Contacts of the strand formed by residues 265 - 277 (chain E) in PDB entry 3J7Y
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 TYR 265 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3204A C 4.8 11.9 + - + +
3205A C 3.3 37.0 - - - -
3206A C 3.1 28.5 + - - -
175E THR* 5.8 2.4 - - - +
177E LYS* 3.3 34.4 + - - -
207E THR* 4.9 1.8 - - - -
208E ALA* 3.4 19.1 - - - -
209E LYS* 3.7 37.5 - - + +
264E ILE* 1.3 76.2 - - - +
266E ARG* 1.3 73.2 + - - +
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Residues in contact with ARG 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3108A U 4.1 15.2 + - - -
3109A U 5.8 5.1 - - - -
3146A G 2.7 62.2 + - - +
3147A G 3.5 13.8 + - - +
3204A C 4.9 1.3 - - - -
207E THR* 3.3 2.1 - - - -
208E ALA 2.8 31.8 + - - +
210E THR* 3.5 30.5 - - + -
264E ILE* 3.5 22.9 + - + +
265E TYR* 1.3 83.9 + - - +
267E THR* 1.3 65.3 + - - +
268E GLU* 5.2 1.1 - - - +
290E PRO* 3.4 12.8 - - + +
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Residues in contact with THR 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3146A G 5.5 1.4 + - - -
3203A A 4.9 4.3 + - - +
3204A C 2.9 29.8 + - - -
205E ASP* 4.1 10.1 - - + -
206E VAL 3.4 5.4 - - - +
207E THR* 3.1 27.0 - - + +
266E ARG* 1.3 75.2 - - - +
268E GLU* 1.3 77.1 + - - +
269E TYR* 3.9 44.2 - - + -
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Residues in contact with GLU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3146A G 2.9 39.2 + - - +
3147A G 3.7 26.0 + - - +
3165A C 4.0 4.0 + - - +
3166A U 4.6 10.1 - - - +
204E VAL 4.1 0.7 - - - +
205E ASP* 3.5 2.1 - - - -
206E VAL 2.8 35.1 + - - +
266E ARG* 5.2 1.2 - - - +
267E THR* 1.3 80.2 + - - +
269E TYR* 1.3 61.0 + - - +
271E LEU* 4.2 23.9 - - + +
288E SER 3.9 12.9 - - - +
290E PRO* 3.6 27.3 - - + +
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Residues in contact with TYR 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3166A U 2.9 34.1 + - - +
3167A U 5.1 4.5 - - - -
3168A C 3.2 28.2 + + - -
3203A A 3.3 38.3 + - - +
205E ASP* 3.5 25.1 - - - +
267E THR* 3.9 30.5 - - + +
268E GLU* 1.3 73.9 - - - +
270E GLY* 1.3 65.7 + - - +
271E LEU* 3.4 7.8 - - - +
303E LYS* 3.4 31.3 + - + -
304E LEU* 3.8 19.7 - - + -
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Residues in contact with GLY 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3166A U 4.3 12.7 - - - +
3167A U 4.6 3.0 + - - -
203E TYR* 3.5 14.9 - - - -
204E VAL 2.8 14.3 + - - -
205E ASP* 3.4 4.8 + - - -
269E TYR* 1.3 76.7 - - - +
271E LEU* 1.3 61.4 + - - +
272E LYS 3.8 0.7 + - - -
286E ASN* 5.5 0.9 + - - -
302E SER* 4.2 8.3 - - - -
304E LEU* 3.6 19.0 - - - +
307E TYR* 4.3 10.2 + - - -
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Residues in contact with LEU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3165A C 4.9 3.1 - - - +
3166A U 3.9 20.2 - - - +
203E TYR* 3.3 2.6 - - - -
204E VAL* 2.8 38.1 + - + +
206E VAL* 3.8 20.6 - - + -
268E GLU* 4.2 22.0 - - + +
269E TYR 3.4 19.5 - - - +
270E GLY* 1.3 74.8 - - - +
272E LYS* 1.3 60.9 + - - +
285E VAL* 3.4 27.8 - - + -
