Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 1D4O
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 GLY 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PRO 4.5 11.4 + - - -
64A ALA 5.0 2.0 + - - -
67A MET 3.1 1.8 + - - -
68A PRO* 1.3 71.8 - - - +
70A GLN* 1.3 65.2 + - - +
71A LEU 3.4 2.5 - - - -
72A ASN* 3.1 20.8 + - - +
73A VAL* 3.0 30.0 + - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.9 8.7 - - - -
34A CYS* 3.9 18.2 - - - -
64A ALA 4.7 2.3 + - - +
65A GLY* 3.4 6.1 - - - -
66A ARG* 2.7 35.2 + - - +
67A MET* 3.0 39.6 + - + +
68A PRO 3.2 2.1 + - - -
69A GLY* 1.3 76.4 - - - +
71A LEU* 1.3 59.5 + - + +
73A VAL* 3.4 5.1 + - - +
74A LEU* 3.0 48.8 + - + +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 3.9 33.0 - - + +
30A GLY 3.6 22.9 - - - +
33A LEU* 4.2 17.0 - - + -
34A CYS* 4.0 20.4 - - + -
60A ILE* 4.1 20.0 - - + -
64A ALA* 3.8 6.0 + - + +
65A GLY* 3.6 36.8 - - - +
69A GLY 3.4 0.8 - - - -
70A GLN* 1.3 78.6 - - + +
72A ASN* 1.3 62.1 + - - +
74A LEU* 4.8 2.2 - - + -
75A LEU* 2.9 33.4 + - + +
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Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ILE* 3.6 29.2 - - - +
61A HIS 5.1 1.2 - - - +
69A GLY* 3.1 20.1 + - - +
71A LEU* 1.3 77.1 + - - +
73A VAL* 1.3 64.7 + - + +
75A LEU* 4.0 2.0 - - - +
76A ALA* 3.0 25.6 + - - +
82A TYR* 5.1 4.7 - - + -
85A VAL* 3.9 24.0 - - - +
86A LEU 5.6 1.2 + - - -
87A GLU* 5.9 5.3 - - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PRO 5.4 1.8 - - - +
69A GLY* 3.0 23.3 + - - +
70A GLN* 3.8 5.6 - - - +
72A ASN* 1.3 78.2 - - + +
74A LEU* 1.3 62.9 + - + +
76A ALA* 3.3 6.4 + - - +
77A GLU* 2.9 53.1 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 6.2 0.2 - - + -
34A CYS* 3.5 30.1 - - + -
39A GLN* 3.9 28.7 - - + +
40A TYR* 5.8 1.6 - - - +
70A GLN* 3.0 39.6 + - + +
71A LEU* 4.3 4.5 - - + +
73A VAL* 1.3 80.9 - - + +
75A LEU* 1.3 63.1 + - + +
77A GLU* 3.5 22.7 + - + +
78A ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 4.1 13.0 - - + -
33A LEU* 4.5 10.3 - - + -
39A GLN* 4.0 24.9 - - + +
42A ILE* 4.6 5.6 - - + -
58A PHE* 3.7 42.2 - - + -
60A ILE* 3.9 17.5 - - + -
71A LEU* 2.9 23.7 + - + +
72A ASN* 4.2 2.7 - - - +
74A LEU* 1.3 78.0 - - + +
76A ALA* 1.3 61.0 + - - +
78A ALA* 3.2 3.9 + - - +
79A GLY 3.2 5.5 + - - -
80A VAL* 3.0 45.6 + - + +
85A VAL* 5.3 4.9 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN 3.0 19.6 + - - +
73A VAL* 3.6 5.8 - - - +
75A LEU* 1.3 75.7 - - - +
77A GLU* 1.3 63.9 + - + +
79A GLY* 2.9 16.5 + - - -
80A VAL 4.0 11.7 + - - +
82A TYR* 3.4 41.1 - - + +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 5.5 2.1 - - + +
73A VAL* 2.9 38.0 + - + +
74A LEU* 3.8 22.2 - - + +
76A ALA* 1.3 75.2 - - + +
78A ALA* 1.3 60.8 + - - +
79A GLY* 3.3 1.4 + - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 3.8 36.8 - - + +
40A TYR* 4.0 21.4 - - + -
43A ALA* 3.8 14.3 - - + +
74A LEU 3.1 17.5 + - - +
75A LEU* 3.7 6.3 - - - +
76A ALA 3.2 0.4 - - - -
77A GLU* 1.3 75.1 - - - +
79A GLY* 1.3 57.6 + - - +
80A VAL* 3.7 0.7 - - + -
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 4.7 4.0 - - - -
47A LYS* 5.8 1.9 + - - -
76A ALA 2.9 11.2 + - - -
77A GLU 3.2 2.3 + - - -
78A ALA* 1.3 79.8 - - - +
80A VAL* 1.3 66.1 + - - +
81A PRO* 3.4 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