Contacts of the helix formed by residues 656 - 667 (chain 3) in PDB entry 6Q8O
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 656 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6383 LEU* 3.7 8.2 - - - +
6393 GLN* 5.5 1.3 - - - +
6543 PHE* 4.8 1.2 - - - +
6553 ARG* 1.3 115.1 + - + +
6573 HIS* 1.3 65.2 + - - +
6583 LEU* 3.4 20.6 - - + +
6593 GLU* 4.2 15.4 + - + +
6603 ALA* 3.5 18.7 + - - +
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Residues in contact with HIS 657 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3523 GLU* 4.0 20.2 + - + -
6113 ARG* 4.2 40.1 - - + +
6123 GLY* 4.7 5.1 - - - -
6133 HIS* 5.2 3.0 + - - -
6383 LEU* 4.4 6.4 - - + +
6563 LEU* 1.3 74.8 - - - +
6583 LEU* 1.3 68.2 + - + +
6603 ALA* 3.2 4.5 + - - +
6613 GLN* 2.9 60.1 + - + +
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Residues in contact with LEU 658 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6563 LEU* 3.4 15.6 - - + +
6573 HIS* 1.3 85.5 - - + +
6593 GLU* 1.3 71.8 + - + +
6613 GLN* 3.1 8.7 + - + +
6623 LYS* 2.9 33.8 + - + +
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Residues in contact with GLU 659 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6533 PRO 5.0 9.9 - - - +
6543 PHE* 4.0 6.1 - - + -
6553 ARG* 4.1 22.9 + - - +
6563 LEU* 4.2 18.9 + - + +
6573 HIS 3.5 0.2 - - - -
6583 LEU* 1.3 87.7 - - - +
6603 ALA* 1.3 56.8 + - - +
6623 LYS* 3.8 24.3 + - - +
6633 ALA* 2.9 31.5 + - - +
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Residues in contact with ALA 660 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3523 GLU* 3.5 30.1 - - + -
6383 LEU* 4.8 3.8 - - + -
6543 PHE* 3.5 23.0 - - + -
6563 LEU 3.5 15.8 + - - +
6573 HIS* 3.2 11.6 + - - +
6593 GLU* 1.3 79.5 - - - +
6613 GLN* 1.3 56.5 + - - +
6633 ALA* 3.4 1.6 + - - +
6643 LEU* 2.9 35.1 + - - +
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Residues in contact with GLN 661 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3523 GLU* 2.6 31.9 + - - -
6133 HIS* 3.2 25.1 + - - -
6573 HIS* 2.9 40.0 + - + +
6583 LEU* 3.1 9.8 + - + +
6603 ALA* 1.3 75.3 - - - +
6623 LYS* 1.3 58.7 + - + +
6643 LEU* 3.3 17.8 + - - +
6653 LYS* 2.9 30.0 + - - +
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Residues in contact with LYS 662 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6583 LEU* 2.9 20.9 + - - +
6593 GLU* 3.8 27.3 + - - +
6613 GLN* 1.3 77.7 - - + +
6633 ALA* 1.3 58.1 + - - +
6643 LEU 3.3 0.2 + - - -
6653 LYS* 3.3 5.9 + - - +
6663 ALA* 2.9 26.7 + - - +
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Residues in contact with ALA 663 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3553 LEU* 4.3 4.9 - - + +
6543 PHE* 3.5 30.3 - - + -
6593 GLU 2.9 17.6 + - - +
6623 LYS* 1.3 75.6 - - - +
6643 LEU* 1.3 57.0 + - - +
6663 ALA* 3.2 10.9 - - - +
6673 ARG* 2.9 29.3 + - - +
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Residues in contact with LEU 664 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513 LEU* 4.1 18.4 - - + +
3523 GLU* 3.8 21.3 - - + +
3553 LEU* 3.6 12.5 - - + +
5473 MET* 3.5 32.5 - - + -
6133 HIS* 5.2 4.0 - - + -
6603 ALA 2.9 20.3 + - - +
6613 GLN* 3.4 33.2 - - - +
6623 LYS 3.2 0.2 - - - -
6633 ALA* 1.3 73.6 - - - +
6653 LYS* 1.3 57.2 - - - +
6673 ARG* 2.7 24.8 + - + +
6683 LYS 2.9 8.1 + - - -
6693 VAL* 3.2 30.6 - - + +
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Residues in contact with LYS 665 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6613 GLN 2.9 16.0 + - - +
6623 LYS* 3.8 5.8 - - - +
6643 LEU* 1.3 74.1 - - - +
6663 ALA* 1.3 58.0 + - - +
6683 LYS* 2.9 23.7 + - - +
6693 VAL* 4.1 11.1 - - - +
6713 GLU* 4.9 16.6 + - - +
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Residues in contact with ALA 666 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6623 LYS 2.9 14.4 + - - +
6633 ALA* 3.2 16.4 - - - +
6643 LEU 3.0 0.2 - - - -
6653 LYS* 1.3 78.7 - - - +
6673 ARG* 1.3 58.8 + - + +
6683 LYS* 3.1 14.6 + - - +
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Residues in contact with ARG 667 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3553 LEU* 4.4 23.2 - - + +
3583 SER* 4.9 5.1 + - - -
3593 GLU* 4.5 15.8 + - - +
5463 ALA 4.0 19.1 + - - -
5473 MET* 4.7 27.4 + - + +
5483 GLY* 5.2 3.4 - - - +
6633 ALA 2.9 13.1 + - - +
6643 LEU* 2.7 17.4 + - - +
6663 ALA* 1.3 69.8 - - - +
6683 LYS* 1.3 69.3 + - - +
6693 VAL* 3.5 1.3 + - - +
6783 PHE* 5.5 6.3 - - - -
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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