Contacts of the helix formed by residues 3969 - 3978 (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 THR3969 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3968D CYS* 1.3 78.9 - - - +
3970D GLY* 1.3 75.4 + - - +
3971D ASN 3.2 1.9 + - - -
3972D GLN* 3.5 1.8 + - - +
3973D GLN* 2.7 37.4 - - - +
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Residues in contact with GLY3970 (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* 6.4 1.1 - - - -
3899D ARG* 4.4 20.6 - - - +
3911D ILE* 6.1 0.2 - - - +
3969D THR* 1.3 84.8 + - - +
3971D ASN* 1.3 63.9 + - - +
3973D GLN* 4.4 2.5 - - - +
3974D SER* 3.3 27.4 + - - -
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Residues in contact with ASN3971 (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* 4.0 27.2 + - - +
3896D ASN* 5.3 0.9 - - - -
3898D LEU* 5.9 1.0 - - - +
3899D ARG* 5.3 3.8 - - - +
3911D ILE* 4.5 19.9 - - + +
3963D TYR* 3.1 50.7 + - + +
3964D ILE* 4.6 5.1 - - + +
3968D CYS* 3.6 22.2 - - - +
3969D THR 3.2 1.2 - - - -
3970D GLY* 1.3 80.4 + - - +
3972D GLN* 1.3 60.1 + - - +
3974D SER* 4.3 2.8 - - - -
3975D LEU* 3.2 31.8 + - + +
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Residues in contact with GLN3972 (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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3964D ILE* 5.2 5.8 - - + -
3967D PRO* 5.2 1.9 - - - +
3968D CYS* 3.2 41.9 + - - +
3969D THR* 3.5 2.1 + - - +
3970D GLY 3.4 0.4 - - - -
3971D ASN* 1.3 76.3 - - - +
3973D GLN* 1.3 75.1 + - - +
3975D LEU* 3.6 3.9 + - - +
3976D ALA* 3.1 25.1 + - - +
4024D SER 5.3 1.9 - - - +
4025D LEU* 4.0 31.5 + - + +
4028D GLY 4.9 7.8 + - - +
4029D ASN* 5.4 9.5 - - - +
4035D ILE* 4.8 27.0 - - + +
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Residues in contact with GLN3973 (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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3969D THR* 2.7 29.8 + - - +
3970D GLY* 4.8 2.2 - - - +
3972D GLN* 1.3 86.0 + - - +
3974D SER* 1.3 64.3 + - - +
3976D ALA* 4.1 4.0 - - - +
3977D HIS* 3.1 47.1 + - + +
4034D MET* 6.3 2.5 - - - -
4035D ILE* 4.9 20.2 - - + +
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Residues in contact with SER3974 (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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3899D ARG* 5.3 3.6 - - - +
3909D ASN* 4.4 16.7 + - - -
3911D ILE* 4.2 24.1 - - - +
3912D ILE* 6.1 2.9 - - - -
3970D GLY 3.3 20.9 + - - -
3971D ASN* 4.3 2.0 - - - -
3972D GLN 3.3 0.6 - - - -
3973D GLN* 1.3 77.3 - - - +
3975D LEU* 1.3 64.4 + - - +
3977D HIS* 3.6 4.0 + - - +
3978D SER* 3.1 25.3 + - - -
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Residues in contact with LEU3975 (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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3911D ILE* 5.1 7.3 - - + +
3915D VAL* 5.2 2.7 - - + -
3960D LEU* 4.1 36.8 - - + +
3963D TYR* 6.5 0.4 - - + -
3964D ILE* 5.5 7.9 - - + -
3971D ASN* 3.2 20.9 + - + +
3972D GLN* 4.1 3.6 - - - +
3974D SER* 1.3 76.7 - - - +
3976D ALA* 1.3 62.8 + - - +
3978D SER* 2.8 20.4 + - - +
3980D LEU* 3.7 27.4 + - + +
3981D TRP 5.0 1.3 + - - +
4025D LEU* 3.7 29.8 - - + -
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Residues in contact with ALA3976 (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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3972D GLN 3.1 19.3 + - - +
3973D GLN* 4.1 4.7 - - - +
3975D LEU* 1.3 82.0 - - - +
3977D HIS* 1.3 68.6 + - + +
3978D SER 3.5 6.8 + - - +
3981D TRP* 5.9 2.6 - - - +
4025D LEU* 6.0 3.6 - - + +
4035D ILE* 5.3 13.0 - - + -
4038D GLN* 4.6 25.6 - - + +
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Residues in contact with HIS3977 (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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3973D GLN* 3.1 35.0 + - + +
3974D SER* 4.2 4.5 - - - +
3976D ALA* 1.3 80.4 + - + +
3978D SER* 1.3 65.8 + - - +
4034D MET* 5.7 10.3 - - + -
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Residues in contact with SER3978 (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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3911D ILE* 5.9 0.8 - - - +
3912D ILE* 6.0 2.5 - - - -
3915D VAL* 3.7 27.7 - - - +
3974D SER 3.1 15.2 + - - -
3975D LEU* 2.8 26.7 + - - +
3976D ALA 3.3 8.4 - - - +
3977D HIS* 1.3 81.7 - - - +
3979D ARG* 1.3 58.7 + - - +
3980D LEU* 3.3 11.4 + - - +
3981D TRP* 4.7 3.6 + - - +
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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