Contacts of the strand formed by residues 272 - 278 (chain A) in PDB entry 1PNG
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 THR 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ASN* 4.7 12.9 + - - +
173A ILE 3.1 12.1 - - - -
174A GLN* 4.0 27.1 - - + +
217A ASN* 4.6 1.7 + - - +
271A SER* 1.3 80.1 - - - +
273A PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 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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172A ASN* 3.3 6.8 - - - +
173A ILE* 2.7 76.3 + - + -
175A LEU* 3.8 28.0 - - + -
184A LEU* 5.8 1.1 - - + -
216A ILE* 3.9 26.0 - - + -
217A ASN* 3.3 26.9 - - - +
264A LEU* 3.9 26.0 - - + -
268A LEU* 4.0 24.0 - - + -
271A SER* 4.3 7.0 - - - +
272A THR* 1.3 75.6 - - - +
274A SER* 1.3 72.8 + - - +
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Residues in contact with SER 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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170A LYS* 4.7 19.0 + - - -
171A LYS 3.4 7.2 - - - -
172A ASN* 3.6 13.0 + - - -
215A ALA 3.5 0.4 - - - +
216A ILE* 3.3 7.6 - - - -
217A ASN* 2.9 50.0 + - - -
218A ASN* 3.8 10.5 + - - -
273A PHE* 1.3 80.2 - - - +
275A TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 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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148A VAL* 3.6 28.9 - - + -
149A ILE* 3.7 11.1 - - + +
169A LEU 3.8 15.0 - - - -
170A LYS* 3.2 6.8 - - - +
171A LYS* 2.8 37.6 + - + +
173A ILE* 3.9 24.2 - - + -
184A LEU* 3.9 20.4 - - + -
214A ILE* 3.8 25.3 - - + +
215A ALA 3.5 3.8 - - - -
216A ILE* 4.6 5.8 - - + -
273A PHE* 4.0 0.4 + - + -
274A SER* 1.3 75.6 - - - +
276A GLU* 1.3 62.1 + - - +
277A TYR* 3.6 30.7 - + + -
297A SER* 2.9 35.1 + - - -
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Residues in contact with GLU 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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169A LEU* 3.3 11.9 - - + +
170A LYS* 3.5 36.8 + - + +
214A ILE* 3.2 6.1 - - - -
215A ALA* 2.9 41.1 + - + +
218A ASN* 4.8 4.9 + - - -
275A TYR* 1.3 81.6 - - - +
277A TYR* 1.3 67.6 + - - +
278A LYS* 3.6 31.9 + - + +
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Residues in contact with TYR 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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149A ILE* 4.4 3.8 - - + -
169A LEU* 3.0 41.3 + - + +
186A THR* 4.2 3.4 - - + -
188A ILE* 3.7 12.5 - - + +
212A HIS* 3.4 34.0 - + + +
213A THR 3.7 1.8 - - - -
214A ILE* 3.6 20.9 - - + -
224A HIS* 3.0 37.2 + + - +
275A TYR* 3.6 26.1 - - + +
276A GLU* 1.3 76.6 - - - +
278A LYS* 1.3 61.8 + - - +
279A PHE* 3.6 31.9 + + - -
295A ILE* 3.8 24.7 - - + -
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Residues in contact with LYS 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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212A HIS* 3.5 4.0 - - - +
213A THR* 2.7 51.0 + - + +
215A ALA* 3.7 25.0 - - + +
218A ASN 5.3 4.0 + - - -
220A ASN* 2.7 30.9 + - - +
276A GLU* 3.9 30.3 - - + +
277A TYR* 1.3 76.1 - - - +
279A PHE* 1.3 65.0 + - - +
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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