Contacts of the helix formed by residues 3891 - 3900 (chain D) 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 ASN3891 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3805D ALA* 5.4 10.5 - - + +
3808D GLN* 4.8 11.5 - - - +
3812D LEU* 5.9 1.0 - - - +
3886D LEU 4.2 8.2 + - - -
3887D CYS* 3.4 27.6 - - - +
3889D GLY* 3.2 8.7 + - - +
3890D HIS* 1.3 74.8 + - - +
3892D ASN* 1.3 61.9 + - - +
3893D ASP* 3.2 22.7 + - - +
3894D PHE* 3.4 19.3 - - - +
3895D GLN* 3.6 17.8 + - - +
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Residues in contact with ASN3892 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3890D HIS 3.7 4.1 + - - +
3891D ASN* 1.3 69.5 - - - +
3893D ASP* 1.3 56.2 + - - +
3894D PHE 3.2 2.5 - - - -
3895D GLN* 3.8 7.8 - - + +
3896D ASN* 2.5 38.9 + - - +
3967D PRO 4.7 14.8 - - - +
3968D CYS* 6.1 2.5 - - + -
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Residues in contact with ASP3893 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3812D LEU* 4.1 24.5 - - + +
3891D ASN* 3.2 27.4 + - - +
3892D ASN* 1.3 75.0 - - - +
3894D PHE* 1.3 64.3 + - - -
3896D ASN* 2.8 23.4 - - - +
3897D TYR* 4.3 4.3 + - - +
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Residues in contact with PHE3894 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3808D GLN* 4.8 9.9 - - + -
3811D MET* 5.0 9.0 - - + -
3812D LEU* 4.1 34.8 - - + -
3815D LEU* 5.2 8.1 - - + -
3824D PHE* 6.3 1.1 - + - -
3886D LEU* 3.6 43.7 - - + -
3887D CYS* 3.7 16.8 - - - -
3891D ASN* 3.4 22.6 + - - +
3892D ASN 3.2 0.2 - - - -
3893D ASP* 1.3 82.8 + - - +
3895D GLN* 1.3 63.4 + - - +
3896D ASN 3.3 1.8 - - - -
3897D TYR* 3.4 22.9 + + + +
3898D LEU* 3.6 35.6 - - + +
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Residues in contact with GLN3895 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3887D CYS* 3.8 14.9 - - - -
3891D ASN 3.6 18.4 + - - +
3892D ASN* 3.5 8.4 + - - +
3894D PHE* 1.3 79.5 - - - +
3896D ASN* 1.3 61.3 + - - +
3897D TYR 3.5 0.2 + - - -
3898D LEU* 3.5 15.2 + - - +
3899D ARG* 3.7 7.4 + - - +
3962D GLU 6.0 0.4 - - - +
3963D TYR* 4.8 11.0 - - + +
3968D CYS* 5.6 4.3 - - + -
3971D ASN* 4.0 28.0 + - - +
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Residues in contact with ASN3896 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3892D ASN* 2.5 27.8 + - - +
3893D ASP* 2.8 18.9 - - - +
3895D GLN* 1.3 76.6 - - - +
3897D TYR* 1.3 81.5 + - - +
3898D LEU 3.3 0.2 - - - -
3899D ARG* 3.4 7.7 + - - +
3900D THR* 3.2 22.0 + - - +
3970D GLY* 6.4 1.1 - - - -
3971D ASN* 5.3 0.9 - - - -
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Residues in contact with TYR3897 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3812D LEU* 5.6 5.8 - - + -
3815D LEU* 3.2 42.7 + - + +
3816D LYS* 3.4 42.6 - - + -
3819D LYS* 5.6 0.9 - - - -
3824D PHE* 3.5 35.5 - + - -
3893D ASP 4.4 3.8 - - - +
3894D PHE* 3.4 22.8 + + + +
3895D GLN 3.3 0.6 - - - -
3896D ASN* 1.3 88.2 + - - +
3898D LEU* 1.3 56.2 + - + +
3900D THR 3.0 9.8 - - - +
3901D GLN* 2.3 54.5 + - + +
3902D THR 5.5 0.2 - - - -
3903D GLY* 5.7 2.4 - - - -
3904D ASN* 5.4 5.9 + - - +
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Residues in contact with LEU3898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3824D PHE* 5.0 12.8 - - + -
3883D LEU* 5.5 3.6 - - + +
3886D LEU* 5.4 7.9 - - + -
3887D CYS* 5.9 2.5 - - - -
3894D PHE* 3.6 43.7 - - + +
3895D GLN* 3.5 11.7 + - - +
3896D ASN 3.3 0.6 - - - -
3897D TYR* 1.3 83.6 - - + +
3899D ARG* 1.3 63.3 + - - +
3901D GLN* 3.4 9.7 + - - +
3909D ASN* 3.9 0.9 - - - +
3910D ILE* 3.7 50.2 + - + +
3911D ILE* 4.4 9.6 - - + +
3963D TYR* 4.2 31.2 - - + +
3971D ASN* 5.9 0.9 - - - +
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Residues in contact with ARG3899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3895D GLN 3.7 9.3 + - - +
3896D ASN* 3.4 10.9 + - - +
3897D TYR 3.3 0.4 - - - -
3898D LEU* 1.3 79.1 - - - +
3900D THR* 1.3 63.1 + - - +
3901D GLN* 4.1 0.7 - - - -
3909D ASN* 3.1 35.1 + - - +
3911D ILE* 4.7 9.1 - - + +
3970D GLY* 4.4 29.4 - - - +
3971D ASN* 5.3 3.1 - - - +
3974D SER* 5.3 2.9 - - - +
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Residues in contact with THR3900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3896D ASN 3.2 12.4 + - - +
3897D TYR* 3.0 15.8 - - - +
3898D LEU 3.5 0.4 - - - -
3899D ARG* 1.3 82.4 - - - +
3901D GLN* 1.3 67.9 + - - +
3902D THR 4.0 1.6 + - - -
3907D THR* 5.8 7.6 - - - -
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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