3.9 25.4 - - + +
231A ASN 4.0 7.2 - - - +
232A GLY* 4.0 2.0 - - - -
233A VAL 3.8 20.6 - - - +
235A ASN* 1.3 79.1 - - - +
237A THR* 1.3 60.9 + - - +
238A PHE* 3.6 12.6 - - + -
253A PRO 3.1 7.0 + - - +
254A TYR* 3.3 24.2 - - + -
255A THR 3.0 23.6 + - - -
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Residues in contact with THR 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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219A TRP 2.9 10.7 + - - +
220A TYR* 3.5 5.7 - - + -
221A THR 3.1 23.6 + - - -
235A ASN* 2.8 25.7 + - - -
236A MET* 1.3 69.9 - - - +
238A PHE* 1.3 73.5 + - - +
255A THR* 3.2 24.4 - - + +
257A LEU* 5.1 0.4 - - + -
497A ILE* 3.9 28.3 - - + -
498A PHE* 4.0 20.9 - - - +
536A TRP 4.5 1.6 - - - +
537A GLY* 3.5 13.5 + - - -
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Residues in contact with PHE 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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220A TYR* 4.6 0.2 - - - -
221A THR* 3.3 18.8 - - - -
229A TRP* 3.5 53.2 - + - -
236A MET* 3.6 20.9 - - + -
237A THR* 1.3 81.6 - - - +
239A SER* 1.3 61.9 + - - +
241A VAL* 4.0 11.0 - - + +
244A ALA* 3.7 24.7 - - + -
245A PRO* 3.5 32.1 - - + -
254A TYR* 3.9 7.6 - + - -
255A THR 2.8 10.2 + - - +
256A THR* 3.4 23.1 - - + +
257A LEU* 2.8 30.0 + - - +
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Residues in contact with SER 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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220A TYR* 2.8 28.6 + - - -
221A THR 3.1 7.1 + - - -
222A ARG* 3.1 3.5 - - - +
223A ASP 2.9 21.8 + - - -
238A PHE* 1.3 74.8 - - - +
240A GLY* 1.3 61.4 + - - +
241A VAL 3.3 1.3 + - - -
257A LEU* 3.4 12.6 - - - -
259A THR 3.8 14.1 - - - -
260A THR* 2.8 25.3 + - - +
497A ILE* 4.1 12.9 - - - +
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Residues in contact with GLY 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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223A ASP* 3.3 11.6 - - - -
224A SER 3.3 0.5 + - - -
239A SER* 1.3 73.4 - - - +
241A VAL* 1.3 59.1 + - - +
257A LEU 3.1 11.9 + - - -
258A GLU 3.3 18.0 + - - -
259A THR* 3.7 2.8 - - - +
287A ALA 3.6 19.5 - - - -
288A ARG* 3.8 4.7 - - - -
289A GLY 2.8 28.1 + - - -
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Residues in contact with VAL 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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221A THR* 3.4 50.9 - - + +
222A ARG* 4.0 2.7 - - - -
223A ASP 4.0 2.0 - - - +
224A SER 3.4 11.0 - - - +
226A VAL* 4.5 13.5 - - + -
238A PHE* 4.0 11.9 - - + +
239A SER 3.3 8.0 - - - +
240A GLY* 1.3 76.4 - - - +
242A GLU* 1.3 74.3 + - - +
244A ALA* 3.5 35.3 + - + +
256A THR* 5.8 0.3 - - - +
257A LEU 4.6 1.4 + - - -
288A ARG* 3.1 18.7 + - - +
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Residues in contact with GLU 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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224A SER 2.9 11.8 + - - +
225A SER* 3.3 22.5 + - - +
226A VAL 2.9 27.1 + - - +
240A GLY 3.7 0.2 + - - -
241A VAL* 1.3 73.2 - - - +
243A GLY* 1.3 60.7 + - - +
244A ALA 3.3 0.6 + - - -
288A ARG* 3.6 35.0 + - + +
289A GLY* 3.7 21.5 + - - -
290A THR 5.0 1.0 + - - -
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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