Contacts of the strand formed by residues 242 - 249 (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 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 3.4 6.5 - - - +
215A VAL 4.9 6.7 + - - -
218A PRO* 5.0 4.2 - - - +
219A LEU* 3.6 23.1 - - - +
234A SER* 4.1 5.7 + - - -
235A GLY 2.7 33.8 + - - +
236A ALA* 3.3 10.6 - - - +
240A GLY 3.6 0.2 + - - -
241A SER* 1.3 74.4 - - - +
243A GLY* 1.3 61.3 + - - +
261A TYR* 3.6 0.9 - - - -
262A MET* 2.8 54.7 + - + +
269A MET* 3.2 26.4 - - - +
272A ARG* 4.0 11.7 - - + +
273A ASN* 2.9 31.7 + - - +
276A ILE* 3.8 20.0 - - + +
302A MES 2.8 27.0 + - - +
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Residues in contact with GLY 243 (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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68A MET* 3.3 12.6 - - - +
70A THR* 4.5 3.6 - - - -
219A LEU* 4.3 3.1 - - - +
234A SER* 3.3 4.3 - - - -
235A GLY 2.9 31.7 + - - +
242A ARG* 1.3 77.3 - - - +
244A ILE* 1.3 66.0 + - - +
260A ILE 3.1 12.3 - - - -
261A TYR* 4.0 2.9 - - - -
276A ILE* 4.8 5.8 - - - -
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Residues in contact with ILE 244 (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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70A THR* 4.5 1.8 - - - +
216A ALA* 4.6 3.8 - - + -
219A LEU* 4.0 25.4 - - + -
220A LEU* 3.9 34.5 - - + -
232A ASP* 3.6 28.0 - - + +
233A LYS 3.4 15.7 - - - +
234A SER* 4.4 0.4 - - - -
243A GLY* 1.3 76.5 - - - +
245A ILE* 1.3 75.7 + - - +
258A VAL 3.9 0.7 - - - +
259A VAL* 3.5 2.3 - - - +
260A ILE* 2.9 49.5 + - + +
261A TYR* 4.9 1.0 - - - -
276A ILE* 4.2 16.2 - - + -
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Residues in contact with ILE 245 (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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70A THR* 4.0 25.8 - - - +
73A VAL* 4.0 25.1 - - + -
185A MET* 3.5 36.6 - - + -
189A LEU* 4.0 21.3 - - + -
210A MET* 4.0 5.6 - - + +
232A ASP* 3.1 5.5 - - - +
233A LYS* 3.0 45.8 + - + +
244A ILE* 1.3 75.8 - - - +
246A ALA* 1.3 62.5 + - - +
258A VAL 3.5 4.3 - - - -
259A VAL* 4.0 8.5 - - + -
261A TYR* 3.8 12.6 - - - +
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Residues in contact with ALA 246 (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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189A LEU* 4.2 6.3 - - - +
210A MET* 4.7 0.9 - - - -
220A LEU* 3.9 26.2 - - + -
230A ILE* 4.2 9.4 - - + -
231A ALA 3.3 5.8 - - - +
232A ASP* 3.9 14.4 - - + -
245A ILE* 1.3 77.9 - - - +
247A ALA* 1.3 60.6 + - - +
248A LEU* 4.1 6.5 - - + -
256A ARG 3.8 0.2 - - - +
257A ILE* 3.2 11.0 - - - +
258A VAL* 2.9 39.7 + - + +
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Residues in contact with ALA 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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50A LEU* 5.6 2.5 - - + -
193A LEU* 4.0 19.3 - - + -
207A ILE* 4.4 8.7 - - + -
210A MET* 4.9 0.8 - - + +
229A PHE* 3.8 2.6 - - - -
230A ILE* 3.2 2.6 - - - -
231A ALA* 2.8 36.3 + - + +
246A ALA* 1.3 72.9 - - - +
248A LEU* 1.3 60.1 + - - +
254A PRO* 4.1 17.0 - - + -
256A ARG 3.3 6.1 - - - +
257A ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 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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220A LEU* 5.1 7.4 - - + +
224A LEU* 4.2 20.6 - - + -
228A TRP* 4.6 1.1 - - + -
229A PHE 3.2 14.1 - - - +
230A ILE* 3.9 17.7 - - + -
246A ALA* 4.6 6.5 - - + +
247A ALA* 1.3 76.5 - - - +
249A GLY* 1.3 60.6 + - - +
254A PRO* 3.5 8.6 - - - +
255A SER 2.8 16.8 + - - -
256A ARG 3.0 23.4 + - - +
258A VAL* 3.7 31.0 - - + -
283A LEU* 4.2 17.9 - - + -
284A ILE* 4.2 12.6 - - + -
287A TRP* 3.7 16.4 - - + -
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Residues in contact with GLY 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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228A TRP* 3.5 12.0 - - - -
229A PHE 2.8 31.5 + - - +
248A LEU* 1.3 77.7 - - - +
250A PRO* 1.3 75.1 - - - +
253A LYS 3.1 13.6 - - - +
254A PRO* 3.7 1.8 - - - +
255A SER* 3.9 3.8 - - - -
287A TRP* 4.0 3.1 - - - -
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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