Contacts of the strand formed by residues 254 - 264 (chain A) in PDB entry 3I5D
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 GLY 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A MET* 4.4 8.8 - - - +
253A GLY* 1.3 74.3 - - - -
255A VAL* 1.3 65.8 + - - +
281A ARG* 4.3 4.3 - - - -
283A ASP* 3.4 17.7 - - - -
295A TYR* 3.6 8.2 - - - +
319A GLY 3.1 6.5 + - - +
320A ILE* 3.1 10.4 - - - +
321A ARG 2.9 22.0 + - - -
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Residues in contact with VAL 255 (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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254A GLY* 1.3 79.5 - - - +
256A MET* 1.3 59.2 + - - +
281A ARG* 3.7 3.9 - - - +
282A LEU* 2.8 58.1 + - + +
283A ASP* 2.9 28.3 + - + +
295A TYR* 3.5 29.8 - - + -
321A ARG* 3.2 31.2 - - + +
323A ASP* 5.4 2.0 - - - +
66B SER* 5.2 3.6 - - - +
68B THR* 4.7 7.0 - - - +
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Residues in contact with MET 256 (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 ILE* 4.1 19.1 - - + +
239A VAL* 4.1 13.0 - - + -
242A ALA* 3.6 20.4 - - + -
249A MET* 4.0 20.2 - - - -
255A VAL* 1.3 72.3 - - - +
257A GLY* 1.3 63.1 + - - +
258A VAL* 3.7 1.3 + - - +
279A PHE* 4.4 2.0 - - + -
280A ARG 2.9 35.7 - - - +
281A ARG* 3.6 15.7 - - - -
282A LEU* 4.1 2.7 - - - -
320A ILE* 3.8 19.0 - - + +
321A ARG 2.9 7.1 + - - +
322A PHE* 3.5 30.8 - - + +
323A ASP* 2.9 27.5 + - - +
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Residues in contact with GLY 257 (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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256A MET* 1.3 70.9 - - - +
258A VAL* 1.3 62.6 + - - +
259A GLN* 3.5 4.1 + - - +
278A THR 4.4 0.2 - - - -
279A PHE* 3.5 6.8 - - - +
280A ARG* 2.7 38.6 + - - +
282A LEU* 3.5 12.9 - - - +
323A ASP 3.6 2.0 - - - -
325A MET* 3.3 25.5 - - - +
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Residues in contact with VAL 258 (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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102A PHE* 5.9 0.7 - - + -
192A ILE* 4.3 21.3 - - + -
233A PHE* 5.7 1.3 - - + -
238A ILE* 4.2 23.3 - - + -
256A MET 4.5 2.0 - - - +
257A GLY* 1.3 73.6 - - - +
259A GLN* 1.3 60.1 + - - +
260A ILE* 3.6 14.3 + - + -
277A TYR* 5.3 5.6 - - + -
278A THR 3.8 5.2 - - - +
279A PHE* 4.2 22.2 - - + -
322A PHE* 4.3 20.4 - - + -
323A ASP 2.9 13.0 + - - +
324A VAL* 3.5 15.8 - - + +
325A MET 3.0 21.1 + - - -
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Residues in contact with GLN 259 (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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257A GLY 3.5 2.4 + - - +
258A VAL* 1.3 71.3 - - - +
260A ILE* 1.3 61.3 + - - +
261A ARG* 4.1 0.7 - - + -
276A ARG 3.4 3.8 - - - +
277A TYR* 3.4 3.1 - - - -
278A THR* 2.9 63.8 + - - +
280A ARG* 2.9 44.9 + - - +
325A MET* 3.3 33.3 - - + +
327A PHE* 4.4 20.6 - - + -
197B ARG* 3.8 20.8 + - - +
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Residues in contact with ILE 260 (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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192A ILE* 4.3 12.8 - - + -
194A ASN* 3.8 22.9 - - + +
207A ASN* 5.7 0.4 - - + +
258A VAL* 3.6 10.1 + - + +
259A GLN* 1.3 75.6 - - - +
261A ARG* 1.3 61.2 + - - +
262A TRP* 3.3 28.0 - - + +
275A PRO* 3.9 20.0 - - + -
276A ARG 3.8 2.7 - - - +
277A TYR* 3.8 28.5 - - + -
324A VAL* 4.1 13.7 - - + -
325A MET 3.0 6.3 + - - +
326A VAL* 3.5 19.3 - - + +
327A PHE* 3.1 29.1 + - - +
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Residues in contact with ARG 261 (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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259A GLN* 4.1 0.9 - - + +
260A ILE* 1.3 74.4 - - - +
262A TRP* 1.3 62.3 + - - +
263A ASP* 2.7 41.2 + - - +
274A VAL 3.8 1.7 - - - +
275A PRO* 3.6 2.8 - - - +
276A ARG* 2.9 62.0 + - - +
278A THR* 5.0 7.7 + - - +
327A PHE* 3.4 41.1 - - + +
199B PRO* 6.0 1.1 - - - -
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Residues in contact with TRP 262 (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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63A VAL* 4.2 8.3 - - + -
194A ASN* 3.0 35.9 + - - -
196A ILE* 3.5 39.1 - - + +
198A TYR* 2.7 33.4 + - + +
205A LYS* 4.1 13.2 - - + -
206A ARG 3.8 7.2 - - - -
207A ASN* 3.7 20.0 - - + -
260A ILE* 3.3 11.9 - - + +
261A ARG* 1.3 69.8 - - - +
263A ASP* 1.3 61.6 + - - +
264A CYS* 3.8 1.8 - - - -
273A CYS* 4.1 17.3 - - - -
274A VAL* 4.2 6.1 - - - -
275A PRO* 3.2 45.5 - - + -
326A VAL* 3.8 20.6 - - + -
327A PHE 3.0 9.8 + - - -
328A GLY* 3.3 0.9 - - - -
329A GLN 3.1 14.9 + - - -
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Residues in contact with ASP 263 (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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261A ARG* 2.7 46.6 + - - +
262A TRP* 1.3 77.0 - - - +
264A CYS* 1.3 63.0 + - - +
265A ASP 4.3 0.2 + - - -
272A TRP 5.7 0.5 - - - +
274A VAL 4.6 5.7 + - - +
327A PHE* 5.6 0.3 - - - -
328A GLY* 3.7 5.7 - - - -
329A GLN* 3.3 22.4 + - - +
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Residues in contact with CYS 264 (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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198A TYR* 4.5 9.4 - - + +
262A TRP* 3.8 4.8 + - - -
263A ASP* 1.3 81.7 - - - +
265A ASP* 1.3 61.1 + - - +
266A LEU* 3.8 17.7 - - + -
272A TRP 5.8 0.9 - - - -
273A CYS* 2.0 63.3 - - + +
274A VAL 3.9 3.6 - - - -
329A GLN 3.3 6.3 + - - +
330A ALA* 3.2 28.2 - - + +
331A GLY 3.7 1.6 + - - -
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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