Contacts of the helix formed by residues 66 - 71 (chain Z) in PDB entry 1XDM
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 ASP 66 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64Z SER 3.6 0.8 + - - -
65Z VAL* 1.3 97.0 - - + +
67Z SER* 1.3 83.7 + - - +
68Z SER* 2.8 30.9 + - - +
69Z ILE* 3.4 10.6 + - - +
324Z GLN* 4.4 1.8 - - - +
328Z MET* 4.2 5.8 - - + -
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Residues in contact with SER 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Z VAL 4.2 1.3 - - - -
66Z ASP* 1.3 78.2 + - - +
68Z SER* 1.3 61.0 + - - -
69Z ILE* 2.9 8.7 + - - +
70Z ASN* 2.8 39.5 + - - +
100Z LYS* 4.5 22.3 - - - +
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Residues in contact with SER 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z ASP* 2.8 17.9 + - - -
67Z SER* 1.3 78.5 + - - +
69Z ILE* 1.3 62.2 + - - +
70Z ASN* 3.1 0.7 - - - -
71Z GLN* 2.9 32.4 - - - +
72Z SER* 5.5 0.3 + - - -
328Z MET* 2.9 23.4 - - - +
332Z MET* 5.7 3.1 - - - +
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Residues in contact with ILE 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Z LEU 5.0 0.7 - - - +
63Z PHE* 6.4 0.7 - - - -
65Z VAL* 3.8 9.4 - - + +
66Z ASP 3.7 11.7 - - - +
67Z SER* 2.9 4.0 - - - +
68Z SER* 1.3 76.9 + - - +
70Z ASN* 1.3 57.4 + - + +
71Z GLN 2.6 18.8 + - - -
72Z SER* 2.7 16.5 + - - +
73Z ILE* 3.0 29.6 + - + -
100Z LYS* 5.2 7.9 - - + -
102Z ILE* 4.1 19.1 - - + -
327Z PHE* 3.2 43.1 - - + -
328Z MET* 3.3 29.2 - - + +
331Z ALA* 4.5 4.9 - - + -
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Residues in contact with ASN 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Z LYS* 3.2 22.2 + - - +
67Z SER* 2.8 30.7 + - - +
68Z SER* 4.8 0.2 - - - -
69Z ILE* 1.3 79.6 - - + +
71Z GLN* 1.3 95.4 + - - +
72Z SER 3.5 0.9 - - - -
73Z ILE 3.7 13.5 - - - +
100Z LYS* 2.7 32.4 + - - +
101Z GLY* 5.0 3.1 - - - -
102Z ILE* 4.5 8.5 - - + +
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Residues in contact with GLN 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Z ASN* 5.6 3.3 - - - +
27Z LYS* 3.7 12.0 - - - +
68Z SER* 2.9 28.5 - - - +
69Z ILE 2.6 6.1 + - - -
70Z ASN* 1.3 111.1 + - - +
72Z SER* 1.3 61.0 + - - +
335Z CYS* 3.6 14.2 - - - -
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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