Contacts of the helix formed by residues 63 - 75 (chain 4) in PDB entry 6AH0
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 SER 63 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134 ALA* 4.0 13.8 - - - +
614 PHE 3.3 2.1 + - - -
624 LEU* 1.3 81.0 + - - +
644 GLU* 1.3 65.8 + - - +
654 GLU 3.4 2.2 - - - -
664 ASP* 3.4 5.8 + - - +
674 ALA* 3.2 17.0 + - - -
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Residues in contact with GLU 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 ASP* 3.6 23.8 - - - +
134 ALA* 4.5 0.8 - - - +
634 SER* 1.3 70.9 - - - +
654 GLU* 1.3 59.9 + - - +
674 ALA* 3.2 1.6 + - - -
684 ASP* 2.8 28.4 + - - -
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Residues in contact with GLU 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6432 PRO* 6.5 0.7 - - - -
634 SER 3.4 0.4 - - - -
644 GLU* 1.3 77.1 - - - +
664 ASP* 1.3 54.9 + - - +
684 ASP* 3.4 1.2 + - - +
694 TYR* 3.0 26.5 + - - -
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Residues in contact with ASP 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6432 PRO* 5.9 4.5 - - - -
6442 SER* 5.7 7.2 - - - +
364 ALA 5.7 0.7 - - - +
374 GLY* 5.9 4.8 - - - -
614 PHE* 5.8 2.7 - - - -
624 LEU 6.1 0.9 - - - +
634 SER* 3.4 9.2 + - - +
644 GLU 3.2 1.0 - - - -
654 GLU* 1.3 72.8 - - - +
674 ALA* 1.3 64.4 + - - +
694 TYR* 3.5 1.4 + - - +
704 ALA* 3.1 18.9 + - - -
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Residues in contact with ALA 67 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 ASP 5.0 5.2 - - - -
134 ALA 4.7 12.1 - - - -
144 THR 6.0 2.5 - - - -
614 PHE* 5.4 3.7 - - - +
634 SER 3.2 13.0 + - - -
644 GLU 3.2 2.9 + - - -
664 ASP* 1.3 74.7 - - - +
684 ASP* 1.3 64.6 + - - +
704 ALA* 3.2 3.5 + - - +
714 ILE* 3.0 20.1 + - - -
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Residues in contact with ASP 68 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 ASP 5.3 0.8 + - - -
644 GLU 2.8 19.3 + - - -
654 GLU* 3.9 1.8 - - - +
674 ALA* 1.3 70.4 - - - +
694 TYR* 1.3 61.6 + - - +
714 ILE* 3.3 2.4 + - - +
724 LYS* 3.1 18.9 + - - -
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Residues in contact with TYR 69 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654 GLU 3.0 17.3 + - - -
664 ASP* 3.9 2.2 - - - +
674 ALA 3.2 0.2 - - - -
684 ASP* 1.3 76.6 - - - +
704 ALA* 1.3 61.6 + - - +
724 LYS* 3.2 3.4 + - - +
734 ILE* 2.9 20.6 + - - -
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Residues in contact with ALA 70 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364 ALA* 5.8 9.1 + - - +
664 ASP 3.1 14.5 + - - -
674 ALA* 3.2 4.2 + - - +
694 TYR* 1.3 76.4 - - - +
714 ILE* 1.3 56.2 + - - +
734 ILE* 4.6 0.9 - - - +
744 MET* 2.8 29.8 + - - -
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Residues in contact with ILE 71 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674 ALA 3.0 13.8 + - - -
684 ASP* 3.3 3.6 + - - +
694 TYR 3.3 0.4 - - - -
704 ALA* 1.3 75.7 - - - +
724 LYS* 1.3 63.3 + - - +
734 ILE 3.3 0.3 + - - -
744 MET* 3.4 6.7 + - - +
754 ASN 3.9 7.6 + - - -
864 VAL* 4.4 24.3 - - - +
874 ASN* 5.8 2.2 - - - +
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Residues in contact with LYS 72 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6352 ALA* 6.1 0.3 - - - -
684 ASP 3.1 13.4 + - - -
694 TYR* 3.2 3.3 + - - +
714 ILE* 1.3 78.0 - - - +
734 ILE* 1.3 60.5 + - - +
754 ASN* 4.5 3.8 + - - +
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Residues in contact with ILE 73 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6322 TRP* 4.8 14.2 - - - +
6352 ALA* 5.7 12.9 - - - +
694 TYR 2.9 14.4 + - - -
704 ALA* 3.9 1.1 - - - +
724 LYS* 1.3 77.8 - - - +
744 MET* 1.3 62.2 + - - +
754 ASN 3.5 7.5 + - - +
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Residues in contact with MET 74 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704 ALA 2.8 17.0 + - - -
714 ILE* 3.4 3.4 + - - +
734 ILE* 1.3 72.7 - - - +
754 ASN* 1.3 67.9 + - - +
764 MET 3.8 0.2 - - - -
774 ILE* 3.0 20.8 + - - -
844 ILE 4.3 3.2 - - - +
864 VAL* 5.6 7.2 - - - +
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Residues in contact with ASN 75 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714 ILE 3.9 8.5 + - - -
724 LYS 4.5 3.2 + - - +
734 ILE 3.5 8.8 + - - +
744 MET* 1.3 75.5 - - - +
764 MET* 1.3 57.6 - - - +
774 ILE 4.1 0.2 - - - +
844 ILE 4.6 5.8 - - - -
854 ARG* 5.9 0.4 - - - +
864 VAL 5.5 5.4 + - - +
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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