Contacts of the strand formed by residues 153 - 166 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.4 5.8 - - - +
75A THR* 2.8 48.4 + - - +
76A LEU 4.9 1.4 - - - -
77A GLY* 5.0 1.4 + - - -
151A LYS* 3.2 42.4 + - + +
152A PHE* 1.3 82.0 - - - +
154A ASP* 1.3 78.3 + - - +
155A PHE* 3.1 4.9 + - - -
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Residues in contact with ASP 154 (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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73A THR* 3.3 10.5 + - - +
75A THR* 3.6 27.3 + - - +
153A THR* 1.3 81.6 - - - +
155A PHE* 1.3 65.7 + - - +
156A LYS* 3.1 10.2 + - - +
153B THR* 3.7 16.8 - - - +
154B ASP* 2.9 48.8 + - - +
155B PHE 4.8 2.3 + - - +
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Residues in contact with PHE 155 (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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72A ALA* 3.5 21.1 - - + -
73A THR 3.4 4.9 - - - -
74A VAL* 3.9 10.8 - - + -
129A GLU 4.5 2.2 - - - -
132A SER* 3.6 13.5 - - - -
133A LYS* 3.5 42.2 - - + -
136A SER* 3.4 29.8 - - - -
152A PHE* 3.7 25.6 - + + -
153A THR 3.1 5.3 + - - -
154A ASP* 1.3 75.6 - - - +
156A LYS* 1.3 59.4 - - - +
157A ILE* 4.0 21.1 - - + -
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Residues in contact with LYS 156 (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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72A ALA* 3.3 3.8 - - - -
73A THR* 2.9 36.3 + - - +
154A ASP 3.1 9.4 + - - +
155A PHE* 1.3 79.8 - - - +
157A ILE* 1.3 69.1 + - - +
158A GLN* 3.6 31.8 + - - +
218A LYS* 4.4 13.3 - - - +
75B THR* 6.3 0.8 - - - +
154B ASP* 4.8 18.5 + - - +
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Residues in contact with ILE 157 (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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70A ILE* 3.9 16.2 - - + -
71A VAL 3.7 4.5 - - - +
72A ALA* 4.1 2.2 - - + -
129A GLU* 3.6 42.6 - - + -
155A PHE* 4.0 26.2 - - + -
156A LYS* 1.3 78.2 - - - +
158A GLN* 1.3 60.9 + - - +
159A ASN 4.0 9.9 - - - +
160A ILE* 3.7 28.9 - - + -
218A LYS* 3.5 32.0 - - - +
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Residues in contact with GLN 158 (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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71A VAL* 2.9 16.3 + - + +
72A ALA* 4.7 0.4 - - - -
73A THR* 2.9 31.5 + - + +
156A LYS* 3.6 30.7 + - - +
157A ILE* 1.3 75.4 - - - +
159A ASN* 1.3 63.7 + - + +
216A GLY 5.3 1.4 - - - +
217A ALA 4.1 2.6 - - - +
218A LYS* 2.7 49.4 + - - +
6C T 3.6 15.2 - - - +
7C A 3.7 41.2 + - - +
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Residues in contact with ASN 159 (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 ASN* 4.6 0.6 - - - +
70A ILE* 3.5 3.5 - - - -
71A VAL* 2.9 38.3 + - + +
157A ILE* 3.7 2.2 - - - +
158A GLN* 1.3 82.2 - - - +
160A ILE* 1.3 67.6 + - - +
161A VAL* 3.9 9.1 - - - +
215A THR* 3.4 3.1 + - - -
216A GLY* 3.1 32.9 + - - -
217A ALA 3.4 6.2 + - - -
5C A 3.4 28.1 + - - -
6C T 3.3 39.9 + - - +
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Residues in contact with ILE 160 (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 LEU* 3.8 34.1 - - + -
69A ASN 3.6 3.6 - - - +
70A ILE* 3.9 19.5 - - + -
129A GLU* 4.6 10.5 - - + +
157A ILE* 3.7 16.8 - - + -
159A ASN* 1.3 81.5 + - - +
161A VAL* 1.3 65.5 + - - +
215A THR* 3.6 18.0 - - - -
217A ALA* 2.9 20.4 + - + +
218A LYS 4.0 11.7 - - - +
219A GLN* 3.9 6.7 - - - -
220A ARG* 3.7 26.5 - - - +
223A ILE* 3.6 17.4 - - + +
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Residues in contact with VAL 161 (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 LEU* 3.5 6.6 - - - +
68A GLN* 2.8 32.4 + - + -
69A ASN* 3.0 24.8 + - + +
159A ASN* 3.9 8.5 - - - +
160A ILE* 1.3 80.5 - - - +
162A GLY* 1.3 66.1 + - - +
213A VAL* 4.3 2.9 - - + -
214A LEU 3.4 9.2 - - - +
215A THR* 3.7 17.0 - - - +
5C A 3.9 8.3 - - + -
25C T 3.4 22.4 - - - +
26C A 3.8 29.2 - - + +
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Residues in contact with GLY 162 (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 THR 3.2 14.1 - - - -
67A LEU* 4.2 7.4 - - - -
68A GLN* 4.3 2.7 - - - -
161A VAL* 1.3 76.8 - - - +
163A SER* 1.3 63.3 + - - -
213A VAL* 3.5 5.4 - - - +
214A LEU* 2.8 37.9 + - - +
223A ILE* 4.1 11.9 - - - +
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Residues in contact with SER 163 (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 PRO* 4.4 1.1 - - - +
66A THR* 2.8 37.9 + - - +
68A GLN* 3.1 27.3 + - - +
162A GLY* 1.3 75.6 - - - -
164A CYS* 1.3 64.1 + - - +
212A ILE 3.1 13.9 - - - -
213A VAL* 4.5 1.1 - - - -
214A LEU* 4.3 2.6 - - - +
26C A 3.8 30.5 + - - -
27C T 5.5 2.2 - - - -
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Residues in contact with CYS 164 (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 ILE* 3.8 15.3 - - + -
64A VAL 4.4 1.6 - - - +
65A PRO* 3.9 20.0 - - + -
66A THR* 5.5 0.9 - - - +
163A SER* 1.3 78.7 - - - +
165A ASP* 1.3 59.6 + - - +
211A LYS* 3.5 7.3 - - - +
212A ILE* 2.8 42.2 + - - +
214A LEU* 4.5 2.5 - - - -
227A PHE* 3.5 44.0 - - - -
27C T 5.9 0.3 - - - +
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Residues in contact with ASP 165 (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 ILE* 3.9 19.9 - - - +
164A CYS* 1.3 78.5 - - - +
166A VAL* 1.3 65.2 + - - +
167A LYS* 3.1 46.1 + - - +
209A SER 4.4 4.3 - - - +
210A GLY 3.6 12.1 - - - +
211A LYS* 3.7 30.9 + - + +
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Residues in contact with VAL 166 (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 ILE* 4.6 9.3 - - - +
165A ASP* 1.3 71.9 - - - +
167A LYS* 1.3 66.2 + - - +
168A PHE* 3.3 58.3 - - + +
170A ILE* 4.5 7.4 - - + -
210A GLY* 3.1 21.2 + - - +
212A ILE* 4.4 2.5 - - + -
227A PHE* 3.8 18.4 - - + -
231A TYR* 3.8 22.8 + - + -
234A LEU* 3.7 24.5 - - + -
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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