Contacts of the helix formed by residues 4069 - 4076 (chain B) in PDB entry 6X34
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 SER4069 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4065B ASP 3.0 14.7 + - - -
4066B ILE* 2.8 26.6 + - - +
4067B VAL 4.4 2.3 - - - +
4068B GLY* 1.3 83.1 - - - +
4070B GLU* 1.3 63.9 + - - +
4071B ALA* 3.5 14.8 + - - +
4072B PHE 4.0 1.0 + - - -
4073B GLN* 3.6 19.1 + - - +
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Residues in contact with GLU4070 (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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4069B SER* 1.3 74.2 - - - +
4071B ALA* 1.3 57.7 + - - +
4072B PHE 3.5 0.2 - - - -
4073B GLN* 3.9 8.1 - - - -
4074B ASP* 3.1 31.1 + - + +
4730H TYR* 4.7 14.1 - - + -
4734H ARG* 4.1 22.9 - - - +
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Residues in contact with ALA4071 (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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4066B ILE* 5.3 6.1 - - + -
4069B SER* 3.2 12.1 + - - +
4070B GLU* 1.3 78.2 - - - +
4072B PHE* 1.3 63.8 + - - +
4074B ASP* 4.2 2.5 - - - +
4075B TYR* 3.2 23.4 + - - +
4090B LYS* 3.6 30.0 - - + +
4729H ILE 5.8 4.3 - - - +
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Residues in contact with PHE4072 (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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4066B ILE* 3.3 33.2 + - + +
4067B VAL* 4.5 9.2 - - + +
4069B SER 4.0 2.7 + - - +
4071B ALA* 1.3 76.5 - - - +
4073B GLN* 1.3 60.8 + - - +
4075B TYR* 4.0 5.7 - - - +
4076B VAL* 3.1 31.5 + - - +
4087B ASP* 6.2 3.4 - - - +
4090B LYS* 4.3 4.9 - - + +
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Residues in contact with GLN4073 (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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4067B VAL 5.5 2.6 + - - +
4069B SER 3.6 16.7 + - - +
4070B GLU* 4.1 8.1 - - - +
4071B ALA 3.3 0.6 - - - -
4072B PHE* 1.3 79.7 - - - +
4074B ASP* 1.3 59.2 + - - +
4076B VAL 2.9 22.2 - - - +
4077B THR* 3.9 6.2 + - - -
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Residues in contact with ASP4074 (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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4070B GLU* 3.1 19.9 + - + +
4071B ALA* 4.2 2.5 - - - +
4073B GLN* 1.3 74.6 - - - +
4075B TYR* 1.3 65.5 + - - +
4076B VAL 4.9 0.5 - - - -
4077B THR* 5.1 1.0 + - - -
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Residues in contact with TYR4075 (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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4071B ALA 3.2 19.5 + - - +
4072B PHE* 4.0 4.5 - - - +
4073B GLN 3.3 0.4 - - - -
4074B ASP* 1.3 80.6 - - - +
4076B VAL* 1.3 60.1 + - + +
4077B THR 4.3 0.5 + - - -
4086B LYS* 6.4 0.4 - - - -
4087B ASP 5.9 5.4 - - - +
4089B GLN 3.3 25.8 - - - +
4090B LYS* 4.3 4.3 - - + -
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Residues in contact with VAL4076 (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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4072B PHE 3.1 15.1 + - - +
4073B GLN* 2.9 16.6 - - - +
4075B TYR* 1.3 77.0 - - + +
4077B THR* 1.3 63.6 + - - +
4078B ASP* 4.8 8.3 - - + +
4083B ILE* 5.8 3.6 - - + -
4084B SER 5.2 6.7 - - - +
4085B LYS 5.5 0.4 - - - +
4086B LYS* 3.7 32.3 - - + -
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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