Contacts of the strand formed by residues 247 - 262 (chain A) in PDB entry 2WMZ
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.2 6.3 - - - -
77A ASP* 3.1 38.1 - - - +
78A MET 4.9 0.9 - - - +
245A LEU* 4.7 4.9 - - + +
246A PRO* 1.3 80.8 - - + +
248A LEU* 1.3 60.6 + - - +
249A ASP* 4.1 11.3 + - - -
287A SER 3.4 4.4 - - - +
288A PHE* 3.4 5.2 - - - -
289A SER* 2.8 44.3 + - - -
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Residues in contact with LEU 248 (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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74A SER* 4.7 0.2 + - - -
75A ILE* 2.9 55.7 + - + +
76A PHE* 2.9 28.6 + - + +
247A THR* 1.3 74.2 - - - +
249A ASP* 1.3 61.7 + - - +
286A LEU* 4.0 34.5 - - + -
287A SER 3.2 15.3 - - - +
288A PHE* 4.4 15.7 - - + +
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Residues in contact with ASP 249 (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 THR* 6.3 2.2 - - + -
73A GLN 3.7 6.5 - - - +
74A SER* 3.8 14.2 + - - -
75A ILE* 4.1 2.9 - - - -
77A ASP* 4.8 3.0 - - - +
80A LYS* 3.8 21.2 + - - -
247A THR* 4.1 17.2 + - - -
248A LEU* 1.3 79.2 + - - +
250A LEU* 1.3 63.3 + - - +
251A THR* 5.4 5.5 + - + -
286A LEU* 3.3 5.5 - - - +
287A SER* 2.8 43.5 + - - +
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Residues in contact with LEU 250 (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 LEU* 4.3 15.0 - - + -
72A THR* 3.5 2.6 - - - -
73A GLN* 2.8 48.6 + - + +
75A ILE* 3.6 24.2 - - + +
249A ASP* 1.3 75.8 - - - +
251A THR* 1.3 81.0 + - - +
252A ALA* 4.3 5.4 - - + +
284A VAL* 5.7 3.1 - - + -
285A GLY 3.2 12.3 - - - +
286A LEU* 4.0 11.2 - - + -
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Residues in contact with THR 251 (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 LEU 3.5 4.5 - - - +
72A THR* 3.5 26.9 - - + -
249A ASP* 4.2 6.2 + - + -
250A LEU* 1.3 80.7 - - - +
252A ALA* 1.3 62.6 + - - +
283A LYS 5.2 0.2 - - - -
284A VAL* 3.2 2.8 - - - -
285A GLY* 2.9 39.2 + - - -
286A LEU 5.6 1.0 - - - -
287A SER* 5.8 5.6 - - - -
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Residues in contact with ALA 252 (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 GLN* 3.6 1.0 - - - +
71A LEU* 2.8 53.2 + - + +
250A LEU* 4.4 5.4 - - + -
251A THR* 1.3 78.6 - - - +
253A SER* 1.3 64.5 + - - +
283A LYS 3.1 12.6 - - - +
284A VAL* 4.4 9.4 - - + -
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Residues in contact with SER 253 (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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68A SER* 5.2 3.1 - - - -
69A LEU 3.3 15.0 - - - -
70A GLN* 3.7 19.5 + - - -
252A ALA* 1.3 79.3 - - - +
254A THR* 1.3 64.7 + - - +
255A GLY 5.4 0.2 - - - -
281A GLN 4.5 0.2 - - - -
282A ASN* 3.4 2.8 - - - +
283A LYS* 2.8 50.7 + - - +
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Residues in contact with THR 254 (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 ALA 4.2 1.0 - - - +
68A SER* 3.7 1.8 - - - -
69A LEU* 3.1 43.8 + - + +
253A SER* 1.3 76.8 - - - +
255A GLY* 1.3 56.9 + - - +
281A GLN 3.1 5.8 - - - -
282A ASN* 2.9 22.9 + - - -
54C TYR* 3.4 16.7 + - - -
