Contacts of the strand formed by residues 246 - 253 (chain A) in PDB entry 1YPN
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 ILE 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG* 3.0 24.9 - - - +
195A ALA* 4.7 3.6 - - - +
196A VAL 5.5 0.5 + - - -
234A MET* 3.9 12.3 - - + -
235A ASN* 3.6 29.8 - - - +
238A LEU* 3.6 27.6 - - + -
240A GLY* 4.3 8.7 - - - -
241A GLY 5.7 0.7 - - - +
244A VAL* 2.8 39.7 + - + +
245A PRO* 1.3 79.5 - - - +
247A GLY* 1.3 71.0 + - - +
248A SER* 5.6 0.2 - - - -
262A LEU* 3.4 4.5 - - - +
263A VAL* 4.0 13.2 - - + -
303A LEU* 4.3 13.9 - - + -
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Residues in contact with GLY 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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131A ARG* 3.9 8.5 - - - -
193A LEU* 3.7 19.1 - - - -
194A PRO 3.8 8.3 - - - -
246A ILE* 1.3 77.7 - - - +
248A SER* 1.3 64.3 + - - -
261A ALA* 3.2 5.4 - - - +
262A LEU* 2.9 37.2 + - - +
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Residues in contact with SER 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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193A LEU* 3.8 1.4 - - - +
194A PRO 3.1 15.6 + - - +
195A ALA 3.8 1.9 - - - +
196A VAL* 3.6 23.6 - - - +
231A GLU* 3.0 36.1 + - - -
234A MET* 4.0 12.7 - - - +
235A ASN* 3.4 21.3 - - - -
246A ILE* 4.7 0.2 - - - -
247A GLY* 1.3 75.1 - - - -
249A TYR* 1.3 61.4 + - - +
259A LEU* 4.2 3.3 - - - +
260A ARG 3.5 7.9 - - - -
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Residues in contact with TYR 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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101A ARG* 3.8 15.3 - - - -
104A PRO* 3.6 35.0 - - + +
189A PRO* 3.8 30.0 - - + +
193A LEU* 3.6 18.1 - - + +
194A PRO* 3.7 18.6 - - + -
227A ARG* 3.9 10.1 + - - -
231A GLU* 3.7 1.8 - - - -
248A SER* 1.3 76.0 + - - +
250A ALA* 1.3 71.4 + - - +
251A GLU* 2.5 46.2 + - + +
258A TRP 3.9 1.6 - - - +
259A LEU* 4.0 1.8 - - - -
260A ARG* 3.0 50.6 + - - +
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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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101A ARG* 3.9 0.5 + - - -
227A ARG* 3.1 46.1 + - - +
230A ALA* 4.6 0.7 - - + -
231A GLU* 2.8 24.8 + - + +
249A TYR* 1.3 76.1 - - - +
251A GLU* 1.3 65.3 + - - +
257A ILE* 4.0 17.3 - - + -
258A TRP 3.3 9.2 - - - +
259A LEU* 3.9 11.0 - - + -
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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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189A PRO* 5.3 2.4 - - - +
227A ARG* 3.6 13.6 + - - +
249A TYR* 2.5 46.5 + - + +
250A ALA* 1.3 72.7 - - - +
252A LEU* 1.3 60.6 + - - +
253A ILE* 3.5 26.8 + - + +
256A GLU 3.4 0.9 - - - +
257A ILE* 3.4 5.4 - - - +
258A TRP* 2.8 39.7 + - + +
260A ARG* 3.9 14.0 + - - +
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Residues in contact with LEU 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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223A GLU* 3.7 38.6 - - + +
226A LEU* 4.3 10.8 - - + -
227A ARG* 3.7 23.3 - - + +
251A GLU* 1.3 70.9 - - - +
253A ILE* 1.3 66.3 + - - +
254A ASP 3.7 3.2 + - - -
255A GLY* 4.2 11.6 + - - +
256A GLU 3.5 24.0 - - - +
257A ILE* 3.5 23.3 - - + -
280A PRO* 4.5 11.0 - - + -
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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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251A GLU* 3.8 28.0 - - + +
252A LEU* 1.3 76.1 - - - +
254A ASP* 1.3 83.8 + - - +
255A GLY 3.4 0.7 - - - -
256A GLU* 2.8 29.3 + - - +
258A TRP* 4.0 31.0 - - + -
277A ARG* 4.0 21.5 + - - +
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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