Contacts of the helix formed by residues 306 - 312 (chain B) in PDB entry 2J2M
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 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A PRO* 2.9 23.7 + - + +
154A ARG 4.3 9.9 - - - +
155A THR 5.3 0.2 - - - -
156A ASN* 3.7 44.2 + - + +
57B ALA 4.9 1.7 + - - -
58B ARG* 5.9 0.2 - - - -
59B GLY* 2.6 35.7 + - - -
60B PHE* 4.6 8.5 - + + -
61B GLY 4.9 0.7 - - - -
93B ARG* 4.6 2.6 + - - -
101B THR* 5.8 0.5 + - - -
243B SER* 5.9 0.7 - - - -
303B VAL* 3.8 11.7 - - + +
305B ASN* 1.3 69.2 - - - +
307B PHE* 1.3 68.0 + + - +
310B THR* 2.9 36.1 + - + +
311B GLU* 2.8 50.4 + - + -
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Residues in contact with PHE 307 (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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153A PRO 4.5 0.8 + - - -
48B GLU 4.0 17.5 - - - -
49B ARG* 5.6 0.2 - - - -
50B VAL* 3.8 33.9 - - + -
305B ASN* 3.3 6.7 + - - +
306B TYR* 1.3 82.4 - - - +
308B ALA* 1.3 58.8 + - - +
311B GLU* 3.3 21.6 - - + +
312B SER* 3.0 38.8 + - - -
369D ASP* 3.2 41.5 - - - +
370D GLY 3.4 26.5 - - - -
373D PRO* 3.4 18.2 - - + -
376D GLN* 3.6 9.6 - - - -
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Residues in contact with ALA 308 (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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305B ASN* 2.9 22.4 + - + +
307B PHE* 1.3 79.6 - - - +
309B GLU* 1.3 63.6 + - + +
312B SER* 3.7 10.8 - - - -
354B LEU* 5.8 0.7 - - - +
355B PRO* 6.1 0.5 - - - +
356B ILE* 3.4 23.0 + - - +
373D PRO* 4.6 10.1 - - + +
376D GLN* 4.0 24.2 - - + +
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Residues in contact with GLU 309 (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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63B HIS* 2.5 36.1 + - - -
91B PHE* 3.9 6.1 - - + -
303B VAL* 3.4 21.0 - - + +
304B ASP* 2.9 31.2 + - - +
305B ASN* 3.0 20.9 + - - +
307B PHE 3.2 0.4 - - - -
308B ALA* 1.3 86.0 - - + +
310B THR* 1.3 62.9 + - - +
311B GLU 3.4 0.2 - - - -
312B SER 3.5 0.2 + - - -
313B VAL* 3.0 35.2 + - - +
356B ILE* 3.6 21.8 - - + +
378D THR* 6.0 0.2 - - - +
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Residues in contact with THR 310 (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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53B ARG* 2.9 23.4 + - - -
60B PHE 3.7 2.7 - - - -
61B GLY* 3.2 33.6 + - - +
91B PHE* 3.7 8.9 - - - -
93B ARG* 3.5 21.0 + - - +
303B VAL* 3.5 22.3 - - - +
306B TYR* 2.9 41.6 + - + +
309B GLU* 1.3 73.8 - - - +
311B GLU* 1.3 58.3 + - - +
313B VAL* 3.4 4.9 - - - +
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Residues in contact with GLU 311 (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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50B VAL* 4.7 9.2 - - + +
51B PRO 4.3 3.3 - - - +
52B GLU* 4.2 21.4 - - - +
53B ARG* 2.8 28.6 + - - +
57B ALA* 4.6 9.8 - - - +
93B ARG* 4.7 1.0 + - - -
101B THR* 4.7 9.2 + - - -
306B TYR* 2.8 36.5 + - + +
307B PHE* 3.3 40.6 - - + +
310B THR* 1.3 73.4 - - - +
312B SER* 1.3 54.2 + - - +
346B ARG* 2.8 35.0 + - - +
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Residues in contact with SER 312 (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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307B PHE* 3.0 29.1 + - - -
308B ALA* 3.7 17.2 - - - -
309B GLU 3.5 0.8 + - - -
310B THR 3.4 0.2 - - - -
311B GLU* 1.3 73.6 - - - +
313B VAL* 1.3 64.5 + - - +
314B GLY 3.5 0.3 + - - -
346B ARG* 4.6 2.5 - - - +
347B ILE* 3.5 18.3 - - - +
354B LEU* 4.1 18.1 - - - +
356B ILE* 3.9 3.4 - - - -
357B ASN* 3.0 20.6 + - - -
373D PRO* 4.2 15.2 - - - +
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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