Contacts of the strand formed by residues 210 - 220 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C ARG* 3.4 41.2 - - + +
43C ILE 3.3 13.5 - - - -
44C LYS* 4.1 26.9 - - + -
203C LYS* 5.3 6.3 - - + -
204C GLU* 3.3 5.8 - - - +
205C ALA* 3.1 54.4 + - + +
206C ASP* 5.4 2.5 - - + +
208C GLU 3.9 0.7 - - - -
209C THR* 1.3 79.2 + - - +
211C VAL* 1.3 72.7 + - - +
212C GLU* 4.4 15.9 - - + +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C MET 3.6 1.4 - - - +
42C ARG* 3.6 0.5 - - - -
43C ILE* 2.6 46.9 + - + +
55C PHE* 3.9 40.6 - - + -
201C ARG* 3.7 33.7 - - - +
203C LYS 3.6 4.3 - - - -
204C GLU* 4.6 1.1 - - + -
208C GLU* 3.6 21.3 - - - +
210C TYR* 1.3 85.4 - - - +
212C GLU* 1.3 66.6 + - - +
213C GLN* 4.2 11.0 - - + +
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 4.2 14.5 - - + +
41C MET 3.3 5.8 - - - +
42C ARG* 3.6 39.4 + - + +
201C ARG* 3.9 0.9 - - - -
202C ILE* 3.0 54.2 + - - +
203C LYS* 2.8 31.7 + - + +
210C TYR* 4.4 8.7 + - + +
211C VAL* 1.3 73.3 - - - +
213C GLN* 1.3 59.5 + - - +
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Residues in contact with GLN 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 3.6 2.9 - - - +
41C MET 3.0 32.3 + - - +
43C ILE* 3.8 18.9 - - + +
55C PHE* 4.2 10.0 - - - -
59C ALA* 3.3 40.9 + - - +
62C PHE* 3.3 25.8 - - - +
63C NRQ 3.5 22.9 - - + +
199C LEU* 3.9 12.9 - - + +
200C GLU 3.3 12.3 - - - +
201C ARG* 4.5 6.0 + - + -
202C ILE* 4.4 1.3 - - - -
211C VAL* 3.9 8.4 - - + +
212C GLU* 1.3 74.3 - - - +
214C HIS* 1.3 60.1 + - - +
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Residues in contact with HIS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 4.0 21.2 - - + +
39C GLN 3.0 22.1 + - - -
40C THR* 3.2 15.0 + - - +
63C NRQ 4.4 2.2 - - - -
198C ARG 5.2 0.9 - - - -
199C LEU* 3.3 3.1 - - - +
200C GLU* 2.5 53.6 + - - +
202C ILE* 3.6 24.2 - - + +
213C GLN* 1.3 75.3 - - - +
215C GLU* 1.3 74.9 + - - +
216C VAL* 4.1 11.0 + - + +
225D PRO 5.8 1.5 + - - -
227D LYS* 4.1 38.2 + - + +
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY 3.8 0.3 - - - +
38C THR* 3.4 2.3 - - - -
39C GLN* 3.0 61.7 + - + +
63C NRQ 3.5 57.3 + - + +
66C SER 4.6 1.5 - - - +
70C ILE* 5.6 1.6 - - - +
197C ARG* 3.7 14.0 - - + -
198C ARG 3.1 18.4 - - - +
199C LEU* 4.1 7.6 - - + -
214C HIS* 1.3 81.2 + - - +
216C VAL* 1.3 65.3 + - - +
217C ALA* 3.8 13.7 - - - +
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU 4.9 2.2 - - - +
37C GLY 3.1 11.7 - - - +
38C THR* 3.7 20.0 - - + -
197C ARG* 3.2 4.2 - - - +
198C ARG* 2.9 44.9 + - + +
214C HIS* 4.1 9.2 + - + +
215C GLU* 1.3 74.0 - - - +
217C ALA* 1.3 65.7 + - - +
218C VAL* 4.3 16.6 - - + -
224D LEU* 3.7 30.3 - - + -
225D PRO* 3.9 25.4 - - + +
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY* 2.7 16.4 + - - -
69C PHE 4.1 7.4 - - - +
70C ILE* 3.9 24.2 - - + -
71C ASN* 2.9 24.5 + - - +
195C VAL* 4.2 4.7 - - + -
196C ASP 3.6 5.6 - - - -
197C ARG* 3.8 13.5 - - + -
215C GLU* 3.8 14.1 - - - +
216C VAL* 1.3 78.0 - - - +
218C VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU 4.8 2.7 - - - +
71C ASN* 3.7 14.8 - - + +
73C THR* 3.8 27.1 - - + -
194C TYR 3.9 0.3 - - - +
195C VAL* 4.4 3.1 - - - +
196C ASP* 3.0 36.2 + - + +
216C VAL* 4.3 11.0 - - + -
217C ALA* 1.3 77.8 - - - +
219C ALA* 1.3 66.1 + - - +
220C ARG* 4.1 2.8 + - + +
224D LEU* 3.5 29.2 - - + -
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ILE* 4.0 8.9 - - + +
71C ASN 2.8 18.8 + - - +
72C HIS* 4.1 5.2 - - + -
73C THR* 2.9 23.6 + - - -
76C ILE* 3.4 12.1 - - + +
193C TYR* 3.7 26.9 - - + -
194C TYR 3.2 10.1 - - - +
195C VAL* 3.9 8.7 - - + +
218C VAL* 1.3 76.0 - - - +
220C ARG* 1.3 62.9 + - - +
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Residues in contact with ARG 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C THR* 5.2 0.9 - - - +
74C GLN* 3.6 10.5 - - + +
76C ILE* 3.7 9.4 - - - -
144C THR* 3.6 13.1 - - - +
193C TYR* 3.4 4.3 - - - +
194C TYR* 2.9 58.0 + - - +
196C ASP* 2.4 44.1 + - - +
218C VAL* 5.0 3.1 - - + +
219C ALA* 1.3 75.5 - - - +
221C TYR* 1.3 67.4 + - - +
222C CYS* 5.0 2.6 - - - +
223C ASP* 3.5 32.8 + - - +
144D THR* 3.7 2.8 + - - -
196D ASP* 3.6 15.1 + - - -
220D ARG* 3.1 20.9 - - - +
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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