Contacts of the strand formed by residues 238 - 247 (chain A) in PDB entry 1YB2
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 HIS 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LEU 3.8 0.9 - - - +
218A MSE 3.3 3.1 - - - -
219A LYS* 2.8 67.2 + - + +
220A ARG* 5.8 0.2 - - - -
221A ARG 6.0 0.4 - - - -
233A SER* 3.1 38.4 + - - -
234A ASP* 5.3 1.1 - - - -
236A LEU* 3.2 29.8 + - + +
237A THR* 1.3 77.0 - - - +
239A THR* 1.3 59.5 + - - +
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Residues in contact with THR 239 (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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192A PRO* 4.2 15.0 - - - +
216A GLU* 3.9 19.7 + - + +
217A LEU 3.3 8.5 - - - +
218A MSE 3.3 16.7 - - + +
237A THR* 4.2 7.9 + - - -
238A HIS* 1.3 74.0 - - - +
240A ALA* 1.3 61.8 + - - +
241A PHE* 3.4 31.0 - - + -
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Residues in contact with ALA 240 (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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190A TYR* 4.5 12.3 - - + -
191A LEU 4.1 4.7 - - - +
192A PRO* 5.5 0.2 - - - -
215A VAL 3.7 0.9 - - - +
216A GLU* 3.5 3.3 - - - -
217A LEU* 2.9 38.0 + - + +
238A HIS 4.4 0.4 - - - -
239A THR* 1.3 75.2 - - - +
241A PHE* 1.3 65.7 + - - +
242A ILE* 4.0 21.3 - - + -
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Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE 3.5 2.9 - - - +
190A TYR* 3.6 1.7 - - - -
191A LEU* 2.9 42.3 + - - +
192A PRO 3.6 9.0 - - - -
193A ASN* 3.5 29.4 - - + +
194A PHE* 3.6 40.8 - + + -
197A SER* 3.8 26.5 - - - +
214A THR* 5.4 1.8 - - + -
215A VAL 3.4 6.7 - - - +
216A GLU* 3.6 42.2 - - + -
239A THR* 3.4 18.8 - - + -
240A ALA* 1.3 74.1 - - - +
242A ILE* 1.3 60.8 + - - +
243A THR* 4.1 0.6 + - - -
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Residues in contact with ILE 242 (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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188A THR* 3.6 29.4 - - + -
189A PHE 3.4 4.0 - - - +
190A TYR* 3.6 34.5 - - + +
213A GLU 3.9 1.0 - - - +
214A THR* 3.2 3.5 - - - +
215A VAL* 2.9 45.7 + - + +
217A LEU* 3.9 32.1 - - + -
240A ALA* 4.2 11.7 - - + -
241A PHE* 1.3 76.1 - - - +
243A THR* 1.3 63.6 + - - +
244A PHE* 3.7 22.7 + - + -
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Residues in contact with THR 243 (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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187A ALA 3.6 1.2 - - - +
188A THR* 3.4 5.2 - - - +
189A PHE* 2.8 55.9 + - + -
191A LEU* 5.0 2.5 - - - +
197A SER* 3.9 9.0 + - - -
200A THR* 4.7 6.9 - - + +
201A VAL* 3.8 10.6 - - + +
204A LEU* 4.0 18.2 - - + -
211A HIS* 3.8 16.4 - - + +
213A GLU 3.6 3.6 - - - -
214A THR* 2.8 28.1 + - - +
241A PHE 4.1 0.7 + - - -
242A ILE* 1.3 71.2 - - - +
244A PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 244 (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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61A MSE 3.6 30.7 - - + -
86A CYS* 4.4 13.0 - - + -
186A VAL* 4.3 7.0 - - + -
187A ALA 3.4 2.2 - - - +
188A THR* 3.3 34.8 - - + -
211A HIS* 3.6 4.7 + - - -
212A LEU* 2.9 40.6 + - + -
213A GLU* 2.8 42.7 + - + +
215A VAL* 4.8 9.4 - - + -
242A ILE* 3.7 26.7 - - + -
243A THR* 1.3 74.6 - - - +
245A ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 245 (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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181A MSE 4.3 0.2 - - - +
186A VAL* 3.2 4.5 - - - +
187A ALA* 2.8 35.4 + - - +
189A PHE* 4.5 3.6 - - + -
204A LEU* 3.9 33.7 - - + -
209A MSE 4.1 17.0 - - + -
210A HIS 3.3 14.1 - - - +
212A LEU* 4.3 4.7 - - - +
244A PHE* 1.3 75.9 - - - +
246A ILE* 1.3 60.4 + - - +
247A LYS 4.2 0.2 + - - -
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Residues in contact with ILE 246 (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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10A VAL* 4.0 4.7 - - + -
54A ILE* 3.9 27.8 - - + -
56A SER* 3.9 24.7 - - - -
62A TYR* 4.0 11.2 - - - +
184A GLY* 3.5 28.7 - - - +
185A SER 3.4 10.8 - - - +
186A VAL* 4.5 0.9 - - + +
209A MSE 3.3 2.8 - - - -
210A HIS* 2.7 59.5 + - + +
212A LEU* 3.8 23.7 - - + +
245A ALA* 1.3 74.1 - - - +
247A LYS* 1.3 67.8 + - - +
248A LYS 3.5 0.9 + - - -
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Residues in contact with LYS 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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43A GLY* 3.6 3.6 - - - -
159A MSE 4.6 6.1 - - - +
178A ALA* 2.9 43.9 + - + +
179A SER* 4.5 4.0 - - - +
181A MSE 3.3 42.3 + - + +
182A LYS 3.6 16.4 - - - +
183A PRO* 3.9 7.4 - - + +
184A GLY* 2.8 29.3 + - - -
185A SER 2.9 9.6 + - - +
207A SER 5.1 1.3 - - - -
208A GLY* 3.7 16.2 - - - +
209A MSE 4.3 4.9 - - + -
246A ILE* 1.3 71.0 - - - +
248A LYS* 1.3 76.3 + - - +
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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