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Residues in contact with GLY 255 (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 ALA 3.5 12.1 - - - -
68A SER* 3.7 12.0 - - - -
253A SER* 4.3 0.6 - - - -
254A THR* 1.3 76.3 + - - +
256A ILE* 1.3 61.5 + - - -
279A MET 4.8 0.3 - - - -
280A GLY* 3.7 0.9 - - - -
281A GLN* 3.1 35.8 + - - +
54C TYR* 3.2 7.5 + - - -
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Residues in contact with ILE 256 (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 THR 5.5 0.7 - - - +
66A SER* 3.4 2.9 - - - -
67A ALA* 3.2 41.3 + - + +
255A GLY* 1.3 74.8 - - - -
257A SER* 1.3 65.9 + - - +
258A ASP* 4.4 12.1 - - - +
279A MET 3.4 9.4 - - - +
54C TYR* 3.0 31.9 - - + +
55C ARG* 3.8 14.6 - - - +
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Residues in contact with SER 257 (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 ALA* 6.5 0.2 - - - -
65A THR 3.3 9.9 - - - -
66A SER* 4.2 10.8 - - - -
256A ILE* 1.3 77.3 - - - +
258A ASP* 1.3 63.3 + - - +
259A THR* 4.0 6.4 + - - -
277A SER 3.6 3.5 - - - +
279A MET* 3.0 47.7 + - - +
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Residues in contact with ASP 258 (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 ASN 3.6 2.6 - - - +
64A ALA* 3.3 2.4 - - - -
65A THR* 2.9 46.5 + - - +
256A ILE* 4.4 9.8 - - - +
257A SER* 1.3 74.2 + - - +
259A THR* 1.3 60.7 + - - +
277A SER 3.4 3.8 - - - -
278A ASN* 3.4 16.7 - - - +
55C ARG* 2.5 45.8 + - - -
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Residues in contact with THR 259 (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 SER* 4.6 7.0 - - - -
63A ASN 3.5 2.9 - - - +
64A ALA* 3.5 25.5 - - + +
257A SER* 4.5 7.6 + - - -
258A ASP* 1.3 76.9 + - - +
260A SER* 1.3 64.8 + - - +
261A TYR* 4.0 32.5 - - + +
276A ASP* 3.3 5.7 - - - +
277A SER* 2.8 42.3 + - - +
278A ASN* 4.9 0.7 - - - +
279A MET* 6.0 0.9 - - - +
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Residues in contact with SER 260 (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 SER* 3.4 2.4 - - - -
63A ASN* 2.9 45.6 + - - +
259A THR* 1.3 77.8 - - - +
261A TYR* 1.3 66.9 + - - +
262A SER* 5.3 0.2 + - - -
276A ASP* 3.5 27.4 - - - -
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Residues in contact with TYR 261 (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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60A ILE* 4.7 10.8 - - + -
61A ASN 3.4 15.5 - - - +
62A SER* 3.7 16.2 - - - -
259A THR* 4.0 26.4 - - + +
260A SER* 1.3 79.6 + - - +
262A SER* 1.3 66.4 + - - +
266A THR* 4.3 7.7 - - + +
273A GLN 4.0 13.9 - - - -
274A TYR* 3.7 50.7 + + + +
275A ASP 4.1 9.4 - - - -
276A ASP* 3.9 7.6 + - - +
277A SER* 5.3 5.0 - - - -
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Residues in contact with SER 262 (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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50A TYR* 5.7 1.0 - - - -
61A ASN* 3.0 45.1 + - - +
62A SER 4.7 0.5 + - - -
63A ASN* 5.1 5.4 + - - -
261A TYR* 1.3 80.4 - - - +
263A GLY* 1.3 60.0 + - - +
266A THR* 3.2 15.8 + - - -
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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