Contacts of the helix formed by residues 69 - 82 (chain D) in PDB entry 1Z6Z
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 ALA 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D ASP* 3.3 22.3 + - + +
67D LEU 3.3 1.5 - - - +
68D GLY* 1.3 81.6 - - - +
70D GLU* 1.3 65.9 + - - +
71D ALA* 3.4 7.6 - - + +
72D GLY 4.4 3.4 - - - +
73D LEU* 3.2 24.1 + - - +
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C SER* 2.5 37.2 + - - -
115C THR* 3.8 22.2 - - + +
118C ASN* 3.3 19.8 + - - +
69D ALA* 1.3 72.9 - - - +
71D ALA* 1.3 58.7 + - - +
73D LEU* 3.1 7.2 + - - +
74D GLN* 2.9 50.0 + - + +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ALA* 3.4 4.8 - - + +
70D GLU* 1.3 78.7 - - - +
72D GLY* 1.3 62.9 + - - +
74D GLN* 3.4 7.2 + - - +
75D GLN* 3.0 34.7 + - - +
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ALA* 3.2 24.1 - - - +
66D ASP* 3.1 33.1 + - - -
67D LEU* 4.3 0.4 - - - +
69D ALA* 3.6 5.7 + - - +
70D GLU 3.3 0.8 - - - -
71D ALA* 1.3 77.6 - - - +
73D LEU* 1.3 60.7 + - - +
75D GLN* 3.3 8.4 + - - +
76D LEU* 3.3 11.3 + - - +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C SER* 3.5 34.3 - - - +
66D ASP 3.7 1.4 + - - -
67D LEU* 4.2 20.9 - - + +
69D ALA 3.2 17.1 + - - +
70D GLU* 3.1 7.4 + - - +
72D GLY* 1.3 76.4 - - - +
74D GLN* 1.3 61.1 + - - +
76D LEU* 3.2 4.4 + - + -
77D LEU* 2.9 45.5 + - + +
122D ALA 6.0 0.4 - - - +
126D THR* 4.8 2.7 - - + -
127D SER* 3.9 42.2 - - - +
130D CYS* 4.4 9.4 - - + -
131D LEU* 5.3 3.8 - - + -
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Residues in contact with GLN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER 5.3 2.4 + - - -
114C SER* 3.6 11.9 + - - +
70D GLU* 2.9 40.6 + - + +
71D ALA* 3.9 6.7 - - - +
73D LEU* 1.3 76.3 - - - +
75D GLN* 1.3 56.3 + - - +
77D LEU* 3.8 27.3 - - - +
78D GLY* 2.7 31.7 + - - -
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 4.0 8.3 - - + +
64D PRO 3.5 19.1 - - - +
65D ALA* 4.0 11.0 - - + +
71D ALA* 3.0 23.2 + - - +
72D GLY* 3.4 13.1 - - - +
74D GLN* 1.3 76.1 - - - +
76D LEU* 1.3 56.5 + - - +
78D GLY* 3.9 0.7 - - - -
79D ALA* 3.1 26.5 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.6 8.5 - - + -
10D THR* 4.2 9.4 - - + -
35D VAL* 4.4 11.4 - - + -
37D SER* 3.9 17.3 - - - +
63D VAL* 3.8 33.6 - - + +
65D ALA* 4.8 0.7 - - + -
67D LEU* 3.7 25.1 - - + -
72D GLY 3.3 7.2 + - - +
73D LEU* 3.2 9.4 + - + +
75D GLN* 1.3 78.2 - - - +
77D LEU* 1.3 64.1 + - + +
79D ALA* 3.3 10.8 + - + +
80D LEU* 3.4 13.8 + - + +
131D LEU* 3.8 36.3 - - + -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C SER* 4.5 17.0 - - - +
73D LEU* 2.9 34.9 + - + +
74D GLN* 3.8 33.7 - - - +
76D LEU* 1.3 76.1 - - - +
78D GLY* 1.3 61.0 + - - +
80D LEU* 3.1 28.6 - - + +
81D ARG* 3.8 3.5 + - - +
130D CYS* 3.9 13.0 - - + +
131D LEU* 4.1 15.7 - - + +
134D SER* 3.2 28.9 - - - +
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Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLN 2.7 22.3 + - - -
75D GLN* 3.9 1.1 - - - -
77D LEU* 1.3 69.8 - - - +
79D ALA* 1.3 59.9 + - - +
80D LEU 3.0 6.1 + - - -
81D ARG* 3.2 18.7 + - - +
82D GLU* 3.6 8.5 + - - +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 5.8 0.9 - - + -
61D VAL* 5.3 3.1 - - + -
63D VAL* 3.8 27.8 - - + -
75D GLN 3.1 14.9 + - - +
76D LEU* 3.3 11.2 + - + +
78D GLY* 1.3 74.7 - - - +
80D LEU* 1.3 61.3 + - - +
82D GLU* 3.4 8.2 + - - +
83D LEU* 3.2 31.1 + - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.0 14.8 - - + -
76D LEU* 3.4 9.1 + - + +
77D LEU* 3.1 25.5 + - + +
78D GLY 3.0 0.4 - - - -
79D ALA* 1.3 73.1 - - - +
81D ARG* 1.3 65.2 + - - +
82D GLU 3.1 1.6 - - - -
83D LEU* 3.2 41.2 + - + +
85D ARG* 3.5 12.9 + - - -
131D LEU* 4.7 4.5 - - + +
134D SER* 3.7 28.7 - - - +
135D VAL* 3.7 37.0 - - + +
138D ALA* 5.2 7.2 - - + +
139D PHE* 4.9 7.1 - - + -
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D LEU 3.8 2.8 + - - +
78D GLY* 3.2 13.2 + - - +
80D LEU* 1.3 78.1 - - - +
82D GLU* 1.3 57.8 + - + +
83D LEU 4.5 2.8 - - - +
85D ARG* 4.8 8.8 + - - +
81F ARG* 4.0 15.9 - - - +
82F GLU* 5.1 2.8 - - - +
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLY 3.6 6.8 + - - +
79D ALA* 3.4 10.6 + - - +
80D LEU 3.1 0.8 - - - -
81D ARG* 1.3 76.7 - - - +
83D LEU* 1.3 65.6 + - - +
84D PRO* 3.6 4.5 - - - +
81F ARG* 3.5 17.2 - - - +
83F LEU 5.4 1.9 - - - +
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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