Contacts of the strand formed by residues 225 - 239 (chain B) in PDB entry 2ARB
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 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 4.1 5.2 - - - +
34B THR* 4.0 4.5 - - - -
35B LYS 6.1 0.2 - - - -
36B THR* 3.6 29.6 - - + -
40B GLY 4.0 7.4 - - - +
42B PRO* 3.6 20.6 - - + +
76B SER 4.7 0.2 + - - -
77B LEU* 3.3 23.6 - - - +
78B LYS* 2.9 41.3 + - + +
224B GLN* 1.3 77.9 - - - +
226B HIS* 1.3 59.9 + - - +
227B THR* 3.9 15.6 + - - -
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Residues in contact with HIS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL 3.7 0.9 - - - +
32B GLN* 3.9 1.9 + - - -
33B LEU* 3.0 31.9 + - + +
34B THR* 2.8 28.8 + - + +
77B LEU* 3.6 24.9 - - + -
85B ALA 3.7 0.4 - - - -
87B GLY 3.1 35.7 + - - -
88B ILE* 4.0 7.6 - - + -
217B ALA* 3.5 18.2 - - + -
218B ALA 3.3 20.9 - - - -
219B SER* 3.4 8.7 - - - -
224B GLN* 3.1 41.3 + - + -
225B THR* 1.3 72.4 - - - +
227B THR* 1.3 59.4 + - - +
228B LEU 3.9 0.6 + - - -
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Residues in contact with THR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.5 24.0 - - + -
31B VAL 3.4 3.4 - - - +
32B GLN* 2.8 37.7 + - - +
75B PHE* 3.1 8.8 - - - +
76B SER* 3.0 45.4 + - - +
77B LEU* 4.8 0.4 - - - +
78B LYS* 4.8 6.9 + - - +
88B ILE* 5.3 0.7 - - - -
225B THR* 4.0 11.4 + - - -
226B HIS* 1.3 71.9 - - - +
228B LEU* 1.3 59.0 + - - +
229B GLU* 3.5 11.5 + - + +
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.8 24.5 - - + -
30B ALA* 3.5 3.3 - - - +
31B VAL* 2.8 40.6 + - + +
33B LEU* 4.9 9.4 - - + -
50B ILE* 3.7 20.4 - - + -
73B PHE* 4.2 6.5 - - + -
74B SER 3.7 14.8 - - - +
75B PHE* 4.2 5.8 - - + -
88B ILE* 4.9 2.2 - - + +
215B PHE* 3.5 58.3 - - + -
226B HIS 3.9 2.0 + - - -
227B THR* 1.3 69.9 - - - +
229B GLU* 1.3 59.7 - - - +
230B SER 3.9 9.6 - - - +
231B TRP* 4.8 0.4 - - + -
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Residues in contact with GLU 229 (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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9B PRO 3.7 9.2 - - - +
10B THR* 3.9 5.9 - - - +
11B PHE* 3.8 11.3 - - - -
29B ASN 4.5 3.1 - - - +
30B ALA* 4.4 8.3 - - + -
74B SER* 2.9 22.0 + - - +
75B PHE 3.9 3.5 - - - -
76B SER* 2.8 30.8 + - - -
169B SER* 2.7 33.1 + - - -
227B THR* 3.9 16.9 - - + +
228B LEU* 1.3 75.5 - - - +
230B SER* 1.3 63.7 + - - +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE 3.3 8.7 - - - -
9B PRO* 3.4 19.5 - - - -
11B PHE* 3.8 6.3 - - - -
72B GLN* 4.4 8.3 + - - -
73B PHE* 3.3 5.9 - - - +
74B SER* 2.8 44.3 + - - +
171B ASN* 5.1 0.9 + - - -
228B LEU* 3.7 4.1 - - - +
229B GLU* 1.3 79.8 - - - +
231B TRP* 1.3 65.7 + - - +
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Residues in contact with TRP 231 (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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6B PHE* 3.7 38.1 - + - -
7B GLY* 3.7 0.3 - - - -
8B PHE* 2.7 58.5 + + + +
11B PHE* 4.0 18.2 - + + -
18B LEU* 4.5 4.9 - - + -
50B ILE* 4.4 15.7 - - + -
52B PHE* 4.1 10.3 - - + -
71B SER* 3.0 21.9 + - - -
72B GLN* 3.3 13.9 - - - +
73B PHE* 4.1 1.6 - - + -
90B PHE* 4.3 8.1 - + - -
213B VAL* 3.8 34.5 - - + -
214B GLY* 4.1 5.4 - - - -
215B PHE* 3.4 34.7 - + + -
228B LEU* 4.8 0.7 - - + -
230B SER* 1.3 77.3 - - - +
232B SER* 1.3 77.1 + - - +
233B PHE* 4.0 4.7 - + + +
