Contacts of the strand formed by residues 203 - 209 (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 203 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201E GLY 3.5 14.1 - - - -
202E GLN* 1.3 83.2 - - - +
204E VAL* 1.3 63.1 + - - +
270E GLY* 3.5 17.9 - - - -
271E LEU 3.3 2.9 - - - -
272E LYS* 3.5 48.5 + - + +
286E ASN* 5.9 0.4 - - - -
301E ASP* 3.9 3.3 - - - +
302E SER* 3.0 36.3 + - - +
307E TYR* 3.1 58.1 + + + -
310E LEU* 4.1 13.2 - - + +
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E PHE* 4.9 9.6 - - + -
202E GLN* 4.6 0.9 - - + -
203E TYR* 1.3 80.8 - - - +
205E ASP* 1.3 65.9 + - - +
206E VAL* 4.0 6.1 - - + -
268E GLU 4.1 0.5 - - - +
269E TYR 3.6 0.9 - - - -
270E GLY 2.8 10.8 + - - -
271E LEU* 2.8 41.9 + - + +
272E LYS 5.1 0.2 - - - -
273E VAL* 3.2 35.0 - - + -
285E VAL* 5.1 6.1 - - + -
299E VAL* 3.3 32.3 - - + -
300E LYS 3.1 18.8 - - - +
302E SER* 3.7 1.7 - - - +
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Residues in contact with ASP 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3203A A 4.4 3.8 + - - +
204E VAL* 1.3 74.5 - - - +
206E VAL* 1.3 61.7 + - - +
207E THR* 4.2 2.1 - - + +
267E THR* 4.1 11.0 - - + -
268E GLU 3.5 6.3 - - - +
269E TYR* 3.5 23.9 - - - +
270E GLY 3.4 15.8 + - - -
298E LYS 3.6 2.3 - - - +
299E VAL* 3.6 0.2 - - - -
300E LYS* 2.8 53.5 + - + +
301E ASP 4.2 2.9 - - - +
302E SER* 3.3 19.7 - - - +
303E LYS* 3.4 25.3 + - - +
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Residues in contact with VAL 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E LEU* 4.1 13.5 - - + -
204E VAL* 4.0 15.2 + - + -
205E ASP* 1.3 76.4 - - - +
207E THR* 1.3 65.6 + - - +
266E ARG 4.0 0.3 - - - +
267E THR* 3.4 0.7 - - - -
268E GLU* 2.8 37.7 + - - +
271E LEU* 3.8 21.8 - - + -
285E VAL* 4.6 3.4 - - + -
289E VAL* 3.4 41.5 - - + -
290E PRO* 4.1 3.8 - - + +
297E VAL* 3.7 19.1 - - + -
298E LYS 3.3 9.6 - - - +
299E VAL* 4.4 2.5 - - + -
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Residues in contact with THR 207 (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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3204A C 4.2 25.4 - - - +
3205A C 3.8 15.1 + - - -
177E LYS* 4.6 2.1 + - - -
205E ASP* 4.9 4.3 - - + +
206E VAL* 1.3 79.7 - - - +
208E ALA* 1.3 65.4 + - - +
265E TYR* 4.9 1.9 - - - -
266E ARG 3.3 7.0 - - - -
267E THR* 3.1 32.3 - - + +
290E PRO* 4.8 0.7 - - - -
297E VAL* 3.4 3.2 - - - +
298E LYS* 2.9 48.4 + - + +
300E LYS* 5.5 1.8 - - + -
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Residues in contact with ALA 208 (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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177E LYS* 5.1 0.4 - - - +
207E THR* 1.3 78.2 - - - +
209E LYS* 1.3 64.1 + - - +
210E THR 3.7 0.9 + - - -
265E TYR* 3.4 15.2 - - - -
266E ARG 2.8 32.8 + - - +
290E PRO* 3.4 24.9 - - + +
295E CYS* 4.3 3.8 - - - -
296E LEU 4.0 9.2 - - - +
297E VAL* 3.4 26.0 - - + -
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Residues in contact with LYS 209 (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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3224A G 4.5 14.1 + - - -
208E ALA* 1.3 73.8 - - - +
210E THR* 1.3 69.9 + - - +
263E ASN* 3.6 40.6 + - - +
264E ILE* 3.4 12.6 - - - +
265E TYR* 3.7 37.1 - - + +
291E GLY* 3.1 19.0 - - - -
292E HIS* 5.3 2.6 - - - -
295E CYS* 4.4 12.6 - - - -
296E LEU 5.1 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