Contacts of the helix formed by residues 4275 - 4286 (chain B) in PDB entry 6W4H
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 ASP4275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4273B ALA 3.4 6.7 + - - +
4274B VAL* 1.3 72.7 - - - +
4276B ALA* 1.3 61.1 + - - +
4277B ALA* 3.6 9.9 + - - +
4278B LYS* 3.1 42.1 + - + +
4279B ALA* 3.1 21.9 + - - +
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Residues in contact with ALA4276 (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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4274B VAL* 3.6 13.2 + - + +
4275B ASP* 1.3 71.1 - - - +
4277B ALA* 1.3 60.8 + - - +
4279B ALA* 3.2 8.5 + - - +
4280B TYR* 2.9 32.6 + - - +
4328B LEU* 3.6 14.2 - - + +
4329B TYR* 4.5 4.2 - - + -
4332B CYS* 5.7 2.2 - - + -
4334B ILE* 3.1 36.8 - - + -
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Residues in contact with ALA4277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4275B ASP* 3.3 8.9 + - - +
4276B ALA* 1.3 79.0 - - - +
4278B LYS* 1.3 62.5 + - - +
4280B TYR* 3.3 2.6 + - - +
4281B LYS* 3.1 40.8 + - - +
4328B LEU* 3.7 11.9 - - - +
4329B TYR* 3.7 21.7 + - - +
4365B LEU* 4.5 12.4 - - + +
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Residues in contact with LYS4278 (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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4275B ASP* 3.1 33.4 + - + +
4277B ALA* 1.3 77.3 - - - +
4279B ALA* 1.3 58.0 + - - +
4281B LYS* 3.3 10.3 + - - +
4282B ASP* 2.9 59.7 + - - +
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Residues in contact with ALA4279 (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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4274B VAL* 6.5 0.2 - - + -
4275B ASP 3.1 14.8 + - - +
4276B ALA* 3.2 12.8 + - - +
4278B LYS* 1.3 78.0 - - - +
4280B TYR* 1.3 57.5 + - - +
4282B ASP* 3.6 6.4 + - - +
4283B TYR* 3.0 27.9 + - - +
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Residues in contact with TYR4280 (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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4276B ALA 2.9 16.0 + - - +
4277B ALA 3.9 3.6 - - - +
4279B ALA* 1.3 75.0 - - - +
4281B LYS* 1.3 61.4 + - + +
4283B TYR* 3.1 33.4 + + - +
4284B LEU* 2.9 49.7 + - + +
4290B PRO* 3.4 4.5 - - - +
4291B ILE* 3.0 46.5 + - + +
4328B LEU* 4.1 15.3 - - + -
4359B ASP* 2.7 20.8 + - - -
4361B VAL* 3.9 7.4 - - + -
4362B GLY* 3.6 20.4 - - - -
4365B LEU* 3.7 19.3 - - + -
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Residues in contact with LYS4281 (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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4277B ALA* 3.1 29.7 + - - +
4278B LYS* 3.3 8.0 + - - +
4280B TYR* 1.3 77.0 - - + +
4282B ASP* 1.3 59.8 + - - +
4284B LEU* 3.4 11.0 + - - +
4285B ALA* 3.0 27.9 + - - +
4365B LEU* 4.1 28.5 + - + -
4366B LYS* 4.3 36.3 - - + +
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Residues in contact with ASP4282 (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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4278B LYS* 2.9 55.0 + - - +
4279B ALA* 3.9 6.6 - - - +
4281B LYS* 1.3 75.6 - - - +
4283B TYR* 1.3 59.7 + - - +
4285B ALA* 3.3 9.1 + - - +
4286B SER* 3.0 32.9 + - - +
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Residues in contact with TYR4283 (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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4279B ALA 3.0 15.9 + - - +
4280B TYR* 3.3 35.4 - + - +
4282B ASP* 1.3 73.6 - - - +
4284B LEU* 1.3 67.1 + - + +
4286B SER* 3.2 14.2 + - - -
4287B GLY 3.5 0.2 + - - -
4288B GLY* 2.9 43.4 + - - -
4289B GLN* 2.7 40.9 + - - +
4291B ILE* 6.1 0.4 - - + -
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Residues in contact with LEU4284 (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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4280B TYR* 2.9 53.7 + - + +
4281B LYS* 3.7 6.5 - - - +
4282B ASP 3.4 0.2 - - - -
4283B TYR* 1.3 76.8 - - + +
4285B ALA* 1.3 57.6 + - - +
4287B GLY* 2.9 22.0 + - - -
4288B GLY 3.7 19.0 + - - +
4290B PRO* 4.1 13.5 - - + -
4359B ASP* 3.2 28.0 - - - +
4362B GLY* 4.4 0.9 - - - -
4366B LYS* 3.8 30.1 - - - +
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Residues in contact with ALA4285 (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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4281B LYS 3.0 15.0 + - - +
4282B ASP* 3.5 13.7 - - - +
4284B LEU* 1.3 75.4 - - - +
4286B SER* 1.3 57.2 + - - +
4287B GLY 3.1 3.6 + - - -
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Residues in contact with SER4286 (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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4282B ASP* 3.0 14.6 + - - +
4283B TYR* 3.6 11.2 - - - -
4284B LEU 3.1 0.6 - - - -
4285B ALA* 1.3 75.6 - - - +
4287B GLY* 1.3 58.3 + - - +
4288B GLY 3.5 1.5 + - - -
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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