Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 5A91
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 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLY 3.7 2.5 - - - +
237A SER* 4.6 2.9 - - - +
242A GLY 2.8 16.1 + - - -
243A THR* 1.3 74.2 - - - +
245A ASN* 1.3 66.4 + - - +
265A PHE* 2.8 33.4 + - - +
274A ASN* 3.2 8.9 - - + +
275A ARG* 2.9 24.6 + - - +
276A ASN* 3.3 52.0 - - - +
279A LEU* 3.4 9.4 - - + +
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Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 5.2 0.7 - - - +
67A ALA 2.8 27.7 + - - -
68A MET* 3.1 18.6 + - - +
69A CYS* 4.2 0.4 - - - +
71A THR* 3.7 7.9 - - + -
235A THR* 3.4 5.9 - - - +
236A GLY 2.8 33.4 + - - +
243A THR* 3.8 10.5 - - - +
244A THR* 1.3 84.2 - - - +
246A ASP* 1.3 65.2 + - - +
263A THR 3.4 4.9 - - - -
264A TYR* 3.2 37.8 - - + +
265A PHE 3.2 8.3 + - - +
276A ASN* 4.8 1.7 - - - +
279A LEU* 3.5 6.4 - - - +
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 4.4 0.4 - - - -
217A GLY 4.7 0.3 - - - +
220A SER* 3.3 11.3 - - - -
221A ILE* 3.0 45.3 + - + +
222A ARG 4.6 0.7 + - - -
233A ASP* 2.5 34.7 - - - +
234A LYS 3.1 17.9 - - - +
235A THR* 3.4 3.2 + - - -
245A ASN* 1.3 77.6 - - - +
247A ILE* 1.3 68.7 + - - +
263A THR* 2.9 32.9 + - - +
279A LEU* 3.9 14.4 - - + -
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Residues in contact with ILE 247 (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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71A THR* 4.0 25.4 - - + +
74A VAL* 4.1 15.7 - - + -
186A MET* 4.0 24.5 - - + -
190A LEU* 3.9 26.5 - - + +
211A LEU* 5.5 1.0 - - + +
233A ASP* 3.1 4.1 - - - +
234A LYS* 2.9 45.4 + - + +
246A ASP* 1.3 79.4 + - - +
248A ALA* 1.3 61.1 + - - +
261A LEU 3.5 4.3 - - - -
262A VAL* 3.8 18.4 - - + -
264A TYR* 3.7 24.7 - - + +
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Residues in contact with ALA 248 (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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190A LEU* 3.6 8.2 - - - +
221A ILE* 3.8 32.1 - - + -
231A VAL* 4.2 8.3 - - + -
232A GLY 3.1 11.2 - - - +
233A ASP* 3.9 8.1 - - + -
247A ILE* 1.3 75.2 - - - +
249A VAL* 1.3 65.1 + - - +
250A ILE* 4.3 6.9 - - + +
259A LEU 4.1 0.2 - - - +
260A VAL* 3.4 3.8 - - - -
261A LEU 2.8 35.2 + - - +
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Residues in contact with VAL 249 (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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190A LEU* 3.9 13.0 - - + +
194A THR* 3.2 34.5 - - + +
195A LEU* 3.9 23.1 - - + -
211A LEU* 5.0 4.0 - - + -
231A VAL* 3.4 4.5 - - - +
232A GLY* 2.8 33.6 + - - +
248A ALA* 1.3 76.5 - - - +
250A ILE* 1.3 64.8 + - - +
251A TRP* 3.4 37.6 - - + -
258A PRO* 4.6 0.9 - - + -
259A LEU 3.6 7.2 - - - +
260A VAL* 4.5 6.3 - - + -
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Residues in contact with ILE 250 (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 ILE* 4.3 7.9 - - + -
225A LEU* 3.8 30.3 - - + -
229A TRP* 3.4 35.4 - - + -
230A VAL 3.6 7.9 - - - +
231A VAL* 4.4 3.8 - - + +
248A ALA* 4.3 9.0 - - + -
249A VAL* 1.3 79.5 - - - +
251A TRP* 1.3 63.3 + - - +
252A PRO* 3.3 6.5 - - + +
258A PRO* 3.2 6.9 - - - +
259A LEU* 2.8 48.9 + - + +
261A LEU* 4.1 30.3 - - + -
287A THR* 4.5 4.9 - - + -
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Residues in contact with TRP 251 (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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194A THR* 5.6 0.4 - - + -
195A LEU* 4.1 14.1 - - + +
204A ARG* 5.6 1.8 - - - -
208A VAL* 3.7 35.4 - - + -
211A LEU* 6.4 1.6 - - + -
212A LYS* 3.7 19.3 - - + -
229A TRP* 4.1 2.7 - - - -
230A VAL* 2.8 54.7 + - + +
232A GLY* 3.7 12.8 - - - -
249A VAL* 3.4 43.3 - - + -
250A ILE* 1.3 75.8 - - - +
252A PRO* 1.3 70.0 - - - +
256A HIS 5.3 0.4 - - - -
258A PRO* 3.7 24.2 - - + +
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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