Contacts of the strand formed by residues 210 - 220 (chain F) in PDB entry 3BXB
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F ARG* 3.6 23.1 - - + +
43F ILE 3.2 16.4 - - - -
44F LYS* 4.0 27.8 - - + -
203F LYS* 4.2 17.9 - - + -
204F GLU* 3.3 4.9 - - - +
205F ALA* 3.0 51.1 + - + +
206F ASP* 5.2 3.4 - - - +
208F GLU 4.2 0.3 - - - -
209F THR* 1.3 81.4 - - - +
211F VAL* 1.3 66.4 + - - +
212F GLU* 2.8 45.7 + - + +
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Residues in contact with VAL 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F MET 3.9 0.7 - - - +
42F ARG* 3.6 0.7 - - - -
43F ILE* 2.6 45.3 + - + +
55F PHE* 4.2 37.2 - - + -
201F ARG* 3.4 42.4 - - - +
203F LYS 3.4 3.6 - - - -
204F GLU* 4.5 1.6 - - + -
208F GLU* 4.1 20.0 - - + +
210F TYR* 1.3 81.6 - - - +
212F GLU* 1.3 73.0 + - - +
213F GLN* 4.4 6.3 - - + +
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Residues in contact with GLU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F THR* 5.0 8.8 - - + +
41F MET 3.3 5.8 - - - +
42F ARG* 3.7 22.9 + - + +
201F ARG 3.8 0.2 - - - -
202F ILE* 2.9 35.7 + - + +
203F LYS* 2.8 43.2 + - + +
210F TYR* 2.8 39.1 + - + +
211F VAL* 1.3 79.0 - - - +
213F GLN* 1.3 59.9 + - - +
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Residues in contact with GLN 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F THR* 3.3 7.5 - - - +
41F MET 2.8 32.6 + - - +
43F ILE* 4.1 16.3 - - + +
55F PHE* 3.6 20.3 - - - -
59F ALA* 3.1 41.9 + - - +
62F PHE* 4.1 7.9 - - - +
63F NRQ 3.5 26.9 - - + +
199F LEU* 3.7 25.0 - - + +
200F GLU 3.7 5.6 - - - +
201F ARG* 4.6 7.2 + - - +
202F ILE* 4.7 0.9 - - - -
211F VAL* 4.5 5.5 - - + +
212F GLU* 1.3 75.9 - - - +
214F HIS* 1.3 61.1 + - - +
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Residues in contact with HIS 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E PRO 5.6 2.7 + - - -
227E LYS* 3.7 37.7 + - + +
38F THR* 4.2 17.2 - - + +
39F GLN 3.0 33.9 + - - +
40F THR* 3.3 16.2 + - + +
63F NRQ 4.5 2.2 - - - -
198F ARG 3.6 1.4 - - - +
199F LEU* 3.3 2.8 - - - +
200F GLU* 2.7 46.1 + - - +
202F ILE* 4.0 20.0 - - + -
213F GLN* 1.3 77.3 - - - +
215F GLU* 1.3 72.0 + - - +
216F VAL* 4.3 7.5 + - + +
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLY 3.6 1.7 - - - +
38F THR* 3.4 2.9 - - - -
39F GLN* 3.0 59.1 + - + +
63F NRQ 3.7 56.3 + - + +
66F SER 5.0 1.1 + - - +
70F ILE* 5.5 2.1 - - - +
197F ARG* 3.8 9.3 - - + +
198F ARG 3.1 15.3 - - - +
199F LEU* 4.4 3.8 - - + -
214F HIS* 1.3 81.1 + - - +
216F VAL* 1.3 69.4 + - - +
217F ALA* 3.6 20.3 - - - +
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Residues in contact with VAL 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU* 3.7 28.3 - - + +
225E PRO* 3.7 33.9 - - + +
36F GLU 4.7 3.6 - - - +
37F GLY 3.4 4.3 - - - +
38F THR* 3.8 23.8 - - + -
196F ASP 4.1 0.4 - - - +
197F ARG* 3.2 3.1 - - - +
198F ARG* 2.8 49.0 + - + +
200F GLU* 5.9 0.2 - - - +
214F HIS* 4.3 8.0 + - + +
215F GLU* 1.3 73.6 - - - +
217F ALA* 1.3 64.1 + - - +
218F VAL* 4.5 7.4 - - + -
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Residues in contact with ALA 217 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F GLY* 2.9 16.8 + - - +
69F PHE 4.1 2.2 - - - +
70F ILE* 3.9 27.4 - - + -
71F ASN 2.9 22.9 + - - -
195F VAL* 4.2 3.6 - - + -
196F ASP 3.3 4.9 - - - +
197F ARG* 4.0 7.6 - - + -
215F GLU* 3.6 21.5 - - - +
216F VAL* 1.3 76.5 - - - +
218F VAL* 1.3 66.8 - - - +
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Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LEU* 3.7 24.7 - - + +
36F GLU 4.8 1.8 - - - +
70F ILE* 4.2 0.6 - - - +
71F ASN* 3.7 20.2 - - + +
73F THR* 3.4 25.4 - - + +
195F VAL* 4.4 0.9 - - - -
196F ASP* 2.8 39.8 + - + +
216F VAL* 4.5 7.4 - - + -
217F ALA* 1.3 77.9 - - - +
219F ALA* 1.3 63.2 + - - +
220F ARG* 3.9 3.4 + - + +
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Residues in contact with ALA 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 3.8 5.2 - - + +
71F ASN 2.9 11.7 + - - +
72F HIS* 3.5 32.5 - - + +
73F THR* 3.1 26.0 + - - -
76F ILE* 3.7 7.0 - - + +
193F TYR* 3.6 17.5 - - + -
194F TYR 3.2 6.7 - - - +
195F VAL* 3.8 9.2 - - + -
218F VAL* 1.3 74.3 - - - +
220F ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E THR* 3.7 9.3 + - - -
196E ASP* 3.3 19.6 + - - +
220E ARG* 3.2 18.6 - - - +
73F THR* 5.6 1.1 - - - -
74F GLN* 4.6 6.1 - - - +
76F ILE* 3.7 10.1 - - - -
144F THR* 4.1 6.7 + - - +
193F TYR* 3.4 5.5 - - - +
194F TYR* 2.8 64.5 + - + +
196F ASP* 2.8 40.5 + - - +
218F VAL* 4.9 3.1 - - + +
219F ALA* 1.3 76.7 - - - +
221F TYR* 1.3 62.8 + - - +
222F CYS* 4.6 5.9 - - - +
223F ASP* 3.2 36.0 + - - +
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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