Contacts of the helix formed by residues 69 - 82 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ASP* 3.2 22.9 + - + +
67B LEU 4.1 1.0 - - - +
68B GLY* 1.3 82.2 - - - +
70B GLU* 1.3 66.0 + - - +
71B ALA* 4.4 7.6 - - + +
72B GLY 4.4 3.4 - - - +
73B LEU* 3.1 23.8 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 2.6 37.5 + - - -
115A THR* 3.9 19.7 - - + +
118A ASN* 3.4 19.9 + - - +
69B ALA* 1.3 71.2 - - - +
71B ALA* 1.3 58.0 + - - +
73B LEU* 3.2 7.3 + - - +
74B GLN* 2.9 50.7 + - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA* 3.4 5.0 - - + +
70B GLU* 1.3 78.3 - - - +
72B GLY* 1.3 61.8 + - - +
74B GLN* 3.5 6.6 + - - +
75B GLN* 3.0 35.1 + - - +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 3.2 20.4 - - - +
66B ASP* 3.1 31.5 + - - -
67B LEU* 4.3 0.6 - - - +
69B ALA* 3.5 6.5 + - - +
70B GLU 3.3 0.4 - - - -
71B ALA* 1.3 77.2 - - - +
73B LEU* 1.3 62.5 + - - +
75B GLN* 3.3 13.8 + - - +
76B LEU* 3.3 11.4 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 3.6 32.1 - - - +
66B ASP 3.7 1.2 + - - -
67B LEU* 4.3 20.6 - - + +
69B ALA 3.1 17.5 + - - +
70B GLU* 3.6 6.5 - - - +
72B GLY* 1.3 76.0 - - - +
74B GLN* 1.3 61.2 + - - +
76B LEU* 3.1 4.1 + - + -
77B LEU* 2.9 50.7 + - + +
122B ALA 5.9 0.4 - - - +
126B THR* 4.7 3.8 - - + -
127B SER* 3.9 41.7 - - - +
130B CYS* 4.4 10.5 - - + -
131B LEU* 5.0 4.0 - - + +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER 5.4 2.0 + - - -
114A SER* 3.7 10.5 + - - +
70B GLU* 2.9 41.6 + - + +
71B ALA* 4.0 6.7 - - - +
73B LEU* 1.3 76.7 - - - +
75B GLN* 1.3 56.2 + - - +
77B LEU* 3.8 25.0 - - - +
78B GLY* 2.8 31.4 + - - -
81B ARG* 4.3 14.4 + - - -
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.0 9.0 - - + +
64B PRO 3.7 17.7 - - - +
65B ALA* 4.0 6.7 - - + +
71B ALA* 3.0 21.9 + - - +
72B GLY* 3.4 19.0 - - - +
74B GLN* 1.3 76.7 - - - +
76B LEU* 1.3 57.1 + - - +
78B GLY* 4.0 1.3 - - - -
79B ALA* 3.1 26.0 + - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.7 7.6 - - + -
10B THR* 4.2 9.0 - - + -
35B VAL* 4.5 11.7 - - + -
37B SER* 3.8 18.6 - - - +
63B VAL* 3.8 32.1 - - + +
65B ALA* 4.8 0.9 - - + -
67B LEU* 3.7 25.4 - - + -
72B GLY 3.3 6.6 + - - +
73B LEU* 3.1 9.2 + - + +
75B GLN* 1.3 77.6 - - - +
77B LEU* 1.3 64.6 + - + +
79B ALA* 3.2 12.5 + - - +
80B LEU* 3.2 19.8 + - + +
131B LEU* 3.9 36.3 - - + -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 4.6 15.7 - - - +
73B LEU* 2.9 32.6 + - + +
74B GLN* 3.8 32.8 - - - +
76B LEU* 1.3 75.9 - - + +
78B GLY* 1.3 62.0 + - - +
80B LEU* 3.4 25.0 + - + +
81B ARG* 3.6 26.2 + - - +
130B CYS* 4.0 13.7 - - + +
131B LEU* 4.1 16.8 - - + +
134B SER* 3.2 29.4 - - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLN 2.8 22.1 + - - -
75B GLN* 4.0 1.6 - - - -
76B LEU 3.2 0.2 - - - -
77B LEU* 1.3 73.3 - - - +
79B ALA* 1.3 61.5 + - - +
81B ARG* 3.3 39.0 + - - +
82B GLU* 3.8 9.9 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B VAL* 5.8 0.4 - - + -
61B VAL* 5.3 6.6 - - + +
63B VAL* 3.8 28.0 - - + -
75B GLN 3.1 14.3 + - - +
76B LEU* 3.2 10.1 + - + +
78B GLY* 1.3 76.8 - - - +
80B LEU* 1.3 63.3 + - + +
82B GLU* 3.3 23.8 + - - +
83B LEU* 3.4 17.1 + - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.7 29.4 - - + -
35B VAL* 5.0 3.1 - - + -
76B LEU* 3.2 19.7 + - + +
77B LEU* 3.5 13.2 - - + +
78B GLY 3.2 0.8 - - - -
79B ALA* 1.3 73.9 - - + +
81B ARG* 1.3 66.4 + - - +
82B GLU 3.0 3.3 + - - -
83B LEU* 3.1 38.9 + - + +
131B LEU* 4.1 13.5 - - + -
134B SER* 4.3 15.3 - - - +
135B VAL* 3.4 29.2 - - + +
138B ALA* 5.2 13.5 - - + +
139B PHE* 5.1 6.2 - - + -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLN* 4.3 17.8 + - - -
77B LEU* 3.6 19.2 + - - +
78B GLY* 3.3 29.4 + - - +
80B LEU* 1.3 77.9 - - - +
82B GLU* 1.3 58.7 + - + +
83B LEU 3.8 3.3 + - - +
138B ALA* 6.0 3.1 - - - -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLY 3.9 10.5 - - - +
79B ALA* 3.6 17.0 - - - +
80B LEU 3.0 1.2 - - - -
81B ARG* 1.3 78.3 - - + +
83B LEU* 1.3 63.0 + - - +
84B PRO* 3.7 5.5 - - - +
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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