Contacts of the strand formed by residues 210 - 220 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42H ARG* 3.0 43.1 - - + +
43H ILE 3.0 21.8 - - - -
44H LYS* 3.1 36.1 - - + +
203H LYS* 4.9 20.6 - - + -
204H GLU* 3.4 3.1 - - - +
205H ALA* 3.2 44.5 + - + +
206H ASP* 5.9 0.7 - - + -
209H THR* 1.3 81.4 + - - +
211H VAL* 1.3 77.2 + - - +
212H GLU* 4.4 12.7 - - + +
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Residues in contact with VAL 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H MET 3.3 2.6 - - - +
42H ARG* 3.5 1.7 - - - -
43H ILE* 2.7 58.9 + - + +
55H PHE* 3.8 40.4 - - + -
201H ARG* 3.6 34.3 - - - +
203H LYS 3.4 5.2 - - - +
204H GLU* 4.6 1.1 - - + -
208H GLU* 4.5 8.1 - - + -
209H THR 5.4 0.2 - - - -
210H TYR* 1.3 89.3 - - - +
212H GLU* 1.3 68.8 + - - +
213H GLN* 4.0 5.4 - - + +
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Residues in contact with GLU 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H THR* 4.1 16.0 - - + +
41H MET 3.3 1.1 - - - -
42H ARG* 3.7 34.8 + - + +
201H ARG* 3.8 2.9 - - - -
202H ILE* 2.8 46.3 + - + +
203H LYS* 2.8 47.5 + - + +
210H TYR* 4.4 8.0 - - + +
211H VAL* 1.3 74.3 - - - +
213H GLN* 1.3 59.3 + - - +
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Residues in contact with GLN 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H THR* 3.0 7.7 - - - +
41H MET* 2.7 46.7 + - + +
43H ILE* 4.0 13.7 - - + -
55H PHE* 3.8 17.0 - - - -
59H ALA* 2.9 47.3 + - - +
62H PHE* 4.2 7.9 - - - +
63H NRQ 3.4 14.6 - - - +
199H LEU* 3.6 31.6 - - + +
200H GLU 3.7 6.3 - - - +
201H ARG* 4.9 5.1 + - - -
202H ILE* 4.6 0.2 - - - -
211H VAL* 4.0 5.8 - - + +
212H GLU* 1.3 74.8 - - - +
214H HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G PRO 5.7 0.4 + - - -
227G LYS* 3.7 42.8 + - + +
38H THR* 4.1 14.9 - - - +
39H GLN* 2.8 33.0 + - - -
40H THR* 3.4 15.8 + - + +
63H NRQ 4.3 2.2 - - - -
198H ARG 3.7 0.7 - - - +
199H LEU* 3.4 4.0 - - - +
200H GLU* 2.9 43.0 + - - +
202H ILE* 3.8 23.7 - - + +
213H GLN* 1.3 76.1 - - - +
215H GLU* 1.3 79.8 + - - +
216H VAL* 4.3 7.9 + - + +
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Residues in contact with GLU 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLY 3.5 3.1 - - - +
38H THR* 3.6 0.5 - - - -
39H GLN* 3.1 44.8 + - + +
63H NRQ 3.2 72.6 + - + +
66H SER 5.5 1.0 - - - +
69H PHE 5.4 0.7 - - - +
70H ILE* 5.5 2.3 - - - +
197H ARG* 3.6 15.8 - - + -
198H ARG 3.2 12.6 - - - +
199H LEU* 3.4 7.6 - - + +
214H HIS* 1.3 81.1 - - - +
216H VAL* 1.3 71.4 + - - +
217H ALA* 3.8 9.4 - - + +
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Residues in contact with VAL 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G LEU* 3.9 14.4 - - + +
225G PRO* 3.6 37.2 - - + +
36H GLU 4.4 6.5 - - - +
37H GLY 2.9 11.9 - - - +
38H THR* 4.1 18.6 - - + -
197H ARG* 3.2 23.7 - - - +
198H ARG* 3.2 23.3 + - + +
200H GLU* 5.7 1.1 - - - +
214H HIS* 4.3 7.4 - - + +
215H GLU* 1.3 73.6 - - - +
217H ALA* 1.3 64.8 + - - +
218H VAL* 4.6 12.8 - - + -
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Residues in contact with ALA 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLY* 2.9 12.4 + - - -
69H PHE 4.2 5.2 - - - +
70H ILE* 3.5 24.1 - - + -
71H ASN* 2.9 24.4 + - - +
195H VAL* 4.0 6.1 - - + -
196H ASP 3.3 5.6 - - - +
197H ARG* 3.6 16.8 - - + -
215H GLU* 3.8 14.6 - - + +
216H VAL* 1.3 76.6 - - - +
218H VAL* 1.3 64.7 + - - +
219H ALA 4.3 0.2 - - - -
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Residues in contact with VAL 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G LEU* 4.1 24.9 - - + -
36H GLU 5.2 2.5 - - - +
71H ASN* 3.6 32.3 - - + +
73H THR* 5.2 3.6 - - - +
194H TYR 4.2 0.2 - - - +
195H VAL* 3.5 3.3 - - - +
196H ASP* 3.1 35.5 + - + +
216H VAL* 4.6 9.9 - - + -
217H ALA* 1.3 78.2 - - - +
219H ALA* 1.3 72.2 + - - +
220H ARG* 4.0 1.6 + - + +
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ILE* 3.9 2.6 - - + +
71H ASN 2.8 17.6 + - - +
72H HIS* 3.8 22.0 - - + +
73H THR* 5.2 2.4 + - - -
74H GLN* 5.2 4.3 - - - +
76H ILE* 3.7 8.8 - - + +
193H TYR* 3.8 16.6 - - + -
194H TYR 3.2 7.2 - - - +
195H VAL* 3.8 19.1 - - + -
218H VAL* 1.3 85.0 - - - +
220H ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G THR* 3.1 12.5 + - - -
196G ASP* 3.0 32.4 + - - +
220G ARG* 3.0 15.3 - - - +
74H GLN* 4.3 8.3 - - - +
76H ILE* 3.4 9.6 - - - +
144H THR* 3.8 6.7 - - - +
193H TYR* 3.7 0.6 - - - +
194H TYR* 2.8 53.1 + - + +
196H ASP* 2.6 31.7 + - - +
218H VAL* 5.0 1.6 - - + +
219H ALA* 1.3 77.5 - - - +
221H TYR* 1.3 64.8 + - - +
222H CYS* 4.5 8.3 - - - +
223H ASP* 3.4 33.6 + - - +
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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