Contacts of the helix formed by residues 1276 - 1281 (chain 1) 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 SER1276 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12721 ILE 4.8 1.6 - - - -
12741 ILE 3.6 0.6 + - - -
12751 GLY* 1.3 70.5 - - - -
12771 GLN* 1.3 64.0 + - - +
12781 ASP 3.0 3.4 - - - +
12791 ALA* 2.9 16.2 + - - +
12801 LEU* 3.4 8.7 + - - -
1103 SER 5.8 2.4 + - - -
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Residues in contact with GLN1277 (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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12731 TYR* 3.6 16.1 + - - +
12741 ILE 3.7 4.0 + - - -
12751 GLY 2.7 6.1 + - - -
12761 SER* 1.3 77.8 - - - +
12781 ASP* 1.3 60.7 + - - +
12791 ALA 3.3 0.5 + - - -
12801 LEU* 3.5 9.9 + - - +
12811 ILE 4.6 2.4 + - - -
1123 CYS 5.0 0.4 - - - -
1133 ARG* 6.3 0.2 - - - -
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Residues in contact with ASP1278 (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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12761 SER* 3.0 2.2 - - - +
12771 GLN* 1.3 79.5 - - - +
12791 ALA* 1.3 61.4 + - - +
12811 ILE 4.3 3.5 + - - -
1103 SER 5.5 4.1 + - - -
1113 GLY* 5.3 3.6 - - - -
1123 CYS 3.5 27.2 + - - +
1133 ARG* 5.8 0.4 - - - +
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Residues in contact with ALA1279 (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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12761 SER* 2.9 12.4 + - - +
12781 ASP* 1.3 80.5 - - - +
12801 LEU* 1.3 67.3 + - - +
12811 ILE 2.8 2.1 + - - -
12821 ALA* 3.8 5.0 + - - -
11663 TYR 5.0 4.5 - - - -
11673 TYR* 4.8 20.6 - - - +
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Residues in contact with LEU1280 (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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12761 SER 3.4 9.1 + - - -
12771 GLN* 3.5 6.0 + - - +
12781 ASP 3.4 1.8 - - - -
12791 ALA* 1.3 75.9 - - - +
12811 ILE* 1.3 50.3 - - - +
12821 ALA* 2.4 2.6 + - - -
12831 HIS* 2.2 39.8 + - - +
12841 TYR 4.8 1.8 - - - -
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Residues in contact with ILE1281 (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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12771 GLN 4.6 2.8 + - - -
12781 ASP 4.3 3.6 + - - -
12791 ALA 2.8 7.3 + - - -
12801 LEU* 1.3 71.4 - - - +
12821 ALA* 1.3 62.3 + - - +
12831 HIS 3.0 1.2 + - - -
12841 TYR* 3.5 10.8 + - - +
387 ASP 6.4 0.4 - - - -
397 SER* 5.8 8.5 - - - +
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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