Contacts of the strand formed by residues 247 - 262 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.1 9.0 - - - +
77B ASP* 3.2 35.9 - - - +
78B MET 4.9 1.1 - - - +
245B LEU* 4.7 5.4 - - + +
246B PRO* 1.3 80.9 - - + +
248B LEU* 1.3 62.3 + - - +
249B ASP* 4.1 13.4 + - - -
287B SER 3.4 4.0 - - - +
288B PHE* 3.4 5.3 - - - +
289B SER* 2.8 43.3 + - - -
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Residues in contact with LEU 248 (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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75B ILE* 2.8 56.1 + - + +
76B PHE* 2.9 27.2 + - + +
247B THR* 1.3 74.3 - - - +
249B ASP* 1.3 61.9 + - - +
286B LEU* 4.0 34.5 - - + -
287B SER 3.3 15.9 - - - +
288B PHE* 4.4 15.9 - - + +
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Residues in contact with ASP 249 (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 THR* 6.2 2.6 - - + -
73B GLN 3.6 7.3 - - - +
74B SER* 3.6 25.2 + - - -
75B ILE* 4.0 3.4 - - - -
77B ASP* 4.9 2.4 - - - +
80B LYS* 3.9 10.5 + - - -
247B THR* 4.1 17.5 + - - -
248B LEU* 1.3 79.8 - - - +
250B LEU* 1.3 63.2 + - - +
251B THR* 5.5 5.3 + - + -
286B LEU* 3.3 4.7 - - - +
287B SER* 2.7 44.0 + - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.2 17.3 - - + -
72B THR* 3.6 2.8 - - - -
73B GLN* 2.9 41.8 + - + +
75B ILE* 3.8 28.5 - - + +
249B ASP* 1.3 75.4 - - - +
251B THR* 1.3 80.8 + - - +
252B ALA* 4.2 4.7 - - + +
284B VAL* 5.7 3.4 - - + -
285B GLY 3.2 12.1 - - - +
286B LEU* 3.9 11.4 - - + -
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Residues in contact with THR 251 (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 LEU 3.5 4.3 - - - +
72B THR* 3.6 27.4 - - + -
249B ASP* 4.3 5.3 + - + -
250B LEU* 1.3 79.8 - - - +
252B ALA* 1.3 62.6 + - - +
284B VAL* 3.1 4.0 - - - -
285B GLY* 2.8 40.5 + - - -
286B LEU 5.6 0.9 - - - -
287B SER* 5.8 5.7 - - - -
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 3.6 1.0 - - - +
71B LEU* 2.9 53.8 + - + +
250B LEU* 4.4 5.4 - - + -
251B THR* 1.3 76.4 - - - +
253B SER* 1.3 65.0 + - - +
283B LYS 3.2 11.9 - - - +
284B VAL* 4.4 9.9 - - + -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 5.2 3.1 - - - -
69B LEU 3.2 15.7 - - - -
70B GLN* 3.8 19.3 - - - -
252B ALA* 1.3 78.7 - - - +
254B THR* 1.3 63.7 + - - +
281B GLN 4.5 0.2 - - - -
282B ASN* 3.4 3.3 - - - +
283B LYS* 2.8 50.5 + - - +
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Residues in contact with THR 254 (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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54A TYR* 3.3 17.7 + - - -
67B ALA 4.2 1.2 - - - +
68B SER* 3.6 1.6 - - - -
69B LEU* 3.1 43.4 + - + +
253B SER* 1.3 77.5 - - - +
255B GLY* 1.3 58.4 + - - +
281B GLN 3.2 6.3 - - - -
282B ASN* 3.1 22.7 + - - -
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.3 8.3 + - - -
67B ALA 3.6 11.2 - - - -
68B SER* 3.8 11.4 - - - -
253B SER* 5.4 0.2 - - - -
254B THR* 1.3 75.2 + - - +
256B ILE* 1.3 60.0 + - - -
279B MET 4.7 0.3 - - - -
280B GLY* 3.7 0.7 - - - -
281B GLN* 3.0 37.7 + - - +
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Residues in contact with ILE 256 (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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54A TYR* 3.1 31.4 - - + +
55A ARG* 3.7 19.3 - - - +
65B THR 5.4 1.1 - - - +
66B SER* 3.3 4.5 - - - -
67B ALA* 3.2 39.8 + - + +
255B GLY* 1.3 74.7 - - - -
257B SER* 1.3 64.8 + - - +
258B ASP* 4.3 13.0 - - - +
279B MET 3.4 5.2 - - - -
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Residues in contact with SER 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 6.4 1.3 - - - -
65B THR 3.4 9.6 - - - -
66B SER* 4.3 11.2 - - - -
256B ILE* 1.3 78.1 - - - +
258B ASP* 1.3 63.5 + - - +
259B THR* 4.0 7.4 + - - -
277B SER 3.6 3.1 - - - +
279B MET* 3.0 48.5 + - - +
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Residues in contact with ASP 258 (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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55A ARG* 2.6 43.1 + - - -
63B ASN 3.4 3.8 - - - +
64B ALA* 3.2 2.8 - - - -
65B THR* 3.0 41.4 + - - +
256B ILE* 4.3 10.1 - - - +
257B SER* 1.3 74.7 + - - +
259B THR* 1.3 62.3 + - - +
277B SER 3.3 3.6 - - - -
278B ASN* 3.4 16.8 - - - +
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER* 4.5 9.6 - - - -
63B ASN 3.5 3.1 - - - +
64B ALA* 3.7 24.5 - - + +
257B SER* 4.5 8.0 + - - -
258B ASP* 1.3 77.3 + - - +
260B SER* 1.3 65.0 + - - +
261B TYR* 4.0 31.0 - - + +
276B ASP* 3.2 6.1 - - - +
277B SER* 2.8 41.9 + - - +
278B ASN* 4.9 0.7 - - - +
279B MET* 6.0 0.5 - - - +
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Residues in contact with SER 260 (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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62B SER* 3.1 3.4 - - - -
63B ASN* 2.8 48.8 + - - +
259B THR* 1.3 75.9 - - - +
261B TYR* 1.3 66.3 + - - +
262B SER* 5.5 0.2 - - - -
276B ASP* 3.4 26.5 - - - -
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Residues in contact with TYR 261 (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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60B ILE* 4.4 15.3 - - + -
61B ASN 3.2 15.5 - - - +
62B SER* 3.8 14.8 - - - -
259B THR* 4.0 26.7 - - + +
260B SER* 1.3 79.3 + - - +
262B SER* 1.3 66.6 + - - +
266B THR* 4.3 8.1 - - + +
273B GLN 4.0 13.7 - - - -
274B TYR* 3.7 48.2 + + + +
275B ASP 4.1 10.1 - - - -
276B ASP* 3.9 8.0 + - - +
277B SER* 5.3 4.2 - - - -
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 5.9 0.9 - - - -
59B GLY 3.4 0.2 - - - +
61B ASN* 2.8 53.4 + - - +
62B SER* 4.7 1.2 + - - -
63B ASN* 5.3 3.1 + - - -
261B TYR* 1.3 80.2 - - - +
263B GLY* 1.3 58.8 + - - +
266B THR* 3.2 15.7 + - - -
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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