Contacts of the strand formed by residues 245 - 251 (chain D) in PDB entry 5ZR1
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 VAL 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D SER* 4.7 0.2 - - - -
95D SER* 2.8 32.5 + - - +
188D LEU* 4.9 4.0 - - + -
212D VAL* 3.3 9.6 - - + +
214D PHE* 3.6 35.0 - - + -
237D MET* 4.1 37.2 - - + +
238D VAL* 3.6 6.7 - - + +
241D SER* 4.9 0.9 - - - +
243D VAL* 3.2 29.8 + - + +
244D PRO* 1.3 73.2 - - - +
246D CYS* 1.3 57.8 + - - +
247D ILE* 3.9 16.3 + - + -
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Residues in contact with CYS 246 (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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85D ILE* 4.3 13.0 - - - -
86D ILE* 5.0 2.9 - - - -
89D SER* 3.3 28.4 + - - +
90D ILE* 6.1 1.6 - - + -
96D HIS 3.8 14.4 - - - -
211D THR* 5.0 1.1 - - - +
212D VAL 3.0 7.3 + - - +
213D VAL* 3.3 15.7 - - + -
214D PHE* 2.6 34.4 + - - +
244D PRO 4.0 1.4 + - - -
245D VAL* 1.3 72.6 - - - +
247D ILE* 1.3 61.5 + - - +
248D PHE* 3.5 33.4 - - - -
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Residues in contact with ILE 247 (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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96D HIS 4.0 4.0 + - - -
97D SER* 3.6 7.9 - - - +
98D VAL* 3.0 31.3 + - - +
214D PHE* 3.5 18.8 - - + -
216D PHE* 5.2 14.4 - - + -
219D ILE* 5.2 3.1 - - + -
234D LEU* 3.3 46.0 - - + +
235D PHE* 4.1 20.2 - - + -
238D VAL* 3.7 14.8 - - + -
245D VAL* 3.9 14.3 + - + -
246D CYS* 1.3 81.9 - - - +
248D PHE* 1.3 72.4 + - - +
249D GLY 4.8 1.1 - - - +
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D ILE* 4.1 13.0 - - + -
85D ILE* 3.7 19.7 - - + -
86D ILE* 3.6 29.4 - - + -
98D VAL* 3.4 23.3 - - + -
100D LEU* 4.0 19.3 - - + -
112D LEU* 3.7 44.4 - - + -
116D LEU* 6.2 0.2 - - + -
213D VAL* 4.4 8.3 - - + -
214D PHE 2.8 18.0 + - - +
215D ILE* 3.4 6.0 - - + -
216D PHE* 2.6 36.8 + - - +
246D CYS* 3.5 24.5 - - - -
247D ILE* 1.3 75.7 - - - +
249D GLY* 1.3 54.7 + - - +
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Residues in contact with GLY 249 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D VAL 3.2 11.1 + - - -
99D ILE* 3.3 7.9 - - - +
100D LEU 2.7 34.6 + - - +
216D PHE* 3.5 5.2 - - - -
219D ILE* 3.8 31.0 - - - +
247D ILE* 4.8 0.2 - - - +
248D PHE* 1.3 74.3 - - - +
250D CYS* 1.3 60.0 + - - -
251D THR 3.8 0.2 - - - -
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Residues in contact with CYS 250 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D LEU* 3.4 20.6 - - - -
108D LYS* 4.0 28.0 - - + +
109D THR* 4.9 2.9 - - - +
112D LEU* 3.7 31.0 - - - -
215D ILE* 5.1 0.7 - - - -
216D PHE 2.5 19.4 + - - +
217D ASP* 3.9 15.7 - - + +
218D GLU* 2.7 34.3 + - - +
219D ILE* 3.6 2.1 + - - +
248D PHE* 5.2 0.7 - - - -
249D GLY* 1.3 71.0 - - - -
251D THR* 1.3 59.7 + - - +
2001D AGS 5.9 3.3 - - - +
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Residues in contact with THR 251 (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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99D ILE* 3.8 15.9 - - + -
100D LEU 3.0 9.2 + - - +
101D VAL* 3.4 31.5 - - + -
102D GLY 3.5 0.2 + - - -
108D LYS* 3.4 13.6 - - - -
218D GLU* 4.8 5.2 - - - +
219D ILE* 3.8 16.4 - - - -
220D ASP* 3.2 27.2 + - - +
249D GLY 3.7 0.6 + - - -
250D CYS* 1.3 74.5 - - - +
252D THR* 1.3 68.7 + - - +
253D LYS 3.4 7.8 + - - +
256D ILE* 3.7 28.3 - - + +
2001D AGS 5.9 0.4 - - - -
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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