Contacts of the strand formed by residues 32 - 38 (chain C) 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 SER 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C GLY 3.4 7.8 + - - -
4C ARG* 3.5 1.0 - - - -
5C ALA 2.9 32.5 + - - +
28C LEU* 3.6 22.2 - - - +
29C SER 2.7 22.6 + - - -
31C GLY* 1.3 83.8 - - - +
33C VAL* 1.3 61.1 + - - +
57C GLY 3.6 1.4 + - - -
58C LEU* 3.7 8.3 - - - -
59C ARG* 3.0 28.5 + - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA 2.8 12.3 + - - +
6C VAL* 3.5 8.5 - - + -
7C CYS* 2.7 34.9 + - - +
28C LEU* 5.2 0.2 - - - -
32C SER* 1.3 80.3 - - - +
34C LEU* 1.3 57.5 + - - +
35C VAL* 4.4 12.8 - - + -
59C ARG* 3.4 38.8 - - + +
61C VAL* 4.3 19.5 - - + -
83C LEU* 4.4 13.5 - - + -
84C PRO* 4.3 17.9 - - + +
86C PRO* 4.1 14.4 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C CYS* 3.4 29.8 - - + +
8C LEU 4.7 0.2 - - - +
9C LEU* 4.9 3.1 - - + -
21C ALA* 4.4 6.5 - - - +
24C LEU* 4.5 8.1 - - + -
25C ALA* 4.0 32.3 - - + +
28C LEU* 4.3 10.5 - - + -
33C VAL* 1.3 73.6 - - - +
35C VAL* 1.3 70.3 + - - +
36C LEU* 3.9 23.3 - - + -
51C LEU* 4.1 17.9 - - + -
58C LEU* 4.8 6.7 - - + +
59C ARG 2.9 11.0 + - - +
60C VAL* 3.4 10.7 - - + +
61C VAL 2.8 26.2 + - - +
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 5.5 0.4 - - + -
7C CYS 2.8 18.1 + - - +
8C LEU* 3.8 22.9 - - + -
9C LEU 2.9 28.4 + - - +
33C VAL* 4.4 6.1 - - + -
34C LEU* 1.3 74.6 - - - +
36C LEU* 1.3 67.5 + - - +
37C SER* 5.5 0.4 - - - -
61C VAL* 3.3 16.4 - - + +
63C VAL* 3.9 22.0 - - + -
76C LEU* 4.4 8.3 - - + -
79C ALA* 5.8 1.6 - - + -
80C LEU* 6.2 0.7 - - + -
83C LEU* 3.8 40.4 - - + -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.6 19.1 - - + -
12C ALA* 3.9 22.7 - - + -
21C ALA* 4.1 9.9 - - + -
34C LEU* 3.9 22.0 - - + -
35C VAL* 1.3 77.7 - - - +
37C SER* 1.3 61.4 + - - +
44C LEU* 4.1 14.9 - - + +
47C LEU* 3.7 24.7 - - + -
48C GLU* 5.0 4.0 - - + +
51C LEU* 4.3 11.2 - - + -
60C VAL* 3.8 25.8 - - + -
61C VAL 2.8 11.8 + - - +
62C ARG* 3.6 5.4 - - + -
63C VAL* 2.9 27.0 + - - +
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Residues in contact with SER 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 6.4 0.4 - - - -
9C LEU 3.1 12.0 + - - -
10C THR* 4.2 11.4 - - - -
11C GLY 3.0 9.5 + - - -
12C ALA* 3.0 26.2 + - - +
35C VAL* 5.5 1.6 - - - -
36C LEU* 1.3 75.1 - - - +
38C ALA* 1.3 59.8 + - - +
44C LEU* 4.0 4.0 - - - -
63C VAL* 2.8 19.0 + - - +
65C ALA* 4.5 7.6 + - - +
67C LEU* 4.8 5.1 - - - +
76C LEU* 3.8 34.5 - - - +
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLY* 4.6 0.7 - - - -
12C ALA 4.1 1.3 - - - +
13C SER* 3.3 40.4 - - - +
37C SER* 1.3 79.3 + - - +
39C ARG* 1.3 61.9 + - - +
40C ASN 4.2 1.6 - - - +
44C LEU* 3.9 10.2 - - + +
63C VAL 3.7 0.8 + - - -
64C PRO* 3.2 8.7 - - - +
65C ALA 2.8 27.2 + - - -
803C NAP 3.7 19.1 - - - +
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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