Contacts of the strand formed by residues 210 - 220 (chain B) in PDB entry 3BX9
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 TYR 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ILE 3.3 4.9 - - - +
44B LYS* 3.9 33.0 - - + -
204B GLU* 3.2 9.1 - - - +
205B ALA* 3.0 45.2 + - + +
206B ASP* 3.1 28.0 - - + -
209B THR* 1.3 98.1 - - + +
211B VAL* 1.3 63.2 + - - +
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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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41B MET 3.5 2.1 - - - +
42B ARG* 3.5 1.5 - - - -
43B ILE* 2.6 48.7 + - + +
55B PHE* 3.8 39.0 - - + -
201B ARG* 3.8 23.8 - - + +
203B LYS 3.6 2.5 - - - -
204B GLU* 4.2 5.6 - - + -
208B GLU* 3.8 33.2 - - + +
209B THR 4.2 0.2 - - - -
210B TYR* 1.3 79.6 - - - +
212B GLU* 1.3 68.5 + - - +
213B GLN* 4.4 4.7 - - + +
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Residues in contact with GLU 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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40B THR* 3.6 28.4 - - + +
41B MET 3.3 5.8 - - - +
42B ARG* 4.6 14.4 - - + +
201B ARG* 3.7 3.3 - - - -
202B ILE* 2.8 55.5 + - + +
203B LYS* 2.9 47.1 + - + +
211B VAL* 1.3 74.1 - - - +
213B GLN* 1.3 59.9 + - - +
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Residues in contact with GLN 213 (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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40B THR* 3.2 5.4 - - - +
41B MET* 2.8 38.2 + - + +
43B ILE* 4.0 16.5 - - + +
55B PHE* 4.0 16.6 - - - -
59B ALA* 3.0 46.6 + - - +
62B PHE* 3.7 11.8 - - - +
63B NRQ 3.5 26.8 - - - +
199B LEU* 3.6 17.3 - - + +
200B GLU 3.3 12.8 - - - +
201B ARG* 4.6 1.8 - - - +
202B ILE* 4.5 0.4 - - - -
211B VAL* 3.9 4.8 + - + +
212B GLU* 1.3 75.2 - - - +
214B HIS* 1.3 62.1 + - - +
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Residues in contact with HIS 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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38B THR* 4.2 8.2 - - + +
39B GLN 3.0 24.7 + - - -
40B THR* 3.3 16.6 - - - +
63B NRQ 4.2 2.9 - - - -
198B ARG 4.1 0.4 + - - +
199B LEU* 3.5 4.0 - - - +
200B GLU* 2.8 47.5 + - + +
202B ILE* 3.5 28.1 - - + +
213B GLN* 1.3 73.7 - - - +
215B GLU* 1.3 75.4 + - - +
216B VAL* 4.3 14.9 + - + +
234B CIT 3.1 17.9 + - - -
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Residues in contact with GLU 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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37B GLY 3.6 0.6 - - - +
38B THR* 3.3 4.7 - - - -
39B GLN* 3.0 48.5 + - + +
63B NRQ 3.2 48.1 + - - +
66B SER 5.0 1.2 + - - +
67B LYS* 5.9 0.3 + - - -
69B PHE 6.0 0.2 - - - +
70B ILE* 5.5 2.0 - - - +
197B ARG* 3.1 32.4 + - + -
198B ARG 3.3 16.4 - - - +
199B LEU* 4.0 6.1 - - + -
214B HIS* 1.3 81.1 + - - +
216B VAL* 1.3 68.2 + - - +
217B ALA* 3.6 14.6 - - + +
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Residues in contact with VAL 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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36B GLU 4.9 2.7 - - - +
37B GLY 3.1 10.1 - - - +
38B THR* 4.2 16.4 - - + -
196B ASP 4.6 0.2 - - - -
197B ARG* 3.2 4.9 - - - +
198B ARG* 3.0 56.6 + - + +
200B GLU* 6.0 0.7 - - - +
214B HIS* 4.3 11.4 - - + +
215B GLU* 1.3 72.6 - - - +
217B ALA* 1.3 64.0 + - - +
218B VAL* 4.6 13.9 - - + -
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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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37B GLY* 2.8 17.2 + - - -
69B PHE 4.2 7.0 - - - +
70B ILE* 4.0 23.8 - - + -
71B ASN 3.1 21.3 + - - -
195B VAL* 4.1 6.3 - - + -
196B ASP 3.4 5.4 - - - -
197B ARG* 4.0 7.4 - - + +
215B GLU* 3.6 22.0 - - - +
216B VAL* 1.3 75.0 - - - +
218B VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 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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36B GLU 4.8 3.1 - - - +
70B ILE* 4.2 2.0 - - - -
71B ASN* 3.7 17.9 - - + +
73B THR* 3.8 26.0 - - + +
194B TYR 3.9 0.5 - - - +
195B VAL* 3.4 1.2 - - - -
196B ASP* 3.0 39.5 + - + +
216B VAL* 4.6 13.7 - - + -
217B ALA* 1.3 80.8 - - - +
219B ALA* 1.3 66.0 + - - +
220B ARG* 4.1 5.9 + - + +
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Residues in contact with ALA 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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70B ILE* 3.6 18.8 - - + +
71B ASN 2.8 13.5 + - - +
72B HIS* 3.8 14.1 - - + -
73B THR* 2.5 39.2 + - - +
76B ILE* 3.7 3.4 - - + -
193B TYR* 3.7 30.5 - - + -
194B TYR 3.2 5.6 - - - +
195B VAL* 3.9 3.1 - - + -
218B VAL* 1.3 70.7 - - - +
220B ARG* 1.3 54.7 + - - +
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Residues in contact with ARG 220 (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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73B THR* 3.8 7.4 - - - +
74B GLN* 3.9 10.1 - - - +
76B ILE* 3.5 10.3 - - - +
144B THR* 3.6 19.0 + - - +
193B TYR* 3.7 2.4 - - - +
194B TYR* 2.8 57.7 + - - +
196B ASP* 2.8 40.4 + - - +
218B VAL* 4.7 7.6 - - + +
219B ALA* 1.3 76.7 - - - +
221B TYR* 1.3 76.8 + - - +
222B CYS* 3.9 10.3 - - - +
223B ASP* 4.4 11.3 - - - +
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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