Contacts of the strand formed by residues 202 - 209 (chain A) in PDB entry 2YD0
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 SER 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL 3.1 7.5 + - - -
62A HIS* 2.5 34.1 + - - +
63A TYR* 2.8 27.0 + - - +
201A ALA* 1.3 76.2 - - - +
203A PHE* 1.3 63.7 + - - +
238A VAL* 3.8 7.1 - - - +
239A THR* 3.5 22.7 - - - -
240A VAL 4.0 4.9 - - - -
241A LYS* 4.0 9.8 + - - +
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Residues in contact with PHE 203 (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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63A TYR* 3.3 50.3 - + + -
65A LEU* 3.9 10.3 - - + -
191A PHE* 4.2 10.5 - + - -
201A ALA* 3.4 24.5 - - + -
202A SER* 1.3 74.8 - - - +
204A SER* 1.3 61.7 + - - +
205A ILE* 4.0 13.1 + - + +
237A ASP 4.0 1.2 - - - +
238A VAL* 3.4 3.0 - - - -
239A THR* 2.8 54.3 + - + +
242A MET* 3.6 28.9 - - + -
243A SER 4.3 1.6 - - - -
244A THR* 3.9 16.4 - - + -
247A VAL* 3.8 25.6 - - + -
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Residues in contact with SER 204 (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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62A HIS* 3.4 20.5 + - - -
63A TYR 3.1 7.4 + - - -
64A ASP* 3.5 11.5 - - - -
65A LEU 2.9 24.8 + - - -
203A PHE* 1.3 70.5 - - - +
205A ILE* 1.3 61.4 + - - +
206A LYS* 3.6 17.4 + - - -
236A PHE 4.6 5.1 + - - -
238A VAL* 3.6 20.2 + - - +
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Residues in contact with ILE 205 (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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65A LEU* 3.6 23.6 - - + +
67A ILE* 5.5 1.3 - - + -
203A PHE* 4.0 20.8 + - + +
204A SER* 1.3 76.4 - - - +
206A LYS* 1.3 66.1 + - - +
207A ILE* 3.9 27.6 - - + -
217A SER* 3.6 26.9 - - - +
218A ASN* 4.0 8.3 - - + +
236A PHE* 2.9 43.5 + - + +
237A ASP 5.1 0.6 + - - -
239A THR* 4.9 4.7 - - + -
247A VAL* 3.9 23.8 - - + -
248A ALA 4.7 0.2 - - - +
249A PHE* 4.6 7.6 - - + -
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Residues in contact with LYS 206 (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 ASP* 3.2 40.6 + - - -
65A LEU 2.8 14.3 + - - +
66A LEU* 3.5 22.0 - - + -
67A ILE* 2.9 26.9 + - - +
204A SER* 3.6 22.6 + - - -
205A ILE* 1.3 75.7 - - - +
207A ILE* 1.3 66.1 + - - +
208A ARG 4.1 0.2 - - - -
233A GLU* 4.3 10.5 - - + +
234A ASP 3.2 8.7 - - - +
235A HIS* 3.6 40.4 + - + +
236A PHE 5.9 0.4 + - - -
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Residues in contact with ILE 207 (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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67A ILE* 3.3 23.6 - - + +
205A ILE* 3.9 15.3 - - + -
206A LYS* 1.3 80.4 - - - +
208A ARG* 1.3 68.5 + - - +
209A ARG* 4.1 2.8 + - + +
215A ALA* 3.7 28.3 - - + -
216A ILE 5.7 0.2 - - - +
217A SER* 5.4 0.2 - - - -
232A ILE 3.7 1.0 - - - +
233A GLU* 3.5 0.8 - - - -
234A ASP* 2.8 32.7 + - - +
236A PHE* 3.8 21.5 - - + -
249A PHE* 4.0 28.0 - - + -
251A ILE* 3.8 25.1 - - + -
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Residues in contact with ARG 208 (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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66A LEU* 4.0 28.9 - - + +
67A ILE 3.0 7.1 + - - -
68A HIS* 3.9 30.7 + - + +
69A ALA 3.8 21.0 + - - +
206A LYS 4.1 0.4 - - - -
207A ILE* 1.3 76.3 - - - +
209A ARG* 1.3 64.5 + - - +
227A VAL* 4.0 22.5 - - + +
231A LEU* 4.2 22.3 - - + +
232A ILE 3.2 6.7 - - - +
233A GLU* 2.6 43.6 + - + +
251A ILE* 4.8 1.6 - - - +
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Residues in contact with ARG 209 (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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69A ALA 5.1 0.7 - - - -
207A ILE* 4.4 12.6 - - + +
208A ARG* 1.3 77.8 - - - +
210A GLU* 1.3 73.9 + - - +
211A PRO* 3.9 13.7 + - - +
213A HIS* 3.1 36.4 + - + +
214A LEU* 4.5 2.0 - - - +
215A ALA 4.2 8.9 - - - +
221A LEU* 5.8 1.0 - - - +
224A SER* 3.9 6.3 + - - -
231A LEU* 3.3 13.5 - - - +
232A ILE* 2.9 55.8 + - - +
234A ASP* 2.8 42.6 + - - +
251A ILE* 4.6 16.6 - - + -
1B NAG 4.4 5.8 - - - -
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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