Contacts of the strand formed by residues 210 - 219 (chain B) in PDB entry 2ARE
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 TRP 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.3 33.7 + - + +
15A GLN* 4.7 4.3 - - - -
16A LYS* 3.4 45.0 - - + +
17A ASN* 4.0 3.6 - - - -
1B GLN* 3.8 29.4 - - - -
55B GLN* 3.8 36.6 - - + +
56B VAL 3.4 20.2 - - - -
57B HIS* 3.4 48.3 + + + -
95B PRO* 3.2 19.3 - - + +
208B PRO* 3.5 10.1 - - - +
209B GLU* 1.3 89.3 - - + +
211B VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 211 (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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55B GLN* 3.4 5.7 - - - -
56B VAL* 2.8 49.7 + - + +
58B LEU* 4.0 24.2 - - + -
92B ILE* 3.5 24.9 - - + -
93B ALA 3.1 17.3 - - - +
95B PRO* 3.9 5.8 - - - -
207B LEU* 4.1 9.2 - - + -
208B PRO* 3.5 21.3 - - + +
210B TRP* 1.3 80.4 - - - +
212B ARG* 1.3 64.7 + - - +
213B VAL* 4.7 2.5 - - + -
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Residues in contact with ARG 212 (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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19B ILE* 3.7 25.5 - - - +
51B LEU* 4.5 21.6 - - + +
52B PHE 3.6 17.9 + - - +
53B SER* 2.9 29.3 + - - +
54B ALA 4.5 4.0 - - - +
55B GLN* 4.1 25.3 - - + +
56B VAL* 5.0 0.9 - - - +
91B PHE 4.1 0.2 - - - +
92B ILE* 3.5 3.8 - - - +
93B ALA* 2.9 32.6 + - - +
94B PRO 4.8 1.1 - - - +
95B PRO* 2.9 46.5 + - + +
97B THR* 5.3 0.7 - - + -
211B VAL* 1.3 77.6 - - - +
213B VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 4.3 10.5 - - + -
51B LEU* 3.4 5.8 - - - -
52B PHE* 3.0 31.1 + - + +
56B VAL* 4.3 20.2 - - + -
90B PHE* 4.2 10.1 - - + -
91B PHE 3.4 4.9 - - - +
92B ILE* 4.0 26.5 - - + -
211B VAL* 4.7 2.9 - - + -
212B ARG* 1.3 80.5 - - - +
214B GLY* 1.3 59.8 + - - +
231B TRP* 3.7 21.1 - - + -
233B PHE* 4.1 26.5 - - + -
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Residues in contact with GLY 214 (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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50B ILE 3.1 14.4 - - - -
51B LEU* 4.0 5.1 - - - +
90B PHE* 3.3 11.2 - - - -
91B PHE* 2.8 34.5 + - - -
213B VAL* 1.3 77.7 - - - +
215B PHE* 1.3 71.4 + - - -
231B TRP* 4.1 8.5 - - - -
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Residues in contact with PHE 215 (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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33B LEU* 4.0 18.6 - - + +
49B ARG* 3.0 6.8 - - - +
50B ILE* 2.9 41.0 + - + +
73B PHE* 3.5 55.0 - + + -
88B ILE* 4.5 9.4 - - + -
89B ALA 3.1 16.6 - - - +
90B PHE* 3.8 20.0 - + + -
91B PHE* 3.6 3.9 - - - -
214B GLY* 1.3 78.4 - - - -
216B SER* 1.3 62.4 + - - +
228B LEU* 3.5 28.5 - - + -
231B TRP* 3.4 36.6 - + - -
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Residues in contact with SER 216 (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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33B LEU* 4.3 2.9 - - - -
48B GLY 3.5 6.7 + - - -
49B ARG* 3.1 29.4 - - - +
88B ILE* 3.4 2.3 - - - +
89B ALA* 2.8 33.3 + - - +
91B PHE* 3.9 3.1 - - - -
108B LEU* 2.7 27.4 + - - +
109B GLY* 3.7 3.6 - - - -
110B LEU* 3.9 18.8 - - - -
215B PHE* 1.3 76.2 - - - +
217B ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 217 (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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33B LEU* 3.8 17.3 - - + -
34B THR* 3.9 2.9 - - + +
47B VAL* 3.5 3.8 - - - +
48B GLY 3.0 29.3 + - - +
87B GLY 3.2 16.6 - - - +
88B ILE* 4.0 1.8 - - - -
108B LEU* 4.2 5.4 - - - -
216B SER* 1.3 76.7 + - - +
218B ALA* 1.3 65.5 + - - +
226B HIS* 3.5 31.9 - - + +
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Residues in contact with ALA 218 (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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34B THR* 3.8 4.9 - - - +
46B THR 3.3 12.6 - - - +
47B VAL* 3.8 15.0 - - + -
86B ASP* 2.8 33.9 + - + +
87B GLY 3.4 4.1 + - - -
105B GLY 3.8 24.9 - - - +
108B LEU* 3.9 14.7 + - - +
109B GLY 4.1 0.4 - - - +
217B ALA* 1.3 78.7 - - - +
219B SER* 1.3 55.7 + - - +
226B HIS* 3.3 6.2 + - - -
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Residues in contact with SER 219 (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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34B THR* 4.3 2.3 - - - +
43B VAL 4.1 1.1 + - - -
45B SER* 3.2 4.9 + - - -
46B THR* 2.9 43.4 + - - +
47B VAL* 5.4 0.2 - - - +
85B ALA 2.7 17.7 + - - -
86B ASP* 3.6 5.2 - - - -
105B GLY* 4.2 6.1 + - - -
218B ALA* 1.3 72.2 + - - +
220B GLY* 1.3 60.3 + - - +
222B GLN 3.5 13.5 - - - -
223B TYR* 3.6 13.3 - - - +
224B GLN 3.6 8.0 + - - -
226B HIS* 3.4 11.6 + - - -
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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