Contacts of the strand formed by residues 248 - 255 (chain A) in PDB entry 4Y2P
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A THR* 3.5 2.2 - - - -
244A VAL* 2.8 40.6 + - + +
245A LYS* 2.8 42.1 + - + +
246A PRO 3.4 0.4 + - - -
247A ARG* 1.3 81.9 - - + +
249A ARG* 1.3 61.9 + - - +
250A LEU* 4.3 8.3 - - + -
294A LYS* 4.1 21.3 - - + -
300A SER* 3.6 6.7 - - - -
302A PRO* 4.6 5.8 - - + -
307A GLU* 3.9 20.9 - - - +
316A GLU* 3.9 17.5 - - - +
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Residues in contact with ARG 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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241A TYR* 3.7 42.5 - - + +
242A VAL 3.2 15.9 - - - +
243A THR* 3.8 17.9 + - + +
247A ARG 4.1 0.6 - - - -
248A VAL* 1.3 75.4 - - - +
250A LEU* 1.3 71.1 + - - +
298A GLU* 4.2 13.1 + - - +
299A SER* 3.4 2.8 - - - -
300A SER* 2.8 40.4 + - - +
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Residues in contact with LEU 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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240A GLY 3.8 0.2 - - - +
241A TYR* 3.3 3.8 - - - -
242A VAL* 2.7 35.4 + - - +
244A VAL* 4.1 27.4 - - + -
248A VAL* 4.3 13.0 - - + -
249A ARG* 1.3 82.0 - - - +
251A HIS* 1.3 60.3 + - - +
252A PHE* 4.2 3.5 + - - -
291A MET* 4.0 17.5 - - + -
292A ASP 4.5 2.0 - - - +
293A MET* 5.4 0.4 - - - -
294A LYS* 4.2 23.6 - - + +
299A SER* 3.5 14.1 - - - +
316A GLU* 4.4 9.2 - - + +
317A MET* 3.9 28.0 - - - -
320A PHE* 4.2 12.1 - - + -
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Residues in contact with HIS 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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239A HIS* 2.7 32.1 + + - -
240A GLY 3.2 14.1 - - - -
241A TYR* 3.5 26.2 - + + -
249A ARG 4.1 0.2 + - - -
250A LEU* 1.3 76.3 - - - +
252A PHE* 1.4 79.7 + - - +
253A VAL* 4.3 3.8 - - + -
271A TRP* 3.7 21.1 - + - -
291A MET* 3.8 3.5 - - - +
292A ASP* 2.6 54.7 + - - +
298A GLU* 3.5 41.6 + - + +
299A SER* 2.9 7.9 + - - +
453A GLN* 5.7 0.2 - - - -
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Residues in contact with PHE 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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239A HIS* 3.6 3.5 - - - -
240A GLY* 2.8 65.4 + - - +
241A TYR 3.8 2.7 - - - -
242A VAL* 4.0 7.9 - - + -
250A LEU 4.3 1.6 - - - -
251A HIS* 1.4 82.8 - - - +
253A VAL* 1.3 73.2 + - - +
254A GLU* 3.8 24.0 - - + -
289A LEU* 3.4 28.0 - - + -
290A ALA 3.2 17.0 - - - +
291A MET* 3.9 15.3 - - - -
292A ASP 4.4 0.2 - - - +
320A PHE* 3.6 28.5 - + - -
324A LEU* 4.1 21.1 - - + -
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Residues in contact with VAL 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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237A MET* 3.7 41.3 - - + -
238A SER 3.3 2.9 - - - +
239A HIS* 3.6 35.0 - - + +
251A HIS* 4.2 1.5 - - + +
252A PHE* 1.3 74.7 - - - +
254A GLU* 1.3 62.6 + - - +
271A TRP* 3.8 37.2 - - + +
278A ILE* 4.3 11.4 - - + +
288A VAL* 3.5 1.4 - - - +
289A LEU* 3.4 3.5 - - - -
290A ALA* 2.8 34.4 + - + +
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Residues in contact with GLU 254 (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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237A MET* 5.0 0.9 - - - +
238A SER* 3.1 41.0 + - - +
240A GLY* 5.8 1.1 - - - +
252A PHE* 3.8 24.1 - - + -
253A VAL* 1.3 78.6 - - - +
255A LEU* 1.3 68.3 + - - +
256A GLY 5.4 1.3 - - - +
287A ARG* 2.8 48.1 + - + -
288A VAL 3.2 10.3 - - - +
289A LEU* 3.7 7.4 - - + +
324A LEU* 5.1 1.1 - - - +
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Residues in contact with LEU 255 (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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145A MET* 6.6 0.2 - - + -
237A MET* 4.3 17.0 - - + -
254A GLU* 1.3 78.9 - - - +
256A GLY* 1.3 66.6 + - - +
278A ILE* 3.7 27.8 - - + +
279A PRO* 3.6 35.0 - - + -
282A ALA* 3.6 11.4 - - + +
288A VAL* 2.7 36.6 + - - +
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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