Contacts of the strand formed by residues 271 - 279 (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 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A CYS* 3.7 31.9 - - - +
135A GLN* 4.3 5.2 - - + -
138A GLU* 3.5 32.8 - - + +
262A LEU* 4.0 26.9 - - + -
263A VAL 3.6 3.4 - - - +
264A GLY* 4.1 7.0 - - - -
265A ALA 4.8 0.2 - - - +
268A GLY* 4.4 11.0 - - - +
269A SER 4.0 1.6 + - - -
270A GLN* 1.3 80.7 - - - +
272A ILE* 1.3 67.1 + - - +
273A ARG* 3.6 35.5 + - + +
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Residues in contact with ILE 272 (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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262A LEU* 3.0 25.5 - - - -
263A VAL* 2.8 24.4 + - + +
270A GLN* 3.7 26.2 - - + +
271A ILE* 1.3 77.1 - - - +
273A ARG* 1.3 65.1 + - - +
294A LEU* 3.5 31.5 - - + +
297A ASN* 3.6 38.1 - - + +
298A GLY* 4.9 0.2 - - - -
299A ALA* 4.3 11.0 - - + +
302A ILE* 4.1 14.4 - - + -
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Residues in contact with ARG 273 (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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135A GLN* 5.0 4.8 - - - +
138A GLU* 2.9 42.4 + - - -
190A GLU 5.3 8.5 + - - -
261A ALA 3.5 6.1 - - - +
262A LEU* 4.2 20.2 - - + +
271A ILE* 3.6 28.6 + - + +
272A ILE* 1.3 81.1 - - - +
274A GLY* 1.3 58.7 + - - +
293A GLU* 4.7 2.9 - - - +
294A LEU* 3.8 10.0 - - - +
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Residues in contact with GLY 274 (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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260A ARG* 3.6 2.4 - - - +
261A ALA 3.1 30.7 + - - +
273A ARG* 1.3 76.7 - - - +
275A GLU* 1.3 62.6 + - - +
290A LEU* 3.6 19.5 - - - -
293A GLU* 4.1 8.1 - - - -
294A LEU* 4.0 5.7 - - - +
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Residues in contact with GLU 275 (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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258A TRP* 2.9 36.3 + - - +
259A LEU 3.1 12.3 - - - +
260A ARG* 4.1 7.9 - - + -
274A GLY* 1.3 75.5 - - - +
276A ARG* 1.3 84.9 + - - +
277A ARG* 4.4 5.5 + - - -
290A LEU* 3.5 5.6 - - - +
293A GLU* 4.8 1.7 + - - +
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Residues in contact with ARG 276 (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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258A TRP* 3.4 6.2 - - - -
259A LEU* 2.8 38.7 + - + +
275A GLU* 1.3 102.5 + - - +
277A ARG* 1.3 65.2 + - - +
286A MET* 3.7 39.9 - - + +
289A SER* 3.5 40.0 + - - -
290A LEU* 3.7 14.5 - - + +
293A GLU* 3.0 32.1 + - - +
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Residues in contact with ARG 277 (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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253A ILE* 4.0 28.8 + - - +
256A GLU* 3.9 33.5 - - + +
257A ILE 3.2 12.3 - - - +
258A TRP* 3.6 44.0 - - + +
275A GLU* 4.4 4.9 + - - -
276A ARG* 1.3 82.9 - - - +
278A GLY* 1.3 61.7 + - - +
286A MET* 4.4 2.7 - - - -
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Residues in contact with GLY 278 (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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256A GLU* 3.4 16.5 - - - -
257A ILE 2.9 32.3 + - - +
277A ARG* 1.3 77.2 - - - +
279A ALA* 1.3 64.8 + - - -
282A ASP* 5.9 1.1 - - - -
286A MET* 3.7 12.5 - - - +
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Residues in contact with ALA 279 (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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255A GLY 4.7 2.0 - - - -
256A GLU* 4.7 3.0 + - - +
278A GLY* 1.3 73.6 - - - -
280A PRO* 1.3 74.6 - - + +
281A GLN* 3.2 26.9 - - - +
282A ASP* 2.9 29.7 + - - +
286A MET* 3.7 5.6 - - - +
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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