Contacts of the helix formed by residues 210 - 217 (chain B) in PDB entry 1SBB
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 GLN 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLY* 3.2 31.4 + - - +
54A SER* 5.8 1.3 - - - -
23B ASN* 2.7 37.9 + - + +
26B VAL* 4.5 5.9 - - - +
27B LEU* 4.0 21.2 - - + +
89B TYR* 3.8 24.4 - - + +
90B TYR 4.9 2.1 + - - -
91B TYR* 5.1 10.7 + - + +
92B GLN* 5.4 0.4 + - - -
208B PHE* 3.5 20.9 + - + +
209B ASP* 1.3 69.7 + - - +
211B SER* 1.3 65.8 + - - +
213B TYR* 4.4 1.6 - - - -
214B LEU* 3.0 32.8 + - - +
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.3 43.0 + - - -
92B GLN* 4.1 20.1 + - - +
115B TYR* 3.3 33.3 + - - -
209B ASP* 3.0 10.5 + - - -
210B GLN* 1.3 81.8 - - - +
212B LYS* 1.3 59.5 - - - +
215B MET* 3.4 3.7 + - - +
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Residues in contact with LYS 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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203B ALA* 4.9 9.3 - - - +
209B ASP* 3.0 29.0 + - + +
211B SER* 1.3 73.9 - - - +
213B TYR* 1.3 67.6 + - - +
215B MET* 3.2 18.4 - - - +
216B MET 4.3 0.9 + - - -
137C ILE* 4.7 1.0 - - - +
139C ASN* 3.3 40.0 - - - +
140C LYS* 4.5 8.6 - - + +
141C GLN* 3.4 27.2 - - - +
142C LYS* 3.5 39.8 - - - +
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Residues in contact with TYR 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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12B HIS* 6.4 0.9 - + - -
24B MET* 3.6 19.7 - - + -
27B LEU* 4.1 7.4 - - + -
28B TYR* 3.4 21.8 - + - -
165B ARG* 2.7 34.0 + - - -
199B ASP* 2.8 20.5 + - + -
200B MET* 3.7 1.6 - - - -
201B MET 4.4 8.7 - - - -
202B PRO* 5.2 1.8 - - + -
208B PHE* 3.7 25.4 - + + -
209B ASP 3.0 16.5 + - - +
210B GLN* 3.8 3.6 - - - +
211B SER 3.4 0.2 - - - -
212B LYS* 1.3 75.1 - - - +
214B LEU* 1.3 78.0 + - + +
215B MET 3.0 5.6 + - - -
216B MET* 3.0 43.0 + - - +
217B TYR* 5.2 0.2 - - - -
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Residues in contact with LEU 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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27B LEU* 3.4 46.2 - - + -
28B TYR* 4.5 2.0 - - - +
87B ALA* 3.5 31.4 - - + +
89B TYR* 3.9 16.8 - - + -
115B TYR* 3.5 21.9 - - + +
210B GLN 3.0 24.4 + - - +
213B TYR* 1.3 87.0 - - + +
215B MET* 1.3 56.2 + - - +
216B MET 2.9 0.7 - - - -
217B TYR* 2.8 53.5 + - + +
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Residues in contact with MET 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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67B GLU* 4.2 8.1 - - - +
115B TYR* 3.3 43.1 - - + +
211B SER* 3.4 12.2 + - - +
212B LYS* 3.2 14.8 - - - +
213B TYR 3.0 0.8 + - - -
214B LEU* 1.3 76.0 - - - +
216B MET* 1.3 54.4 + - - +
217B TYR 2.9 2.9 + - - -
218B ASN* 2.9 43.1 - - - +
140C LYS* 3.7 24.6 - - + +
141C GLN* 2.8 45.3 - - + +
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Residues in contact with MET 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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69B LYS* 5.9 0.5 + - - -
165B ARG* 3.9 6.7 - - - +
198B TYR* 3.5 58.6 + - + -
199B ASP 5.1 2.5 - - - +
212B LYS 4.3 1.0 + - - +
213B TYR* 3.0 42.1 + - + +
214B LEU 2.8 3.0 + - - +
215B MET* 1.3 76.5 - - - +
217B TYR* 1.3 99.7 + - + +
218B ASN* 3.5 3.1 - - - +
219B ASP* 3.8 11.6 - - - +
140C LYS* 5.3 9.3 - - + +
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Residues in contact with TYR 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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28B TYR* 3.1 20.2 + - - -
87B ALA* 5.1 4.3 - - + -
115B TYR* 3.4 25.2 - - + +
116B GLY* 3.5 4.0 - - - -
117B GLY 4.6 0.5 + - - -
158B GLN* 3.2 57.7 + - + +
161B ASP* 2.9 26.8 + - - +
198B TYR* 4.3 11.7 - + - -
214B LEU* 2.8 44.5 + - + +
216B MET* 1.3 109.7 - - + +
218B ASN* 1.3 60.3 + - - +
219B ASP* 3.1 11.6 + - - +
220B ASN* 3.1 12.3 + - - -
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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