Contacts of the strand formed by residues 271 - 278 (chain A) in PDB entry 1YZ3
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 GLY 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU* 2.9 31.8 + - - +
256A TYR 3.0 14.1 - - - -
258A MET* 3.9 6.5 - - - -
269A VAL* 3.0 15.2 - - - +
270A LYS* 1.3 80.8 - - - +
272A VAL* 1.3 66.9 + - - +
257B ILE* 4.2 5.6 - - - -
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Residues in contact with VAL 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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53A VAL* 4.1 8.7 - - + -
56A TRP* 3.6 16.7 - - + -
57A LYS* 4.7 3.4 - - + -
182A PHE* 3.8 20.9 - - + -
214A ILE* 4.1 5.2 - - + -
215A GLY 3.3 13.7 - - - +
217A LEU* 3.8 5.4 - - - +
255A THR* 3.4 2.3 - - - -
256A TYR* 2.7 48.7 + - + -
258A MET* 3.6 26.9 - - + -
271A GLY* 1.3 80.0 - - - +
273A PHE* 1.3 70.3 + - - +
3001A SKA 3.9 13.2 - - + -
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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
----------------------------------------------------------
56A TRP* 3.9 3.1 - - - -
185A GLU* 4.0 8.5 - - - -
194A PHE* 5.3 4.3 - + - -
213A LEU* 3.8 31.2 - - + -
214A ILE* 3.4 10.3 - - - +
215A GLY* 2.9 74.7 + - - +
216A ALA 3.8 8.5 - - - -
217A LEU* 3.5 31.6 - - + -
234A VAL* 4.4 2.2 - - + -
236A GLU* 5.5 1.1 - - + -
239A VAL* 3.7 40.8 - - + -
253A LEU* 4.6 9.2 - - + -
254A ARG 3.2 8.7 - - - +
255A THR* 4.5 2.5 - - - +
272A VAL* 1.3 76.1 - - - +
274A PHE* 1.3 67.8 + - - +
275A ALA* 4.3 3.6 - - + -
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Residues in contact with PHE 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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56A TRP* 3.6 19.9 - - + -
60A CYS* 3.5 37.5 - - + -
61A LEU* 3.9 22.2 - - + -
64A THR* 3.1 30.5 - - - -
212A LEU* 4.2 17.3 - - + -
213A LEU 3.4 2.5 - - - -
214A ILE* 3.7 18.8 - - + -
252A ASP* 3.8 22.0 - - - -
253A LEU* 3.1 8.8 - - - +
254A ARG* 2.8 41.1 + - + +
273A PHE* 1.3 75.3 - - - +
275A ALA* 1.3 65.3 + - - +
276A TRP* 4.0 13.2 - - + -
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Residues in contact with ALA 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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211A LEU 3.5 1.2 - - - +
212A LEU* 3.4 4.5 - - - -
213A LEU* 2.6 53.3 + - + +
239A VAL* 4.9 0.9 - - + -
243A LEU* 3.8 22.0 - - + -
252A ASP 3.4 4.0 - - - +
253A LEU* 3.2 21.8 - - + -
273A PHE* 4.4 6.5 - - + -
274A PHE* 1.3 79.5 - - - +
276A TRP* 1.3 61.6 + - - +
277A ALA* 3.9 0.7 - - + +
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Residues in contact with TRP 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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64A THR* 3.8 20.9 - - + -
67A THR* 3.9 24.7 - - + -
69A GLU* 3.8 15.7 - - + -
70A VAL* 3.8 18.1 - - + +
210A HIS* 3.1 29.3 + + - -
211A LEU 3.6 3.4 - - - -
212A LEU* 3.7 18.4 - - + -
250A VAL* 3.7 0.9 - - - -
251A ARG* 2.7 86.3 + - + +
252A ASP* 2.7 34.5 + - + +
274A PHE* 4.0 13.6 - - + -
275A ALA* 1.3 71.9 - - - +
277A ALA* 1.3 58.0 + - - +
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Residues in contact with ALA 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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210A HIS* 3.4 4.0 + - - -
211A LEU* 2.6 48.1 + - + +
243A LEU* 4.1 24.5 - - + -
248A TYR* 3.8 28.9 - - + -
250A VAL* 4.3 7.2 - - - +
251A ARG* 4.2 3.8 - - - +
275A ALA* 3.9 1.1 - - + -
276A TRP* 1.3 80.0 - - - +
278A GLN* 1.3 58.2 + - - +
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Residues in contact with GLN 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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208A GLY* 2.9 27.9 + - - +
209A GLY 3.2 13.0 - - - +
210A HIS* 2.9 31.0 + - + +
248A TYR* 3.5 4.0 - - - -
249A LYS* 2.9 40.2 + - + +
251A ARG* 3.1 28.9 + - + -
277A ALA* 1.3 76.4 - - - +
279A LYS* 1.3 65.3 + - - +
280A VAL* 3.2 3.9 + - + -
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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