Contacts of the helix formed by residues 69 - 82 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66F ASP* 3.3 22.7 + - + +
67F LEU 3.3 1.1 - - - +
68F GLY* 1.3 80.0 - - - +
70F GLU* 1.3 67.5 + - - +
71F ALA* 4.4 7.9 - - + +
72F GLY 4.4 3.1 - - - +
73F LEU* 3.1 23.6 + - - +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E SER* 2.6 37.5 + - - -
115E THR* 3.9 21.6 - - + +
118E ASN* 3.5 17.5 + - - +
69F ALA* 1.3 73.1 - - - +
71F ALA* 1.3 58.1 + - - +
73F LEU* 3.1 7.6 + - - +
74F GLN* 2.9 51.3 + - + +
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ALA* 3.4 4.8 - - + +
70F GLU* 1.3 78.3 - - - +
72F GLY* 1.3 62.2 + - - +
74F GLN* 3.5 6.6 + - - +
75F GLN* 3.1 34.2 + - - +
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Residues in contact with GLY 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ALA* 3.3 20.7 - - - +
66F ASP* 3.1 30.9 + - - -
67F LEU* 4.3 0.8 - - - +
69F ALA* 3.5 6.1 + - - +
70F GLU 3.3 0.4 - - - -
71F ALA* 1.3 77.6 - - - +
73F LEU* 1.3 62.5 + - - +
75F GLN* 3.3 20.7 + - - +
76F LEU* 3.3 4.3 + - - +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E SER* 3.7 31.2 - - - +
66F ASP 3.7 1.6 + - - -
67F LEU* 4.3 20.9 - - + +
69F ALA 3.1 15.9 + - - +
70F GLU* 3.1 8.8 + - - +
72F GLY* 1.3 76.4 - - - +
74F GLN* 1.3 62.6 + - - +
76F LEU* 3.1 4.9 + - + +
77F LEU* 2.9 51.1 + - + +
122F ALA 6.0 0.2 - - - +
126F THR* 4.8 3.4 - - + -
127F SER* 3.9 41.3 - - - +
130F CYS* 4.4 9.6 - - + -
131F LEU* 5.0 4.7 - - + +
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Residues in contact with GLN 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E SER 5.4 2.2 + - - -
114E SER* 3.8 10.7 + - - -
70F GLU* 2.9 41.2 + - + +
71F ALA* 4.0 6.7 - - - +
73F LEU* 1.3 75.1 - - - +
75F GLN* 1.3 56.8 + - - +
77F LEU* 3.8 28.1 - - - +
78F GLY* 2.7 31.7 + - - -
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Residues in contact with GLN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.0 8.4 - - + +
64F PRO 3.7 18.2 - - - +
65F ALA* 4.0 6.5 - - + +
71F ALA* 3.1 21.3 + - - +
72F GLY* 3.3 19.8 - - - +
73F LEU 3.2 0.2 - - - -
74F GLN* 1.3 77.2 - - - +
76F LEU* 1.3 56.7 + - - +
78F GLY* 3.9 0.7 - - - -
79F ALA* 3.1 27.0 + - - +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 4.7 8.5 - - + -
10F THR* 4.2 9.0 - - + -
35F VAL* 4.4 11.7 - - + -
37F SER* 3.8 16.8 - - - +
63F VAL* 3.8 34.7 - - + +
65F ALA* 4.8 0.9 - - + -
67F LEU* 3.7 26.0 - - + -
72F GLY 3.3 6.8 + - - +
73F LEU* 3.1 9.0 + - + +
75F GLN* 1.3 77.8 - - - +
77F LEU* 1.3 64.5 + - - +
79F ALA* 3.2 13.3 + - + +
80F LEU* 3.4 13.3 + - + +
131F LEU* 3.8 36.6 - - + -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E SER* 4.8 10.8 - - - +
114E SER* 6.1 0.2 - - - -
73F LEU* 2.9 33.8 + - + +
74F GLN* 3.8 35.4 - - - +
76F LEU* 1.3 76.5 - - + +
78F GLY* 1.3 62.3 + - - +
80F LEU* 3.3 27.2 - - + +
81F ARG* 4.0 7.4 + - - +
130F CYS* 4.0 17.0 - - + +
131F LEU* 4.1 15.7 - - + -
134F SER* 3.2 29.2 - - - +
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Residues in contact with GLY 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F GLN 2.7 23.2 + - - -
75F GLN 3.9 1.3 - - - -
77F LEU* 1.3 71.0 - - - +
79F ALA* 1.3 63.3 + - - +
80F LEU 3.2 1.0 + - - -
81F ARG* 3.3 23.2 + - - +
82F GLU* 4.0 4.9 + - - +
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL* 5.8 1.6 - - + -
61F VAL* 5.3 7.4 - - + +
63F VAL* 3.8 27.6 - - + -
75F GLN 3.1 14.5 + - - +
76F LEU* 3.2 11.4 + - + +
78F GLY* 1.3 75.1 - - - +
80F LEU* 1.3 61.3 + - - +
82F GLU* 3.6 5.2 + - - +
83F LEU* 3.2 22.4 + - - +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 4.0 22.0 - - + -
35F VAL* 6.3 0.9 - - + -
76F LEU* 3.4 7.2 + - + +
77F LEU* 3.3 25.5 + - + +
78F GLY 3.1 0.4 - - - -
79F ALA* 1.3 77.7 - - - +
81F ARG* 1.3 65.4 + - + +
82F GLU 3.1 1.4 + - - -
83F LEU* 3.2 21.4 + - + +
131F LEU* 4.8 4.3 - - + +
134F SER* 3.8 28.0 - - - +
135F VAL* 3.6 37.2 - - + +
138F ALA* 5.1 10.0 - - + +
139F PHE* 4.6 21.2 - - + -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG 4.0 10.0 - - - +
82D GLU* 3.5 27.5 - - - +
77F LEU 4.3 8.1 - - - +
78F GLY* 3.3 14.8 + - - +
80F LEU* 1.3 76.4 - - + +
82F GLU* 1.3 58.7 + - + +
83F LEU 4.1 2.3 + - - +
138F ALA* 6.3 1.1 - - - -
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG 5.1 3.4 - - - +
83D LEU 3.9 11.4 - - - +
84D PRO* 4.0 1.3 - - - -
85D ARG* 2.9 59.9 + - + +
78F GLY 4.0 6.1 + - - +
79F ALA* 3.6 7.8 + - - +
80F LEU 3.1 0.6 - - - -
81F ARG* 1.3 78.1 - - + +
83F LEU* 1.3 63.0 + - - +
84F PRO* 3.8 1.6 - - - +
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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