Contacts of the helix formed by residues 3969 - 3978 (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 THR3969 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3968B CYS* 1.3 80.4 - - - +
3970B GLY* 1.3 76.1 + - - +
3971B ASN 3.2 2.1 + - - -
3972B GLN* 3.5 1.8 + - - +
3973B GLN* 2.7 36.9 + - - +
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Residues in contact with GLY3970 (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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3896B ASN* 6.4 0.9 - - - -
3899B ARG* 4.4 20.2 - - - +
3969B THR* 1.3 83.9 + - - +
3971B ASN* 1.3 64.9 + - - +
3973B GLN* 4.4 2.7 - - - +
3974B SER* 3.3 27.7 + - - -
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Residues in contact with ASN3971 (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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3895B GLN* 4.0 27.2 + - - +
3896B ASN* 5.3 1.0 - - - -
3898B LEU* 5.9 0.8 - - - +
3899B ARG* 5.3 3.6 - - - +
3911B ILE* 4.5 20.5 - - - +
3963B TYR* 3.1 49.6 + - + +
3964B ILE* 4.6 5.2 - - + +
3968B CYS* 3.6 22.3 - - - +
3969B THR 3.2 1.2 - - - +
3970B GLY* 1.3 79.6 + - - +
3972B GLN* 1.3 60.5 + - - +
3974B SER* 4.0 2.9 - - - -
3975B LEU* 3.2 31.4 + - - +
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Residues in contact with GLN3972 (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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3964B ILE* 5.2 6.5 - - + -
3967B PRO* 5.2 2.3 - - - +
3968B CYS* 3.2 40.9 + - - +
3969B THR* 3.5 2.1 + - - +
3970B GLY 3.4 0.2 - - - -
3971B ASN* 1.3 77.0 - - - +
3973B GLN* 1.3 74.5 + - - +
3975B LEU* 3.6 3.8 + - - +
3976B ALA* 3.1 24.9 + - - +
4024B SER 5.3 2.4 - - - +
4025B LEU* 4.0 29.0 + - + +
4028B GLY 4.9 7.4 + - - +
4029B ASN* 5.4 9.5 - - - +
4035B ILE* 4.8 27.1 - - + +
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Residues in contact with GLN3973 (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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3969B THR* 2.7 29.5 + - - +
3970B GLY* 4.8 2.5 - - - +
3971B ASN 3.5 0.2 - - - -
3972B GLN* 1.3 86.0 + - - +
3974B SER* 1.3 63.9 + - - +
3976B ALA* 4.6 3.6 - - - +
3977B HIS* 3.1 48.0 + - + +
4034B MET* 6.3 2.5 - - - -
4035B ILE* 4.9 19.6 - - + +
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Residues in contact with SER3974 (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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3899B ARG* 5.3 3.2 - - - +
3909B ASN* 4.4 16.1 + - - -
3911B ILE* 4.2 24.5 - - - +
3912B ILE* 6.1 2.7 - - - -
3970B GLY 3.3 21.3 + - - -
3971B ASN 4.2 1.8 - - - -
3972B GLN 3.3 0.2 - - - -
3973B GLN* 1.3 77.9 - - - +
3975B LEU* 1.3 63.5 + - - +
3977B HIS* 3.6 4.3 + - - +
3978B SER* 3.1 24.9 + - - -
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Residues in contact with LEU3975 (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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3911B ILE* 5.1 7.1 - - + +
3915B VAL* 5.2 3.1 - - + -
3960B LEU* 4.1 38.6 - - + +
3963B TYR* 6.5 0.4 - - + -
3964B ILE* 5.5 7.6 - - + -
3971B ASN 3.2 21.2 + - - +
3972B GLN* 4.1 3.1 - - - +
3974B SER* 1.3 76.3 - - - +
3976B ALA* 1.3 62.0 + - - +
3978B SER* 2.8 20.9 + - - +
3980B LEU* 3.7 27.6 - - + +
3981B TRP 5.0 1.1 + - - +
4025B LEU* 3.7 29.2 - - + -
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Residues in contact with ALA3976 (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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3972B GLN 3.1 18.2 + - - +
3973B GLN* 4.1 5.4 - - - +
3974B SER 3.3 0.2 - - - -
3975B LEU* 1.3 81.6 - - - +
3977B HIS* 1.3 68.1 + - + +
3978B SER 3.5 6.8 + - - +
3981B TRP* 5.9 2.6 - - - +
4025B LEU* 6.2 3.1 - - + -
4035B ILE* 5.3 13.2 - - + -
4038B GLN* 4.6 27.1 - - + +
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Residues in contact with HIS3977 (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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3973B GLN* 3.1 35.1 + - + +
3974B SER* 3.6 4.0 + - - +
3976B ALA* 1.3 81.9 - - + +
3978B SER* 1.3 64.6 + - - +
4034B MET* 5.7 10.8 - - + -
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Residues in contact with SER3978 (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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3911B ILE* 6.2 0.7 - - - -
3912B ILE* 6.0 2.5 - - - -
3915B VAL* 3.7 28.2 - - - +
3974B SER 3.1 13.4 + - - -
3975B LEU* 2.8 27.3 + - - +
3976B ALA 3.3 8.3 - - - +
3977B HIS* 1.3 83.1 - - - +
3979B ARG* 1.3 60.5 + - - +
3980B LEU* 3.3 11.3 + - - +
3981B TRP* 4.7 3.1 + - - +
3982B ASP 5.5 0.2 + - - -
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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