Contacts of the helix formed by residues 234 - 244 (chain A) in PDB entry 3NAV
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 GLY 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.7 28.0 - - - +
64A ILE* 4.7 0.9 - - - -
211A GLY 4.8 4.0 + - - -
214A ILE 4.5 3.6 + - - +
232A ILE* 4.1 4.2 + - - +
233A SER* 1.3 76.0 + - - +
235A SER* 1.3 66.6 + - - +
236A ALA 3.0 3.1 + - - -
237A VAL 3.3 8.3 + - - -
238A VAL* 3.6 8.5 + - - +
601A EDO 4.0 22.2 - - - -
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 3.6 27.4 + - - +
64A ILE* 4.5 13.2 + - - +
234A GLY* 1.3 73.5 - - - +
236A ALA* 1.3 59.7 + - - +
238A VAL* 3.2 3.1 + - - -
239A LYS* 2.8 31.6 + - - +
601A EDO 5.1 2.3 + - - -
60B ASP* 5.7 0.7 + - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE 4.2 1.7 + - - +
215A SER* 3.8 28.9 - - - +
233A SER* 3.6 16.3 + - - +
234A GLY 3.0 2.4 + - - -
235A SER* 1.3 80.2 - - - +
237A VAL* 1.3 62.5 + - - +
239A LYS* 3.7 8.1 + - - +
240A ILE* 3.5 25.3 + - - +
258A PHE* 3.8 17.3 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.7 1.6 - - + -
21A PRO* 3.6 24.5 - - + -
22A PHE 3.6 8.7 - - - +
23A VAL* 3.7 22.4 - - + -
40A LEU* 4.0 12.8 - - + -
233A SER* 4.0 15.9 + - - +
234A GLY 3.3 1.2 + - - +
235A SER 3.3 0.6 - - - -
236A ALA* 1.3 76.2 - - - +
238A VAL* 1.4 65.9 + - - +
240A ILE* 3.1 23.7 + - - +
241A ILE* 3.4 5.1 + - - +
255A LEU* 3.3 27.8 - - + +
258A PHE* 3.8 22.2 - - + -
259A THR* 5.6 0.2 - - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.7 35.0 - - + +
23A VAL* 4.1 10.5 - - + -
24A THR 4.5 3.8 - - - +
27A ASP* 4.0 4.0 - - - +
63A THR* 3.5 24.0 - - + +
64A ILE* 4.4 6.1 - - + -
67A ALA* 3.6 27.8 - - + -
70A ARG* 3.9 9.2 - - - +
234A GLY 3.6 7.4 + - - +
235A SER 3.2 3.5 + - - +
237A VAL* 1.4 75.8 - - - +
239A LYS* 1.3 63.2 + - - +
241A ILE* 3.1 13.8 + - + +
242A GLU* 3.0 17.7 + - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 3.6 19.3 + - + +
235A SER 2.8 20.6 + - - +
236A ALA* 3.7 10.1 - - - +
238A VAL* 1.3 73.2 - - - +
240A ILE* 1.3 58.7 + - + +
242A GLU* 3.1 29.1 + - - +
243A THR* 2.9 42.9 + - - +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 3.5 11.4 - - - +
237A VAL* 3.1 8.0 + - - +
239A LYS* 1.3 76.9 - - + +
241A ILE* 1.3 65.3 + - - +
243A THR* 3.3 6.2 + - - -
244A HIS* 3.2 28.7 + - + +
251A GLN* 4.1 4.0 - - - +
254A GLU* 3.7 31.9 - - + +
255A LEU* 3.9 26.0 - - + +
258A PHE* 3.4 48.2 - - + -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.2 25.8 - - + -
27A ASP* 4.0 28.7 - - + +
28A PRO* 4.0 23.1 - - + -
36A ILE* 3.7 26.2 - - + -
70A ARG* 4.4 1.6 - - - +
237A VAL 3.9 12.6 - - - +
238A VAL* 3.1 11.6 + - + +
240A ILE* 1.3 80.9 - - - +
242A GLU* 1.3 62.5 + - - +
244A HIS 3.4 2.4 + - - -
245A LEU* 3.2 22.8 + - + +
251A GLN* 3.8 18.2 + - - +
255A LEU* 4.1 12.8 - - + -
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 4.1 18.7 + - - +
66A GLY* 5.7 2.1 - - - -
70A ARG* 3.6 30.7 + - - +
238A VAL 3.0 11.6 + - - +
239A LYS* 3.1 36.6 + - + +
241A ILE* 1.3 77.5 - - - +
243A THR* 1.3 61.1 + - - +
244A HIS 3.4 0.7 + - - -
245A LEU* 3.5 27.2 + - + +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LYS* 2.9 32.2 + - - +
240A ILE* 3.3 7.5 + - - -
242A GLU* 1.3 76.6 - - - +
244A HIS* 1.3 82.8 + - + +
245A LEU 3.6 1.0 + - - -
246A ASP* 4.3 4.5 - - - +
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Residues in contact with HIS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 3.2 33.7 + - + +
241A ILE 3.6 0.4 - - - -
243A THR* 1.3 98.5 + - + +
245A LEU* 1.3 63.6 + - - +
246A ASP* 3.1 11.9 + - - +
247A ASN* 3.0 14.7 + - + +
250A LYS* 3.9 33.5 - - + +
251A GLN* 2.8 42.4 + - + +
254A GLU* 3.7 20.0 + - + +
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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