Contacts of the helix formed by residues 305 - 311 (chain B) in PDB entry 3NNJ
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 ILE 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 4.2 5.2 - - + -
288B MSE 4.0 14.6 - - - -
289B VAL* 3.9 26.5 - - + -
292B ALA* 4.0 23.6 - - + -
297B LEU* 4.3 14.1 - - + -
301B TYR 3.8 3.1 + - - +
302B LEU* 3.0 45.3 + - + +
304B ASP* 1.3 75.6 - - - +
306B PRO* 1.3 76.4 - - + +
307B HIS* 3.8 9.4 - - + +
308B VAL* 2.8 28.2 + - + -
309B GLN 2.9 9.7 + - - -
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Residues in contact with PRO 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 5.0 8.3 - - + -
295B LYS* 6.4 2.2 - - + -
297B LEU* 5.1 6.3 - - + -
298B LYS* 6.0 3.4 - - - +
304B ASP 3.3 8.7 - - - +
305B ILE* 1.3 87.5 - - + +
307B HIS* 1.3 56.8 + - - +
309B GLN* 3.5 6.3 + - + +
310B GLN* 2.9 47.0 + - + +
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Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.6 36.6 - - + +
71B VAL* 4.5 14.9 - - + +
288B MSE 4.0 24.7 - - + +
305B ILE* 3.3 4.5 - - + +
306B PRO* 1.3 78.7 - - - +
308B VAL* 1.3 59.0 + - - +
310B GLN* 3.8 16.3 + - - +
311B THR* 2.9 30.5 + - + +
315B ARG* 3.5 20.5 + - - -
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MSE 4.4 0.9 - - - -
98B MSE 3.7 33.7 - - + -
288B MSE 4.1 21.1 - - + -
289B VAL* 6.2 0.2 - - + -
302B LEU* 3.4 27.6 - - + +
303B ARG* 4.1 10.8 - - - -
305B ILE* 2.8 25.2 + - + +
307B HIS* 1.3 71.1 - - - +
309B GLN* 1.3 65.6 + - - +
311B THR* 3.0 16.1 + - - -
312B LEU* 3.1 15.5 + - + -
315B ARG* 3.3 21.2 + - - +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ARG* 2.8 26.7 + - - +
304B ASP* 4.1 13.4 - - - +
305B ILE 2.9 14.1 + - - +
306B PRO* 3.7 7.2 - - + +
308B VAL* 1.3 77.6 - - - +
310B GLN* 1.3 63.4 + - + +
312B LEU* 3.3 38.9 + - - +
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Residues in contact with GLN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO* 2.9 40.1 + - - +
307B HIS* 4.0 17.7 - - - +
308B VAL 3.2 0.4 - - - -
309B GLN* 1.3 78.0 - - + +
311B THR* 1.3 65.3 + - + +
312B LEU 3.4 1.0 + - - -
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Residues in contact with THR 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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74B ASP* 6.0 2.5 - - - +
307B HIS* 2.9 19.8 + - + +
308B VAL 3.0 1.7 + - - -
310B GLN* 1.3 81.4 - - + +
312B LEU* 1.3 65.5 + - - +
313B ALA 3.5 1.8 - - - -
314B ALA* 3.1 21.8 + - + +
315B ARG* 2.6 48.9 + - - +
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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
------------------------------------------------------------
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