Contacts of the helix formed by residues 290 - 297 (chain B) in PDB entry 2VDY
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 LEU 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.2 20.9 - - + -
32B LEU* 4.4 16.6 - - + -
48B ILE* 4.0 21.5 - - + -
288B TYR* 3.9 28.0 - - + +
289B ASP* 1.3 72.2 - - - +
291B GLY* 1.3 57.1 + - - +
292B ASP 3.3 0.7 - - - -
293B VAL* 3.0 6.7 + - + -
294B LEU* 2.7 45.7 + - + +
323B VAL* 2.9 34.9 + - + +
325B HIS* 3.9 22.4 - - + -
342B MET* 4.0 12.1 - - - -
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Residues in contact with GLY 291 (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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289B ASP* 3.3 12.8 + - - -
290B LEU* 1.3 75.6 - - - +
292B ASP* 1.3 63.3 + - - +
294B LEU* 3.6 2.8 + - - +
295B GLU* 3.2 30.4 + - - +
303B PHE* 3.8 24.2 - - - -
323B VAL* 4.0 8.3 + - - +
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Residues in contact with ASP 292 (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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35B LEU* 6.0 3.1 - - + -
289B ASP* 4.5 7.5 + - - +
290B LEU 3.3 0.6 - - - -
291B GLY* 1.3 74.7 - - - +
293B VAL* 1.3 63.6 + - + +
295B GLU* 3.3 16.3 + - - +
296B GLU* 3.0 37.5 + - + +
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Residues in contact with VAL 293 (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 LEU* 3.9 25.4 - - + -
31B HIS* 3.8 27.1 - - + -
32B LEU* 3.8 22.4 - - + -
35B LEU* 3.8 25.4 - - + -
289B ASP 4.2 12.8 - - - +
290B LEU* 3.0 12.5 + - + +
292B ASP* 1.3 78.1 - - + +
294B LEU* 1.3 61.3 + - - +
296B GLU* 3.2 19.8 + - - +
297B MET* 3.2 16.7 + - - +
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Residues in contact with LEU 294 (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 PHE* 4.4 13.9 - - + -
28B LEU* 4.8 9.0 - - + -
48B ILE* 5.0 2.7 - - + -
52B LEU* 3.8 32.8 - - + -
290B LEU* 2.7 31.1 + - + +
291B GLY 3.8 4.0 - - - +
293B VAL* 1.3 72.7 - - - +
295B GLU* 1.3 58.7 + - - +
297B MET* 3.2 13.4 + - - +
298B GLY 3.4 0.2 + - - -
299B ILE* 2.9 50.7 + - + +
302B LEU* 5.5 2.9 - - + -
303B PHE* 4.0 19.3 - - + -
323B VAL* 4.0 28.9 - - + -
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Residues in contact with GLU 295 (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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291B GLY 3.2 18.3 + - - +
292B ASP* 3.6 19.0 - - - +
294B LEU* 1.3 75.8 - - - +
296B GLU* 1.3 60.6 + - - +
298B GLY* 3.3 12.5 + - - -
299B ILE 3.3 17.8 + - - +
300B ALA* 4.1 17.4 - - + +
303B PHE* 3.5 29.8 - - + +
304B THR* 5.9 1.2 - - - +
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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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31B HIS* 4.0 32.4 + - + +
35B LEU* 4.2 25.2 - - - +
292B ASP* 3.0 16.5 + - + +
293B VAL* 3.2 20.0 + - - +
295B GLU* 1.3 75.8 - - - +
297B MET* 1.3 58.6 + - - +
298B GLY 3.3 1.5 + - - -
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Residues in contact with MET 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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24B PHE* 3.7 34.1 - - + -
27B SER* 3.5 23.1 - - - +
28B LEU* 3.6 41.5 - - - +
31B HIS* 3.7 24.7 - - + +
70B GLY* 4.7 15.9 - - - +
293B VAL* 3.2 17.6 + - - +
294B LEU* 3.2 11.6 + - - +
295B GLU 3.2 1.0 - - - -
296B GLU* 1.3 75.8 - - - +
298B GLY* 1.3 59.7 + - - +
299B ILE* 3.6 7.0 - - + -
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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