Contacts of the helix formed by residues 391 - 396 (chain 1) in PDB entry 6Q8W
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 LEU 391 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3671 MET* 3.5 34.8 - - + -
3871 LEU* 3.5 24.0 - - + +
3881 GLU* 4.2 6.1 - - - +
3901 LEU* 1.3 76.6 - - - +
3921 PRO* 1.3 69.2 - - + +
3941 ILE* 2.9 7.7 + - - +
3951 GLU* 2.9 25.6 + - - +
4071 VAL* 4.2 21.2 - - + +
4101 VAL* 4.0 23.3 - - + -
4111 LYS* 4.0 26.5 - - + +
4141 LEU* 4.2 13.7 - - + -
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Residues in contact with PRO 392 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3881 GLU 3.9 6.5 - - - +
3891 ALA* 3.2 22.0 - - - +
3911 LEU* 1.3 92.5 - - + +
3931 LEU* 1.3 62.8 + - + +
3941 ILE 3.1 1.1 + - - -
3951 GLU* 3.6 18.9 + - + +
3961 GLY* 3.7 8.8 + - - -
3971 ARG* 3.1 20.1 + - - +
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Residues in contact with LEU 393 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3581 PRO* 5.0 2.3 - - - +
3891 ALA 4.0 13.7 - - - +
3901 LEU* 3.6 23.6 - - + +
3911 LEU 3.1 0.8 + - - -
3921 PRO* 1.3 77.8 - - + +
3941 ILE* 1.3 57.8 + - - +
3971 ARG* 3.0 54.1 + - - +
1023 GLU* 4.6 11.4 - - + +
1033 ALA* 4.5 4.9 - - - +
1063 GLY* 4.1 25.1 - - - -
1073 MET* 4.4 9.7 - - + +
1093 GLU* 5.6 2.5 - - - +
1103 PHE* 3.8 31.9 - - + -
1563 ARG* 5.1 7.4 - - - +
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Residues in contact with ILE 394 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3581 PRO* 4.8 7.0 - - - +
3591 CYS* 4.6 6.5 - - - +
3621 GLY* 4.5 6.5 - - - -
3631 VAL* 3.9 23.8 - - + +
3671 MET* 3.4 36.3 - - + -
3901 LEU* 3.8 13.5 - - + +
3911 LEU 2.9 4.0 + - - +
3931 LEU* 1.3 83.6 - - - +
3951 GLU* 1.3 66.6 + - - +
3961 GLY 3.6 0.2 - - - -
3971 ARG 3.7 4.6 + - - -
3981 SER* 3.0 26.1 + - - +
4031 ALA* 3.5 25.1 - - + -
4041 ASP* 3.9 3.1 - - - +
4071 VAL* 3.8 12.8 - - + -
1103 PHE* 4.4 14.8 - - + -
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Residues in contact with GLU 395 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3911 LEU* 2.9 15.4 + - - +
3921 PRO* 3.6 11.9 + - + +
3941 ILE* 1.3 78.1 - - - +
3961 GLY* 1.3 68.0 + - - +
3971 ARG* 3.2 0.3 + - - -
3981 SER 4.6 1.6 + - - -
4041 ASP* 2.9 33.4 - - - +
4071 VAL* 3.5 24.6 - - + +
4081 TRP* 2.4 42.4 + - + +
4111 LYS* 4.5 19.5 + - - +
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Residues in contact with GLY 396 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3921 PRO 3.7 10.0 + - - -
3941 ILE 3.6 0.2 - - - -
3951 GLU* 1.3 84.4 - - - +
3971 ARG* 1.3 60.7 + - - +
3981 SER 4.0 2.0 + - - +
783 LYS* 3.4 36.0 - - - +
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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