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Residues in contact with SER 232 (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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6B PHE* 3.3 11.2 - - - -
7B GLY* 4.1 7.9 - - - -
70B GLN 4.0 0.4 - - - +
71B SER* 3.4 1.0 - - - -
72B GLN* 2.8 52.3 + - - +
231B TRP* 1.3 82.1 - - - +
233B PHE* 1.3 61.6 - - - +
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Residues in contact with PHE 233 (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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4B LEU* 4.6 4.3 - - + -
5B SER* 3.1 4.9 - - - -
6B PHE* 2.9 68.3 + + + +
56B VAL* 4.0 19.5 - - + -
69B PHE* 4.0 36.3 - + + -
70B GLN 3.4 12.3 - - - -
71B SER* 3.9 13.2 - - - -
90B PHE* 4.4 7.6 - + - -
92B ILE* 6.2 0.2 - - + -
213B VAL* 4.1 30.5 - - + -
231B TRP* 4.0 5.2 - - - +
232B SER* 1.3 76.6 - - - +
234B THR* 1.3 63.2 + - - +
235B SER* 3.6 26.2 - - - -
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Residues in contact with THR 234 (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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4B LEU 3.4 6.5 + - - -
5B SER* 3.7 14.8 - - - -
68B ASN 4.6 0.4 - - - +
69B PHE* 3.1 5.4 - - - +
70B GLN* 2.9 62.0 + - + +
233B PHE* 1.3 80.9 - - - +
235B SER* 1.3 65.9 + - - +
236B THR* 5.7 1.6 - - - +
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Residues in contact with SER 235 (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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2B ASP 4.4 1.2 + - - -
3B SER* 3.2 4.7 - - - -
4B LEU* 2.9 41.0 + - - +
56B VAL* 3.5 23.7 - - - +
57B HIS 5.4 1.2 + - - -
67B ALA* 4.7 7.0 - - - -
68B ASN 3.3 6.7 - - - -
69B PHE* 3.9 9.9 - - - -
233B PHE* 3.6 15.8 - - - -
234B THR* 1.3 79.9 + - - +
236B THR* 1.3 63.2 + - - +
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Residues in contact with THR 236 (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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2B ASP* 3.4 6.2 + - - +
3B SER* 3.8 15.4 - - - -
67B ALA* 4.0 4.2 - - - +
68B ASN* 2.9 27.5 + - + +
234B THR* 5.7 1.6 - - - +
235B SER* 1.3 78.2 - - - +
237B LEU* 1.3 59.8 + - - +
238B LEU* 2.8 49.3 - - + +
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Residues in contact with LEU 237 (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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2B ASP* 3.0 31.6 + - + +
57B HIS* 3.5 51.8 - - + +
58B LEU 3.8 5.6 - - - +
59B TRP* 4.0 11.7 - - - -
60B GLU* 4.5 4.7 - - + -
65B ARG* 3.8 47.1 + - + +
66B VAL* 3.8 8.1 - - - +
67B ALA* 3.6 20.2 - - + +
236B THR* 1.3 77.2 + - - +
238B LEU* 1.3 64.9 + - - +
239B TYR* 5.5 2.4 - - - -
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Residues in contact with LEU 238 (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 ARG* 3.3 8.4 - - - +
66B VAL 3.1 33.4 + - - +
67B ALA 4.3 0.2 - - - -
68B ASN* 3.1 32.3 - - + +
178B PRO* 4.5 6.3 - - + -
236B THR* 2.8 42.8 - - + +
237B LEU* 1.3 78.4 - - - +
239B TYR* 1.3 72.9 + - + +
240B THR* 3.3 7.1 + - - +
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Residues in contact with TYR 239 (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 SER* 5.3 5.4 - - - -
64B SER 4.9 0.2 - - - -
65B ARG* 3.9 37.4 + - + -
179B SER* 5.3 1.9 + - - -
237B LEU 5.5 1.8 - - - -
238B LEU* 1.3 81.0 - - + +
240B THR* 1.3 63.3 + - - +
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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