Contacts of the helix formed by residues 1001 - 1009 (chain E) in PDB entry 6BAA
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 CYS1001 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000E ALA* 1.3 68.9 - - - +
1002E THR* 1.3 60.4 + - - +
1003E LYS 3.1 5.8 - - - -
1004E TYR* 3.1 25.3 + - - +
1005E LEU* 3.8 2.1 + - - +
1309E LEU* 3.9 31.0 - - + -
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Residues in contact with THR1002 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E ALA* 3.1 7.2 - - - -
1001E CYS* 1.3 74.9 - - - +
1003E LYS* 1.3 60.3 + - - +
1004E TYR 3.2 0.2 - - - -
1005E LEU* 3.1 14.7 + - - +
1006E SER* 2.9 27.4 + - - -
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Residues in contact with LYS1003 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E ALA* 3.5 16.9 + - + +
1001E CYS 3.1 0.8 - - - -
1002E THR* 1.3 75.4 - - - +
1004E TYR* 1.3 60.2 + - - +
1006E SER* 3.4 8.1 + - - +
1007E SER* 2.9 28.2 + - - -
1312E VAL* 5.6 5.8 - - + -
1316E HIS* 3.8 34.1 - - + +
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Residues in contact with TYR1004 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001E CYS* 3.1 15.0 + - - +
1003E LYS* 1.3 79.0 - - - +
1005E LEU* 1.3 56.0 + - - +
1007E SER* 3.3 7.8 + - - -
1008E ALA* 2.9 27.4 + - - +
1093E VAL* 5.2 4.0 - - + +
1140E LEU* 6.5 0.4 - - + -
1309E LEU* 5.4 10.3 - - + -
1312E VAL* 4.6 21.1 - - + +
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Residues in contact with LEU1005 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001E CYS 3.8 1.3 + - - +
1002E THR* 3.1 20.6 + - - +
1004E TYR* 1.3 77.1 - - - +
1006E SER* 1.3 59.2 + - - +
1008E ALA* 2.9 21.8 + - - +
1009E GLY* 3.0 16.8 + - - +
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Residues in contact with SER1006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E THR 2.9 15.8 + - - -
1003E LYS* 3.7 9.0 - - - -
1005E LEU* 1.3 75.7 - - - +
1007E SER* 1.3 61.1 + - - +
1009E GLY* 3.8 7.9 + - - -
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Residues in contact with SER1007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E LYS 2.9 16.9 + - - -
1004E TYR* 3.6 8.7 - - - -
1006E SER* 1.3 76.6 - - - +
1008E ALA* 1.3 60.4 + - - +
1092E LYS* 4.8 2.4 - - - +
1093E VAL* 4.2 27.5 + - - -
1096E ARG* 4.5 15.0 - - - +
1097E LEU* 5.6 7.2 - - - -
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Residues in contact with ALA1008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004E TYR 2.9 13.4 + - - +
1005E LEU* 2.9 14.6 + - - +
1007E SER* 1.3 79.9 - - - +
1009E GLY* 1.3 65.6 + - - +
1012E LEU* 4.7 11.6 - - + +
1013E LEU* 5.9 3.4 - - + +
1089E THR* 5.4 15.7 - - - -
1092E LYS* 5.0 9.6 - - - +
1093E VAL* 5.1 9.2 - - + +
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Residues in contact with GLY1009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005E LEU 3.0 12.4 + - - +
1006E SER* 3.8 7.1 + - - -
1007E SER 3.5 2.0 - - - -
1008E ALA* 1.3 85.8 - - - +
1010E ILE* 1.3 64.3 + - - -
1011E LEU 3.3 3.0 + - - -
1012E LEU 4.0 1.5 + - - -
1013E LEU* 3.6 17.7 + - - +
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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