286E ASN* 3.4 19.1 - - - +
288E SER 4.1 10.5 - - - +
289E VAL* 4.0 12.8 - - + -
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Residues in contact with LYS 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLY* 3.9 20.2 - - - +
202E GLN 3.6 3.8 - - - -
203E TYR* 3.5 39.0 + - + +
270E GLY 3.8 1.0 + - - -
271E LEU* 1.3 71.8 - - - +
273E VAL* 1.3 69.9 + - - +
274E TRP* 3.2 32.1 + - + -
285E VAL* 3.6 1.5 - - - -
286E ASN* 2.9 47.6 + - + +
334E ASP* 3.1 28.7 + - - -
336E ASN* 4.2 10.7 - - - +
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Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E PHE* 4.4 11.2 - - + -
199E ARG 3.8 17.7 - - - +
200E PRO* 4.1 2.2 - - + -
201E GLY* 2.8 30.0 + - - -
202E GLN* 2.9 19.0 + - + +
204E VAL* 3.2 29.6 - - + -
272E LYS* 1.3 73.9 - - - +
274E TRP* 1.3 61.4 + - - +
275E ARG 3.6 22.7 - - - +
276E ILE* 3.9 17.0 - - + -
283E ILE* 3.9 15.5 - - + -
284E TYR 3.4 8.1 - - - +
285E VAL* 4.5 2.2 - - + +
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Residues in contact with TRP 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E LEU* 3.6 30.5 - - + -
111E THR* 4.3 11.7 - - + -
117E HIS* 3.6 37.5 - + - +
119E VAL* 3.6 25.4 - - + -
200E PRO* 4.2 2.0 - - - -
272E LYS* 3.2 46.5 + - + -
273E VAL* 1.3 73.3 - - - +
275E ARG* 1.3 61.8 - - + +
284E TYR* 2.8 12.1 + - + +
286E ASN* 3.4 32.6 - - + +
333E TYR* 3.6 0.7 - - - -
334E ASP* 2.8 46.1 + - + +
336E ASN* 4.1 15.7 - - + -
337E VAL* 3.7 15.8 - - + +
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Residues in contact with ARG 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E MET* 4.2 6.7 - - - +
109E LEU* 4.9 12.8 - - + +
200E PRO* 4.2 2.7 - - - -
273E VAL* 3.6 3.5 - - - +
274E TRP* 1.3 82.6 - - + +
276E ILE* 1.3 72.4 + - - +
277E ASN* 5.4 3.2 - - - +
284E TYR* 2.8 82.0 + - + +
331E ASP* 3.1 28.3 + - - +
332E LEU 3.2 12.8 - - - +
333E TYR* 3.6 43.2 + - + -
340E PRO* 5.2 2.0 - - - +
94Q ILE* 5.8 0.2 - - - +
98Q ASP* 3.1 34.3 + - - -
145Q LEU* 5.7 0.2 - - - +
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Residues in contact with ILE 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ALA* 4.2 2.5 - - + +
196E ALA* 4.2 19.1 - - + +
198E PHE 3.2 26.7 - - - +
200E PRO* 4.3 4.7 - - + +
273E VAL* 3.9 11.9 - - + -
275E ARG* 1.3 84.2 - - - +
277E ASN* 1.3 59.7 + - - +
278E THR* 3.2 35.0 - - - +
282E ILE 3.4 8.5 - - - +
283E ILE* 3.8 22.2 - - + -
284E TYR* 4.4 0.2 - - - -
331E ASP* 3.2 3.6 - - - +
332E LEU* 2.8 62.5 + - + +
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Residues in contact with ASN 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ALA* 5.4 0.2 - - - -
275E ARG* 5.4 3.2 - - - +
276E ILE* 1.3 70.8 - - - +
278E THR* 1.3 61.8 + - - +
279E LYS* 3.2 14.6 + - - +
280E HIS* 3.1 29.6 + - - +
281E ASN* 2.9 19.9 + - - -
282E ILE* 2.8 19.7 + - + +
284E TYR* 3.9 29.1 + - + +
330E GLU 3.1 17.6 - - - +
331E ASP* 3.9 9.1 + - + +
94Q ILE* 4.6 8.3 - - - +
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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