Contacts of the strand formed by residues 153 - 166 (chain B) in PDB entry 1YTB
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 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ASP* 3.7 18.2 - - - +
74B VAL* 3.3 6.8 - - - +
75B THR* 2.8 46.2 + - - +
76B LEU 5.1 0.2 - - - -
77B GLY* 5.1 1.9 + - - -
151B LYS* 3.1 38.9 + - + +
152B PHE* 1.3 80.9 - - - +
154B ASP* 1.3 72.2 + - - +
155B PHE* 3.2 5.3 + - - -
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 2.9 39.7 + - - +
156A LYS* 4.8 20.0 + - - +
73B THR* 3.3 9.9 + - - +
74B VAL* 4.2 0.2 - - - -
75B THR* 3.3 30.8 + - - +
153B THR* 1.3 81.3 + - - +
155B PHE* 1.3 66.0 + - - +
156B LYS* 3.2 9.2 + - - +
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASP* 4.8 3.2 + - - +
72B ALA* 3.5 15.7 - - + -
73B THR 3.3 7.2 - - - -
74B VAL* 3.9 17.9 - - + -
129B GLU* 3.8 17.5 - - + -
132B SER* 3.3 29.4 - - - -
133B LYS* 3.8 31.2 - - + -
136B SER* 3.7 11.4 - - - -
152B PHE* 3.6 29.8 - + + -
153B THR 3.2 4.1 + - - -
154B ASP* 1.3 76.7 - - - +
156B LYS* 1.3 61.7 + - - +
157B ILE* 3.8 23.1 - - + -
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.2 3.3 - - - -
73B THR* 2.9 39.6 + - - +
154B ASP 3.9 7.2 - - - +
155B PHE* 1.3 80.1 - - - +
157B ILE* 1.3 73.3 + - - +
158B GLN* 3.5 28.5 + - - +
218B LYS* 5.5 6.3 - - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ILE* 4.0 18.6 - - + -
71B VAL 3.6 9.4 - - - +
72B ALA* 4.2 1.6 - - + -
129B GLU* 3.4 47.1 - - + +
155B PHE* 3.8 21.0 - - + -
156B LYS* 1.3 82.3 - - - +
158B GLN* 1.3 61.5 + - - +
159B ASN 3.8 6.5 - - - +
160B ILE* 3.7 33.9 - - + -
218B LYS* 3.5 34.0 - - - +
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 2.8 15.9 + - + +
72B ALA* 4.7 0.4 - - - -
73B THR* 2.9 33.4 + - + +
156B LYS* 3.5 34.7 + - - +
157B ILE* 1.3 74.7 - - - +
159B ASN* 1.3 64.3 + - + +
216B GLY 5.2 0.7 - - - +
217B ALA 3.9 1.5 - - - +
218B LYS* 2.9 46.9 + - - +
6D T 3.4 18.3 - - + +
7D A 3.5 43.4 + - - +
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Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN 4.7 0.4 - - - -
70B ILE* 3.5 2.4 - - - -
71B VAL* 2.8 37.1 + - + +
157B ILE* 3.7 2.1 - - - +
158B GLN* 1.3 81.5 - - - +
160B ILE* 1.3 66.3 + - - +
161B VAL* 3.8 10.1 - - - +
215B THR* 3.5 3.2 + - - -
216B GLY* 2.9 36.0 + - - -
217B ALA 3.1 7.6 + - - -
5D A 3.3 31.4 + - - -
6D T 3.4 36.0 + - - +
24D A 5.5 0.2 - - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.1 21.1 - - + -
69B ASN 3.5 8.1 - - - +
70B ILE* 4.1 18.2 - - + -
129B GLU* 6.5 0.4 - - + -
157B ILE* 3.7 24.5 - - + -
159B ASN* 1.3 80.0 + - - +
161B VAL* 1.3 65.9 + - - +
216B GLY 3.6 16.3 + - - -
217B ALA* 2.9 17.5 + - + +
218B LYS 4.2 0.4 - - - +
219B GLN* 3.7 13.0 - - - +
220B ARG* 3.6 30.5 - - + +
223B ILE* 3.6 29.2 - - + +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.6 4.3 - - - -
68B GLN* 2.8 31.3 + - + -
69B ASN* 2.9 28.5 + - + +
71B VAL* 6.0 0.2 - - + -
159B ASN* 3.8 13.7 - - - +
160B ILE* 1.3 79.9 - - - +
162B GLY* 1.3 67.7 + - - +
213B VAL* 4.4 1.6 - - + -
214B LEU 3.5 9.2 - - - +
215B THR* 3.4 21.5 - - - +
5D A 3.8 3.8 - - + -
25D T 3.4 22.0 - - - +
26D A 3.8 29.4 - - + +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR 3.2 12.1 - - - -
67B LEU* 4.2 2.9 - - - -
68B GLN* 4.2 2.9 - - - -
161B VAL* 1.3 75.2 - - - +
163B SER* 1.3 64.2 + - - -
213B VAL* 3.6 6.6 - - - +
214B LEU* 2.8 37.0 + - - +
223B ILE* 3.9 17.4 - - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO* 4.5 1.0 - - - +
66B THR* 2.9 36.9 + - - +
68B GLN* 3.0 31.5 + - - +
162B GLY* 1.3 76.1 - - - -
164B CYS* 1.3 65.1 + - - +
212B ILE 3.2 13.2 - - - -
213B VAL* 4.5 3.4 - - - -
214B LEU* 4.3 2.8 - - - +
26D A 4.0 24.9 + - - -
27D T 5.5 2.5 - - - -
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Residues in contact with CYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.0 16.8 - - + -
64B VAL 4.6 1.1 - - - +
65B PRO* 4.1 15.5 - - + -
66B THR* 5.8 0.2 - - - -
163B SER* 1.3 78.1 - - - +
165B ASP* 1.3 60.5 + - - +
166B VAL* 5.4 0.2 - - - -
210B GLY 3.9 0.5 - - - +
211B LYS* 3.5 6.4 - - - +
212B ILE* 2.9 41.5 + - - +
214B LEU* 4.3 4.0 - - - -
227B PHE* 3.3 46.0 - - - -
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.2 14.6 - - - +
164B CYS* 1.3 77.4 - - - +
166B VAL* 1.3 62.5 + - - +
167B LYS* 3.0 48.5 + - - +
209B SER 4.3 3.8 - - - +
210B GLY 3.2 15.9 - - - +
211B LYS* 3.8 28.8 - - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 4.1 10.0 - - + +
165B ASP* 1.3 70.8 - - - +
167B LYS* 1.3 65.9 + - - +
168B PHE* 3.1 58.1 + - + +
170B ILE* 4.2 6.1 - - + -
210B GLY* 3.0 23.7 + - - +
212B ILE* 4.6 3.6 - - + -
227B PHE* 3.7 23.6 - - + -
231B TYR* 3.6 27.2 + - + -
234B LEU* 4.0 13.2 - - + -
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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