Contacts of the strand formed by residues 242 - 253 (chain A) in PDB entry 5YUS
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 SER 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.1 25.2 + - - +
241A LYS* 1.3 79.4 - - - +
243A VAL* 1.3 65.5 + - - +
335A HIS* 3.5 22.8 + - - -
336A VAL 3.3 13.9 - - - -
337A THR* 4.7 2.5 - - - -
338A LEU* 4.5 2.0 - - - -
843B G 3.6 15.5 - - - +
844B T 2.6 31.1 + - - +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.6 24.5 - - - +
242A SER* 1.3 81.2 - - - +
244A GLY* 1.3 65.1 + - - +
270A LEU* 3.7 20.9 - - + +
273A ARG* 4.0 25.6 - - + +
274A LEU* 4.5 7.9 - - + +
277A VAL* 4.6 10.5 - - + -
335A HIS* 3.6 4.2 - - - -
336A VAL* 2.9 39.4 + - + +
338A LEU* 4.5 14.6 - - + -
843B G 3.5 14.4 - - - +
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Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A VAL* 1.3 77.5 - - - +
245A VAL* 1.3 71.9 + - - +
246A GLU* 5.6 2.9 - - - -
270A LEU* 4.3 1.3 - - - -
273A ARG* 3.7 4.7 + - - -
334A LEU 3.2 11.9 - - - -
335A HIS* 4.2 10.0 - - - -
842B G 3.3 23.7 - - - +
843B G 2.8 13.3 + - - -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY* 1.3 81.0 - - - +
246A GLU* 1.3 67.7 + - - +
266A LEU* 3.9 29.0 - - + +
269A GLU* 4.2 15.7 - - + -
270A LEU* 3.7 38.1 - - + +
273A ARG* 3.9 23.8 - - - +
333A GLY* 3.3 1.2 - - - -
334A LEU* 2.8 33.4 + - + +
842B G 3.3 13.7 - - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY* 5.6 2.1 - - - -
245A VAL* 1.3 80.6 + - - +
247A ARG* 1.3 62.6 + - - +
266A LEU* 4.4 4.9 - - - +
289A LYS* 3.1 35.6 + - - -
331A LEU* 4.1 19.4 - - + +
332A VAL 3.4 6.3 - - - +
333A GLY* 3.6 13.7 - - - -
334A LEU 5.6 1.0 - - - +
841B G 3.7 44.9 + - + +
842B G 2.7 36.2 + - - +
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 3.0 43.0 - - - +
246A GLU* 1.3 76.0 - - - +
248A THR* 1.3 71.7 + - - +
249A MET* 3.6 21.4 - - + +
262A ILE* 5.2 4.9 - - + -
265A ARG* 3.6 30.6 - - - +
266A LEU* 4.0 19.0 - - + +
331A LEU* 3.3 4.2 - - - -
332A VAL* 3.0 31.1 + - - +
841B G 3.4 10.3 - - - -
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Residues in contact with THR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 4.4 16.0 + - - +
38A ARG* 4.5 10.3 - - + +
247A ARG* 1.3 84.9 + - - +
249A MET* 1.3 71.9 + - - +
250A ALA 4.1 0.7 + - - -
291A LYS* 5.6 0.2 - - - +
330A ARG* 3.3 40.9 + - - +
331A LEU* 3.4 15.3 - - - +
840B A 3.7 17.2 + - - +
841B G 2.7 33.9 + - - -
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 5.2 1.6 - - - +
38A ARG* 2.7 32.6 + - - +
247A ARG* 3.6 31.4 - - + +
248A THR* 1.3 80.7 - - - +
250A ALA* 1.3 57.9 + - - +
251A GLU 3.2 15.3 - - - +
253A ILE* 4.0 15.7 - - + -
262A ILE* 3.6 37.2 - - + -
329A VAL 3.8 13.2 - - - +
330A ARG 2.9 32.6 + - - +
331A LEU* 4.0 7.2 - - - +
332A VAL* 4.5 3.6 - - + -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.5 26.3 - - - +
37A ARG* 4.5 18.8 - - + +
38A ARG* 3.3 24.1 + - - +
247A ARG* 6.1 0.2 - - - +
248A THR 4.1 0.4 + - - -
249A MET* 1.3 74.5 - - - +
251A GLU* 1.3 77.6 + - + +
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU 5.6 0.2 - - - +
38A ARG* 3.5 5.4 - - - +
249A MET* 3.4 19.7 - - - +
250A ALA* 1.3 96.9 - - + +
252A ASP* 1.3 70.6 + - - +
253A ILE* 3.6 4.9 + - - +
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 2.8 38.9 + - - +
251A GLU* 1.3 81.1 - - - +
253A ILE* 1.3 60.4 + - - +
254A HIS* 3.6 27.7 + - + -
293A ASP* 3.2 30.5 - - - +
328A GLY* 4.3 1.1 - - - -
329A VAL 3.2 19.5 - - - +
330A ARG* 3.5 10.4 + - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A MET* 4.0 21.3 - - + -
251A GLU 4.1 5.6 - - - +
252A ASP* 1.3 77.3 - - - +
254A HIS* 1.3 65.2 + - - +
255A HIS 4.8 0.2 - - - +
258A GLU* 3.3 26.2 - - + +
259A CYS* 3.7 34.8 - - + +
262A ILE* 4.0 18.2 - - + -
320A TRP* 3.9 18.5 - - + -
328A GLY* 3.5 2.1 - - - -
329A VAL* 2.8 45.9 + - + +
332A VAL* 4.3 7.6 - - + -
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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