Contacts of the helix formed by residues 25 - 29 (chain G) in PDB entry 6AHU
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 ARG 25 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B PRO 3.1 27.2 + - - -
438B LEU* 4.1 16.6 - - + +
440B HIS* 3.2 20.4 - - - -
441B SER* 3.4 34.3 - - - +
490B LEU 3.9 2.8 + - - -
491B GLY* 4.4 11.4 + - - -
493B ILE 2.3 32.3 + - - -
494B THR* 3.2 34.6 + - + +
525B PRO 5.1 0.4 - - - -
526B ASN* 3.4 42.1 - - + +
24G LYS* 1.3 74.3 - - - +
26G LEU* 1.3 58.7 + - - +
27G PRO* 3.4 2.2 - - - +
28G SER* 2.9 30.9 + - - +
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Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B ASN* 3.7 17.0 - - - +
528B GLU* 6.4 1.1 - - + -
24G LYS* 3.2 45.2 - - + +
25G ARG* 1.3 69.8 - - - +
27G PRO* 1.3 55.4 - - + +
28G SER 3.1 5.6 - - - -
29G ARG* 2.8 43.3 + - - +
30G LEU* 2.6 57.9 + - + -
38G TYR* 5.6 0.2 - - - +
70G TYR* 4.9 4.3 - - - +
72G HIS* 6.2 2.5 - - + -
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Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ASN* 4.9 14.0 - - - +
23G ARG* 4.2 9.0 - - - +
24G LYS 3.3 19.7 - - - +
25G ARG 3.5 1.6 - - - +
26G LEU* 1.3 88.9 - - + +
28G SER* 1.3 57.4 + - - +
29G ARG 3.4 0.2 - - - -
30G LEU* 4.9 0.4 - - + -
31G PRO* 3.3 18.1 - - + +
36G ASP* 3.4 24.2 - - - +
38G TYR* 3.3 32.1 - - + +
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Residues in contact with SER 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ASN* 5.0 6.1 - - - -
438B LEU* 3.7 42.2 - - - +
525B PRO* 4.3 16.6 - - - +
25G ARG* 2.9 21.2 + - - +
27G PRO* 1.3 76.8 - - - +
29G ARG* 1.3 59.0 + - - +
31G PRO* 4.1 7.0 - - - +
32G ARG* 5.4 7.8 + - - +
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Residues in contact with ARG 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B PRO* 3.8 37.9 - - + -
526B ASN* 4.6 5.4 + - - -
528B GLU* 4.9 19.5 + - - +
26G LEU* 2.8 38.7 + - - +
28G SER* 1.3 80.1 + - - +
30G LEU* 1.3 72.1 + - - +
31G PRO* 3.4 2.7 - - - -
32G ARG* 3.0 31.1 + - + +
33G ARG 4.3 1.6 + - - -
34G PRO* 4.6 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