Contacts of the strand formed by residues 153 - 165 (chain O) in PDB entry 5FYW
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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74O VAL* 3.4 5.8 - - - +
75O THR* 2.8 48.7 + - - +
76O LEU 4.9 1.2 - - - -
77O GLY* 5.3 1.0 - - - -
151O LYS* 3.2 42.2 + - + +
152O PHE* 1.3 80.6 - - - +
154O ASP* 1.3 78.5 + - - +
155O PHE* 3.1 6.1 + - - -
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Residues in contact with ASP 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O THR* 3.3 10.7 + - - +
75O THR* 3.6 27.5 + - - +
153O THR* 1.3 81.2 + - - +
155O PHE* 1.3 65.1 + - - +
156O LYS* 3.1 9.9 + - - +
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Residues in contact with PHE 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ALA* 3.5 20.0 - - + -
73O THR 3.4 4.9 - - - -
74O VAL* 3.9 12.1 - - + -
129O GLU 4.5 2.2 - - - -
132O SER* 3.6 14.1 - - - -
133O LYS* 3.5 42.4 - - + -
136O SER* 3.4 29.8 - - - -
152O PHE* 3.7 25.1 - + + -
153O THR 3.1 4.7 + - - -
154O ASP* 1.3 75.0 - - - +
156O LYS* 1.3 61.1 + - - +
157O ILE* 4.0 20.6 - - + -
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Residues in contact with LYS 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ALA* 3.3 3.7 - - - -
73O THR* 2.9 36.3 + - - +
154O ASP 3.1 9.6 + - - +
155O PHE* 1.3 78.8 - - - +
157O ILE* 1.3 71.9 + - - +
158O GLN* 3.6 32.4 + - - +
218O LYS* 4.4 13.9 - - - +
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Residues in contact with ILE 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O ILE* 3.9 15.9 - - + -
71O VAL 3.7 3.8 - - - -
72O ALA* 4.1 2.5 - - + -
129O GLU* 3.6 43.1 - - + +
155O PHE* 4.0 25.9 - - + -
156O LYS* 1.3 79.4 - - - +
158O GLN* 1.3 61.9 + - - +
159O ASN 4.0 9.4 - - - +
160O ILE* 3.7 28.9 - - + -
218O LYS* 3.5 31.6 - - - +
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Residues in contact with GLN 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N T 3.6 23.4 - - - +
27N A 3.9 29.2 + - - +
71O VAL* 2.9 15.4 + - + +
72O ALA* 4.7 0.4 - - - -
73O THR* 2.9 38.6 + - + +
156O LYS* 3.6 29.9 + - - +
157O ILE* 1.3 73.7 - - - +
159O ASN* 1.3 62.6 + - + +
216O GLY 5.3 1.7 - - - +
217O ALA 4.1 2.2 - - - +
218O LYS* 2.7 49.9 + - - +
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Residues in contact with ASN 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N A 3.7 24.7 + - - +
26N T 3.5 38.4 + - + +
69O ASN 4.1 0.8 - - - +
70O ILE* 3.5 3.6 - - - -
71O VAL* 2.9 41.5 + - + +
157O ILE* 3.7 2.4 - - - +
158O GLN* 1.3 81.8 - - - +
160O ILE* 1.3 67.7 + - - +
161O VAL* 3.9 10.1 - - - +
215O THR* 3.4 5.3 + - - -
216O GLY* 3.1 33.6 + - - -
217O ALA 3.4 5.6 + - - -
47T A 4.9 0.6 - - - -
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Residues in contact with ILE 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O LEU* 3.8 34.3 - - + -
69O ASN 3.6 3.8 - - - +
70O ILE* 3.9 20.2 - - + -
129O GLU* 4.6 10.3 - - + +
157O ILE* 3.7 17.0 - - + -
159O ASN* 1.3 80.0 + - - +
161O VAL* 1.3 66.3 + - - +
215O THR* 3.6 17.7 - - - -
216O GLY 3.7 1.0 + - - -
217O ALA* 2.9 20.4 + - + +
218O LYS 4.0 11.7 - - - +
219O GLN* 3.9 6.3 - - - -
220O ARG* 3.7 27.4 - - - +
223O ILE* 3.6 16.5 - - + +
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Residues in contact with VAL 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N A 4.6 2.2 - - - +
67O LEU* 3.5 6.8 - - - +
68O GLN* 2.8 32.1 + - + -
69O ASN* 3.0 26.9 + - + +
71O VAL* 6.0 0.2 - - + -
159O ASN* 3.9 13.5 - - - +
160O ILE* 1.3 80.8 - - - +
162O GLY* 1.3 66.8 + - - +
213O VAL* 4.3 7.0 - - + -
214O LEU 3.4 9.2 - - - +
215O THR* 3.7 16.4 - - - +
48T T 3.9 20.0 - - + +
49T A 4.1 25.6 - - + +
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Residues in contact with GLY 162 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65O PRO* 5.1 0.2 - - - -
66O THR 3.2 12.8 - - - -
67O LEU* 4.2 7.9 - - - -
68O GLN* 4.3 3.4 - - - -
161O VAL* 1.3 76.6 - - - +
163O SER* 1.3 63.5 + - - -
213O VAL* 3.5 5.2 - - - +
214O LEU* 2.8 38.4 + - - +
223O ILE* 4.1 11.4 - - - +
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Residues in contact with SER 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O PRO* 4.4 1.5 - - - +
66O THR* 2.8 38.1 + - - +
68O GLN* 3.1 28.8 + - - +
162O GLY* 1.3 76.2 - - - -
164O CYS* 1.3 62.6 + - - +
212O ILE 3.1 15.3 - - - -
213O VAL* 4.5 9.4 - - - -
214O LEU* 4.3 2.8 - - - +
49T A 4.7 14.0 + - - -
50T T 5.4 2.9 + - - -
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Residues in contact with CYS 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O ILE* 3.8 15.9 - - + -
64O VAL 4.4 1.3 - - - +
65O PRO* 3.9 19.7 - - + -
66O THR* 5.5 1.3 - - - +
163O SER* 1.3 78.3 - - - +
165O ASP* 1.3 62.0 + - - +
211O LYS* 3.5 7.2 - - - +
212O ILE* 2.8 40.4 + - - +
214O LEU* 4.5 2.2 - - - -
227O PHE* 3.5 44.0 - - - -
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Residues in contact with ASP 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O ILE* 3.9 21.1 - - - +
164O CYS* 1.3 78.3 - - - +
166O VAL* 1.3 62.9 + - - +
167O LYS* 3.1 47.8 + - - +
209O SER 4.4 4.3 - - - +
210O GLY 3.6 12.4 - - - +
211O LYS* 3.7 30.1 + - + +
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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