Contacts of the strand formed by residues 245 - 255 (chain A) in PDB entry 4BEI
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A PRO* 3.9 5.2 - - - -
243A PRO 3.6 1.2 + - - -
244A ALA* 1.3 75.4 - - - +
246A GLU* 1.3 62.1 + - - -
247A TYR* 3.7 6.2 - - - -
269A VAL* 3.3 6.6 - - - -
270A LYS 2.7 43.7 + - - +
210B ASP* 4.6 12.1 - - - -
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Residues in contact with GLU 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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144A LYS* 2.8 30.8 + - - -
207A VAL 3.8 1.4 - - - +
208A GLY* 3.4 19.4 - - - -
209A PRO* 3.6 6.3 - - - +
245A GLY* 1.3 71.2 - - - -
247A TYR* 1.3 66.1 + - - +
248A THR* 4.9 6.5 + - - +
267A THR* 4.1 25.7 + - - +
268A VAL 4.0 2.9 - - - +
269A VAL* 4.4 11.4 - - + +
1272A O4B 4.5 11.6 - - - +
210B ASP* 3.8 14.9 + - - +
211B GLY* 3.6 25.0 - - - +
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Residues in contact with TYR 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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206A ALA* 4.5 7.4 - - + -
207A VAL 3.5 1.3 - - - -
208A GLY* 3.8 14.6 - - - -
209A PRO* 3.5 17.9 - - + -
212A LEU* 4.9 3.1 - - + -
214A ILE* 3.7 27.4 - - + -
238A PHE* 3.6 34.5 - + + -
242A TYR* 3.6 9.3 - - + +
243A PRO* 2.7 53.5 + - - +
245A GLY 3.7 10.5 - - - -
246A GLU* 1.3 74.9 - - - +
248A THR* 1.3 61.3 + - - +
249A ILE* 3.6 6.8 + - + -
267A THR* 3.4 4.3 - - - -
268A VAL* 2.7 46.3 + - - +
270A LYS* 3.8 15.7 - - + -
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Residues in contact with THR 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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81A LYS* 4.5 0.7 - - - +
205A THR 3.7 0.2 - - - +
207A VAL* 2.7 41.0 + - - +
246A GLU* 4.9 9.9 + - - +
247A TYR* 1.3 71.0 - - - +
249A ILE* 1.3 63.6 + - - +
250A ASN* 3.3 5.6 + - + +
265A SER* 4.3 8.1 - - - -
266A MET 3.7 7.6 - - - +
267A THR* 4.6 3.1 - - - +
1272A O4B 3.5 77.2 + - - +
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Residues in contact with ILE 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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186A PHE* 3.7 36.1 - - + -
204A MET* 4.0 24.5 - - + -
205A THR 3.6 5.6 - - - +
206A ALA* 3.5 26.5 - - + -
216A VAL* 4.9 6.3 - - + -
236A ILE* 4.4 8.1 - - + -
238A PHE* 4.0 22.2 - - + -
247A TYR* 4.5 5.2 - - + +
248A THR* 1.3 70.0 - - - +
250A ASN* 1.3 60.3 - - - +
265A SER* 3.2 5.0 - - - -
266A MET* 2.6 52.7 + - + +
268A VAL* 4.0 12.3 - - + -
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Residues in contact with ASN 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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203A TRP* 5.5 0.2 - - - -
204A MET* 3.2 4.9 - - - +
205A THR* 2.7 54.4 + - - +
207A VAL* 4.9 1.8 - - + -
248A THR* 3.3 7.2 + - + +
249A ILE* 1.3 76.6 - - - +
251A ALA* 1.3 61.6 + - - +
252A GLN* 2.9 37.4 + - - +
263A GLU* 3.0 17.2 - - - +
264A GLN 3.6 2.7 - - - +
265A SER* 2.8 23.0 + - - +
1272A O4B 3.6 16.3 - - - +
87B TYR* 4.5 10.9 + - - +
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Residues in contact with ALA 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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166A ILE* 6.4 0.2 - - - -
168A ILE* 3.5 34.3 - - + -
202A PHE* 4.5 2.0 - - + -
203A TRP 3.4 4.7 - - - +
204A MET* 3.7 26.0 - - + -
249A ILE 4.3 0.2 - - - -
250A ASN* 1.3 72.9 - - - +
252A GLN* 1.3 65.2 + - - +
253A VAL* 5.6 0.2 - - - -
263A GLU* 3.3 4.0 - - - +
264A GLN 2.8 40.3 + - - +
266A MET* 5.3 0.4 - - + -
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Residues in contact with GLN 252 (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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201A GLU 4.1 0.4 - - - +
202A PHE* 3.4 1.6 - - - -
203A TRP* 2.8 71.5 + - + +
250A ASN* 2.9 27.0 + - - +
251A ALA* 1.3 78.9 - - - +
253A VAL* 1.3 68.0 + - - +
261A ARG* 3.2 37.3 - - + +
262A VAL 3.4 8.1 - - - +
263A GLU* 3.5 11.2 - - + -
85B GLY 3.1 19.8 - - - +
86B ILE* 4.1 1.2 - - - +
87B TYR 3.8 12.5 + - - +
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Residues in contact with VAL 253 (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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161A LEU* 3.6 22.8 - - + +
164A LEU* 4.7 1.1 - - + -
166A ILE* 3.6 38.4 - - + -
168A ILE* 5.4 1.1 - - + -
190A LEU* 4.4 9.9 - - + -
200A VAL* 3.9 21.8 - - + -
201A GLU 3.4 10.1 - - - +
202A PHE* 3.8 19.7 - - + -
252A GLN* 1.3 80.7 - - - +
254A VAL* 1.3 64.5 + - - +
261A ARG* 3.4 2.2 - - - -
262A VAL* 2.9 36.9 + - + +
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Residues in contact with VAL 254 (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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161A LEU* 4.0 3.4 - - - -
200A VAL* 3.1 7.1 - - - +
201A GLU* 2.8 38.1 + - + +
203A TRP* 3.3 35.2 - - + -
253A VAL* 1.3 75.6 - - - +
255A ASP* 1.3 73.1 + - - +
256A ILE* 3.4 0.5 + - - +
259A GLY* 4.1 11.4 - - - +
260A GLU 3.5 11.9 - - - +
261A ARG* 3.9 19.1 - - + -
123B TYR* 3.8 29.8 - - + +
124B MET* 4.2 7.6 - - + -
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Residues in contact with ASP 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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161A LEU* 3.6 17.8 - - + +
194A ARG* 2.7 36.2 + - - +
199A ASN 3.5 11.8 + - - +
200A VAL* 4.3 3.1 - - + -
254A VAL* 1.3 72.3 - - - +
256A ILE* 1.3 56.2 + - - +
257A VAL* 2.9 21.1 + - - +
258A SER* 3.1 30.1 + - - +
259A GLY* 2.8 34.1 + - - -
260A GLU* 2.9 12.1 + - + +
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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