Contacts of the strand formed by residues 261 - 270 (chain D) 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 ARG 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C GLU* 2.5 46.3 + - - +
85C GLY 3.9 2.0 + - - -
86C ILE* 3.4 23.9 - - - +
124C MET* 5.7 2.0 - - - -
84D GLU* 4.6 9.3 + - - +
161D LEU* 3.9 1.7 - - - +
203D TRP* 4.5 2.5 - - - -
252D GLN* 3.2 32.8 + - + +
253D VAL 3.4 9.9 - - - +
254D VAL* 3.9 22.9 - - + +
259D GLY 3.4 5.2 + - - +
260D GLU* 1.3 76.2 - - - +
262D VAL* 1.3 73.7 + - - +
263D GLU* 3.2 25.1 + - - +
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Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D PRO* 3.7 27.1 - - + -
160D GLU 4.1 15.3 - - - +
161D LEU* 3.7 17.3 - - + -
166D ILE* 3.9 34.5 - - + -
252D GLN* 3.4 5.7 - - - +
253D VAL* 2.9 36.7 + - + +
261D ARG* 1.3 78.6 - - - +
263D GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU 4.1 5.5 - - - +
85C GLY* 3.6 11.9 - - - +
83D PRO* 5.8 2.9 - - - -
84D GLU 4.2 13.3 + - - -
85D GLY 4.8 0.7 + - - -
159D PRO* 3.5 19.0 - - - +
166D ILE* 5.7 1.8 - - - -
250D ASN* 3.0 17.5 - - - +
251D ALA 3.3 5.4 - - - +
252D GLN* 3.5 28.1 - - + +
261D ARG* 3.2 20.6 + - - +
262D VAL* 1.3 80.3 - - - +
264D GLN* 1.3 64.9 + - - +
265D SER* 5.0 0.9 - - - +
1272D O4B 3.5 19.3 - - - +
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Residues in contact with GLN 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D SER 5.5 1.0 + - - -
158D LEU* 5.0 5.1 - - - +
159D PRO* 3.7 21.6 - - + +
166D ILE* 3.6 18.1 - - + +
167D ASP* 4.2 1.9 - - - +
168D ILE* 3.4 52.2 + - + +
249D ILE 4.0 0.3 - - - +
250D ASN* 3.7 0.2 - - - +
251D ALA* 2.8 35.8 + - - +
263D GLU* 1.3 75.4 - - - +
265D SER* 1.3 73.3 + - - +
266D MET* 4.1 4.9 - - + +
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Residues in contact with SER 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D THR* 4.3 5.4 - - - -
249D ILE 3.2 8.5 - - - -
250D ASN* 2.8 26.5 + - - -
263D GLU* 4.2 1.4 + - - +
264D GLN* 1.3 78.5 - - - +
266D MET* 1.3 70.5 + - - +
1272D O4B 3.1 44.7 - - - +
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Residues in contact with MET 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 3.7 45.1 - - + +
170D ASN* 4.0 17.5 - - + +
186D PHE* 4.0 26.7 - - + -
204D MET* 5.2 0.2 - - + -
248D THR* 3.5 3.6 - - - -
249D ILE* 2.6 65.2 + - + +
251D ALA 5.1 1.3 - - - +
264D GLN* 4.1 7.6 - - + +
265D SER* 1.3 86.2 - - - +
267D THR* 1.3 64.4 + - - +
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Residues in contact with THR 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ASN* 5.1 1.6 - - - +
175D ASN* 4.2 17.2 + - - +
246D GLU* 4.1 23.8 + - - +
247D TYR 3.4 7.5 + - - -
248D THR* 4.8 8.5 - - + -
266D MET* 1.3 78.6 - - - +
268D VAL* 1.3 69.4 + - - +
269D VAL* 4.9 5.3 + - - +
1272D O4B 5.3 15.0 - - - +
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Residues in contact with VAL 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ASN* 4.3 2.5 - - - +
174D ILE 4.2 13.7 - - - +
175D ASN 3.7 9.2 - - - +
176D SER* 4.3 8.5 - - - -
177D VAL* 4.7 2.0 - - + +
184D VAL* 4.4 11.9 - - + -
186D PHE* 4.1 15.3 - - + -
238D PHE* 3.7 33.4 - - + -
246D GLU* 4.9 0.2 - - - -
247D TYR* 2.7 47.8 + - - +
249D ILE* 4.0 17.9 - - + -
266D MET* 5.4 0.4 - - + -
267D THR* 1.3 80.8 + - - +
269D VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ASN 3.1 16.0 + - - +
176D SER* 3.1 14.3 - - - -
177D VAL 3.1 23.6 + - - -
245D GLY* 3.3 14.6 - - - +
246D GLU* 4.5 10.8 - - + +
267D THR* 5.0 7.2 - - - +
268D VAL* 1.3 79.0 - - - +
270D LYS* 1.3 71.1 + - - +
271D LYS* 4.2 16.6 - - + +
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Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D VAL* 3.6 15.5 - - + -
178D GLU 4.0 13.0 - - - +
179D SER* 2.9 30.9 + - - +
181D GLY* 4.6 0.9 - - - -
238D PHE* 4.6 11.7 - - + -
239D ASP 3.3 20.6 - - - -
240D LYS* 2.9 8.7 + - - +
242D TYR* 2.6 37.0 + - + +
243D PRO 3.7 10.2 - - - +
244D ALA* 3.3 2.2 - - - +
245D GLY* 2.7 35.7 + - - +
247D TYR* 3.8 20.7 - - + -
268D VAL 4.1 0.8 + - - -
269D VAL* 1.3 75.5 - - - +
271D LYS* 1.3 70.3 + - - +
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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