Contacts of the helix formed by residues 295 - 306 (chain B) in PDB entry 2OB1
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 PRO 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.1 12.6 - - + -
293B GLN 3.2 12.1 - - - +
294B ILE* 1.3 89.6 - - - +
296B GLU* 1.3 67.0 + - - +
297B SER* 3.9 17.0 - - - +
298B GLU* 3.0 30.7 + - + -
299B ARG* 3.1 9.4 + - - -
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Residues in contact with GLU 296 (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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294B ILE 3.9 0.2 + - - -
295B PRO* 1.3 73.7 - - - +
297B SER* 1.3 57.3 + - - +
299B ARG* 3.0 22.5 + - - +
300B LYS* 2.8 33.1 + - + +
303B ARG* 2.7 32.1 + - - -
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Residues in contact with SER 297 (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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97A GLU* 3.8 22.5 + - - +
295B PRO* 3.2 15.8 - - - +
296B GLU* 1.3 77.3 - - - +
298B GLU* 1.3 61.4 + - - +
300B LYS* 3.6 8.3 - - - +
301B ARG* 2.9 27.2 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 4.3 15.7 - - - +
27B SER* 2.6 25.4 + - - -
29B GLY* 5.7 1.7 + - - -
30B LEU* 4.1 6.3 - - + -
79B TYR* 2.6 30.4 + - - +
294B ILE* 3.5 7.4 - - + -
295B PRO* 3.0 29.2 + - + +
297B SER* 1.3 81.9 + - - +
299B ARG* 1.3 60.5 + - - +
301B ARG* 2.9 38.6 + - - +
302B LEU* 2.8 34.6 + - - +
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Residues in contact with ARG 299 (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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76B TYR* 4.6 2.7 + - + -
290B PHE* 2.6 60.9 + - + -
291B ASN* 3.2 29.9 + - - +
294B ILE* 3.0 29.3 + - + -
295B PRO 3.1 6.8 + - - +
296B GLU* 3.0 26.2 + - - +
298B GLU* 1.3 78.8 - - - +
300B LYS* 1.3 62.5 + - - +
302B LEU* 3.3 6.8 + - - +
303B ARG* 3.0 44.6 + - - +
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Residues in contact with LYS 300 (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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296B GLU* 2.8 19.0 + - + +
297B SER* 3.6 8.3 - - - +
299B ARG* 1.3 77.7 - - - +
301B ARG* 1.3 63.2 + - - +
303B ARG* 3.2 27.3 + - + +
304B SER* 3.1 22.6 + - - -
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Residues in contact with ARG 301 (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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121A HIS* 6.3 0.4 - - - -
23B GLY 2.9 25.5 + - - -
24B TYR 2.7 23.4 + - - -
26B PRO 3.9 7.7 + - - -
27B SER* 3.7 10.7 - - - +
79B TYR* 3.8 0.4 - - - -
297B SER 2.9 18.2 + - - +
298B GLU* 2.9 43.8 + - - +
300B LYS* 1.3 74.9 - - - +
302B LEU* 1.3 75.8 + - - +
304B SER* 2.9 26.3 + - - +
305B LEU* 3.3 21.4 + - + +
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Residues in contact with LEU 302 (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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24B TYR* 3.6 32.2 - - + -
76B TYR* 3.4 39.9 - - + +
79B TYR* 3.7 38.6 - - + -
290B PHE* 5.9 0.4 - - + -
294B ILE* 5.6 1.1 - - + -
298B GLU 2.8 26.7 + - - +
299B ARG* 3.7 3.6 - - - +
301B ARG* 1.3 103.8 - - - +
303B ARG* 1.3 62.3 + - - +
305B LEU* 3.0 2.6 + - + -
306B GLN 3.0 26.5 + - - +
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Residues in contact with ARG 303 (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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76B TYR* 4.0 8.0 + - - +
296B GLU* 2.7 29.3 + - - -
299B ARG* 3.0 28.9 + - - +
300B LYS* 3.3 33.5 - - + +
302B LEU* 1.3 75.4 - - - +
304B SER* 1.3 61.1 + - - +
305B LEU 3.5 0.3 + - - -
306B GLN 4.3 4.7 - - - -
307B PHE* 3.6 55.6 + - + +
308B LEU* 5.8 1.6 - - + +
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Residues in contact with SER 304 (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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300B LYS* 3.1 9.9 + - - -
301B ARG* 2.9 20.2 + - - +
303B ARG* 1.3 80.3 - - - +
305B LEU* 1.3 66.8 + - - +
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Residues in contact with LEU 305 (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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22B VAL* 3.4 24.3 - - - +
23B GLY* 3.3 36.6 - - - +
24B TYR* 3.8 13.9 - - + +
301B ARG* 3.4 35.0 - - + +
302B LEU* 3.0 5.8 + - - +
304B SER* 1.3 85.3 - - - +
306B GLN* 1.3 63.6 + - - +
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Residues in contact with GLN 306 (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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22B VAL* 3.6 25.2 - - + +
24B TYR* 2.8 33.1 + - + +
70B SER* 5.1 4.2 + - - -
71B PHE* 4.7 2.6 - - - +
72B PRO* 3.3 39.3 - - + +
75B ASN* 3.0 27.6 + - - +
76B TYR* 4.2 1.9 - - - -
302B LEU 3.0 13.1 + - - +
303B ARG* 3.9 0.8 - - - -
304B SER 3.6 0.4 - - - -
305B LEU* 1.3 80.6 - - - +
307B PHE* 1.3 65.0 + - - +
308B LEU 3.5 1.9 + - - -
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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