Contacts of the strand formed by residues 261 - 270 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLU* 2.5 46.3 + - - +
85G GLY 3.9 2.0 + - - -
86G ILE* 3.4 25.0 - - - +
124G MET* 5.7 2.0 - - - -
84H GLU* 4.6 8.8 + - - +
161H LEU* 3.9 2.0 - - - +
203H TRP* 4.5 2.5 - - - -
252H GLN* 3.2 33.2 + - + +
253H VAL 3.4 10.8 - - - +
254H VAL* 3.9 22.7 - - + -
259H GLY 3.4 6.1 + - - +
260H GLU* 1.3 75.6 - - - +
262H VAL* 1.3 74.2 + - - +
263H GLU* 3.2 25.5 + - - +
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Residues in contact with VAL 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H PRO* 3.7 26.5 - - + -
160H GLU 4.1 14.4 - - - +
161H LEU* 3.7 17.0 - - + -
166H ILE* 3.9 35.0 - - + -
252H GLN* 3.4 4.7 - - - +
253H VAL* 2.9 38.0 + - + +
261H ARG* 1.3 77.6 - - - +
263H GLU* 1.3 66.8 + - - +
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Residues in contact with GLU 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G GLU 4.1 4.9 - - - +
85G GLY* 3.6 9.5 - - - +
83H PRO* 5.3 3.3 - - - +
84H GLU 4.2 13.4 + - - -
85H GLY 4.8 0.7 + - - -
159H PRO* 3.5 19.5 - - - +
166H ILE* 5.8 1.6 - - - -
250H ASN* 3.0 17.5 - - - +
251H ALA 3.3 5.8 - - - +
252H GLN* 3.5 27.6 - - + +
261H ARG* 3.2 20.5 + - - +
262H VAL* 1.3 82.2 - - - +
264H GLN* 1.3 63.2 + - - +
265H SER* 4.2 1.2 + - - +
1272H O4B 3.4 20.1 - - - +
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Residues in contact with GLN 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H LEU* 5.0 4.4 - - - +
159H PRO* 3.7 22.3 - - + +
166H ILE* 3.6 17.7 - - + +
167H ASP* 4.2 1.9 - - - +
168H ILE* 3.4 54.3 + - + +
249H ILE 4.0 0.3 - - - +
250H ASN* 3.6 0.2 - - - -
251H ALA* 2.8 36.4 + - - +
263H GLU* 1.3 74.5 - - - +
265H SER* 1.3 73.7 + - - +
266H MET* 4.1 4.9 - - + +
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Residues in contact with SER 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H THR* 4.3 5.2 - - - -
249H ILE 3.2 8.1 - - - -
250H ASN* 2.8 26.3 + - - -
263H GLU* 4.2 1.7 + - - +
264H GLN* 1.3 79.0 - - - +
266H MET* 1.3 69.6 + - - +
1272H O4B 3.2 43.3 + - - +
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Residues in contact with MET 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H ILE* 3.7 46.0 - - + +
169H LYS* 4.2 0.9 - - - -
170H ASN* 4.0 17.3 - - + +
186H PHE* 4.0 26.2 - - + -
204H MET* 5.2 0.4 - - + -
248H THR* 3.5 3.9 - - - -
249H ILE* 2.6 65.8 + - + +
250H ASN 4.9 0.2 - - - +
251H ALA 5.1 1.3 - - - +
264H GLN* 4.1 7.6 - - + +
265H SER* 1.3 86.1 - - - +
267H THR* 1.3 64.0 + - - +
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Residues in contact with THR 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H ASN* 5.1 1.4 + - - -
175H ASN* 4.2 17.2 + - - +
246H GLU* 4.1 24.6 + - - +
247H TYR 3.4 7.3 + - - -
248H THR* 4.6 6.5 - - - +
266H MET* 1.3 79.8 - - - +
268H VAL* 1.3 68.7 + - - +
269H VAL* 5.0 4.7 - - - +
1272H O4B 5.0 17.3 - - - -
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Residues in contact with VAL 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H ASN* 4.2 2.9 - - - +
174H ILE 4.2 14.4 - - - +
175H ASN 3.7 8.5 - - - +
176H SER* 4.3 8.5 - - - -
177H VAL* 4.7 1.3 - - + +
184H VAL* 4.4 12.6 - - + -
186H PHE* 4.1 15.3 - - + -
238H PHE* 3.7 32.8 - - + -
247H TYR* 2.7 47.4 + - - +
249H ILE* 4.0 18.2 - - + -
266H MET* 4.1 0.8 + - + -
267H THR* 1.3 82.3 + - - +
269H VAL* 1.3 69.2 + - - +
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Residues in contact with VAL 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H ASN 3.1 16.9 + - - +
176H SER* 3.1 14.0 - - - -
177H VAL 3.0 23.6 + - - -
245H GLY* 3.3 14.8 - - - +
246H GLU* 4.5 10.5 - - + +
267H THR* 5.0 7.0 - - - +
268H VAL* 1.3 77.3 - - - +
270H LYS* 1.3 70.3 + - - +
271H LYS* 4.3 16.4 - - + +
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Residues in contact with LYS 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H VAL* 3.6 14.6 - - + -
178H GLU 4.0 13.0 - - - +
179H SER* 2.8 31.8 + - - +
181H GLY* 4.6 0.7 - - - -
238H PHE* 4.6 11.7 - - + -
239H ASP 3.3 20.2 - - - -
240H LYS* 2.9 8.9 + - - +
242H TYR* 2.6 37.2 + - + +
243H PRO 3.7 10.4 - - - +
244H ALA* 3.4 2.4 - - - +
245H GLY* 2.7 35.9 + - - +
247H TYR* 3.8 20.2 - - + -
268H VAL* 4.1 1.6 + - - +
269H VAL* 1.3 74.3 - - - +
271H LYS* 1.3 69.7 + - - +
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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