Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 4IBR
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 ARG 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLU* 2.5 40.9 + - + -
48A LEU 3.2 13.5 - - - +
49A ASP* 4.7 2.0 - - - +
50A LEU* 3.9 3.2 - - - +
56A LEU* 3.9 17.9 - - + +
246A ALA 3.8 0.2 - - - +
247A ALA* 3.3 5.5 - - - +
248A LEU* 3.0 33.2 + - + +
254A PRO* 3.8 0.9 - - - +
255A SER* 1.3 88.4 + - - +
257A ILE* 1.3 66.3 + - - +
258A VAL* 4.1 2.2 - - + -
283A LEU* 4.3 4.2 + - - +
286A HIS 5.1 1.2 + - - -
287A TRP* 2.5 85.4 + - + +
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Residues in contact with ILE 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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46A ILE 3.7 0.9 - - - +
47A GLU* 3.3 5.2 - - - +
48A LEU* 2.8 47.7 + - + +
50A LEU* 3.8 30.1 - - + -
186A ALA* 3.9 35.6 - - + +
189A LEU* 4.3 13.7 - - + -
190A ARG* 4.2 19.1 - - + -
193A LEU* 4.5 11.9 - - + -
246A ALA 3.2 6.5 - - - +
247A ALA* 3.9 24.9 - - + -
256A ARG* 1.3 74.8 - - - +
258A VAL* 1.3 64.5 + - - +
259A VAL* 4.4 3.4 - - + -
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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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45A TYR* 3.7 29.4 - - + +
46A ILE 3.4 2.7 - - - +
47A GLU* 4.3 16.2 - - + -
220A LEU* 4.6 12.1 - - + +
244A ILE* 3.9 1.5 - - + +
245A ILE* 3.5 1.2 - - - -
246A ALA* 2.9 34.6 + - - +
248A LEU* 3.7 17.5 - - + -
256A ARG* 4.1 2.7 - - + -
257A ILE* 1.3 80.3 - - - +
259A VAL* 1.3 69.1 + - - +
260A ILE* 4.2 13.2 - - + -
283A LEU* 3.7 30.1 - - + -
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Residues in contact with VAL 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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44A GLY 3.8 0.3 - - - +
45A TYR* 3.3 5.2 - - - -
46A ILE* 3.0 41.5 + - + +
182A PRO* 3.9 14.8 - - + +
185A MET* 4.2 4.3 - - + -
186A ALA* 3.4 35.7 - - + +
189A LEU* 5.3 0.9 - - + -
244A ILE 3.5 2.9 - - - -
245A ILE* 4.0 18.6 - - + -
257A ILE* 4.4 3.6 - - + -
258A VAL* 1.3 80.0 - - - +
260A ILE* 1.3 63.9 + - - +
261A TYR* 3.4 37.9 - - + -
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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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43A VAL* 4.5 12.1 - - + -
44A GLY 3.3 9.0 - - - +
45A TYR* 3.6 18.8 - - + -
220A LEU* 4.3 13.5 - - + -
243A GLY* 3.1 3.5 - - - -
244A ILE* 2.9 44.0 + - + +
258A VAL* 4.2 6.3 - - + -
259A VAL* 1.3 78.5 - - - +
261A TYR* 1.3 75.0 + - - +
262A MET* 4.7 3.8 - - + -
276A ILE* 4.2 31.2 - - + -
279A ILE* 3.7 38.6 - - + -
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Residues in contact with TYR 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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43A VAL* 3.4 4.2 - - - +
44A GLY* 2.7 37.0 + - - +
65A PHE* 3.5 33.2 - - + -
66A PRO 3.7 23.8 - - - -
67A MET 3.8 5.6 - - - -
68A MET* 3.7 20.2 - - + -
70A THR* 2.8 27.5 + - + -
180A THR* 3.7 25.0 - - + +
182A PRO* 4.4 13.0 - - + -
185A MET* 3.5 20.0 - - + +
242A ARG 3.6 2.2 - - - -
243A GLY* 4.0 0.7 - - - -
244A ILE 4.9 0.2 - - - -
245A ILE* 3.8 3.8 - - + +
259A VAL* 3.4 32.5 - - + -
260A ILE* 1.3 78.5 - - - +
262A MET* 1.3 65.0 + - - +
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Residues in contact with MET 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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35A ALA* 6.3 0.2 - - - -
39A LEU* 3.7 21.5 - - + -
42A ARG 3.3 6.7 - - - +
43A VAL* 4.0 21.5 - - + -
65A PHE* 4.3 3.0 - - - +
66A PRO* 5.3 1.0 - - - +
68A MET* 5.0 1.6 - - - +
240A GLY 4.3 1.1 - - - +
241A SER* 3.1 4.8 - - - -
242A ARG* 2.8 39.0 + - + +
260A ILE* 4.7 5.4 - - + -
261A TYR* 1.3 81.2 - - - +
263A THR* 1.3 65.4 + - - +
265A SER* 5.3 4.3 - - - -
272A ARG* 3.2 47.8 - - + +
275A GLN* 5.2 2.0 - - - -
276A ILE* 3.9 30.7 - - - -
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Residues in contact with THR 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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40A GLY 4.7 0.2 - - - +
41A GLY* 3.1 1.7 - - - -
42A ARG* 2.7 63.9 + - - +
65A PHE* 3.9 10.5 - - + -
66A PRO* 3.9 19.2 - - + +
171A ALA* 4.2 4.2 + - - +
174A ASN 6.2 2.0 - - - +
239A ARG 4.0 4.9 + - - -
240A GLY 4.5 1.8 - - - +
241A SER* 2.7 26.5 + - - +
262A MET* 1.3 78.1 - - - +
264A GLY* 1.3 59.8 + - - +
265A SER* 3.4 6.6 - - - +
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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