Contacts of the strand formed by residues 44 - 50 (chain V) in PDB entry 1ZGL
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 GLN 44 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35V TYR* 4.2 2.2 - - - -
36V GLN* 2.9 54.1 + - - +
41V GLN* 4.4 18.0 - - + +
42V GLY 4.4 4.3 - - - +
43V LEU* 1.3 73.6 - - - +
45V PHE* 1.3 66.1 + - - +
46V LEU* 3.6 3.8 + - - +
59V ASN* 4.6 16.3 - - + +
60V PHE* 3.6 24.6 - - + -
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Residues in contact with PHE 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U TYR 4.1 4.0 - - - -
103U LYS* 3.5 50.9 - - + -
104U LEU 5.8 0.2 - - - +
33V SER* 3.3 26.5 - - - -
34V TRP 4.0 0.2 - - - -
35V TYR* 3.7 24.5 - + + -
43V LEU 4.3 0.4 + - - -
44V GLN* 1.3 74.9 - - - +
46V LEU* 1.3 59.3 + - - +
47V PHE* 3.4 23.3 - - - -
48V GLU* 3.6 5.6 - - + -
56V ASN* 3.4 25.1 - - + -
58V GLY* 3.2 41.7 - - - -
59V ASN 3.8 8.8 + - - -
60V PHE* 3.2 18.6 - - - -
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Residues in contact with LEU 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34V TRP* 2.9 28.1 + - + +
35V TYR 3.4 9.2 - - - +
36V GLN* 3.3 44.0 - - + +
44V GLN 3.6 2.2 + - - +
45V PHE* 1.3 76.1 - - - +
47V PHE* 1.3 90.0 + - + +
57V LYS 2.6 28.4 - - - +
58V GLY* 3.8 1.0 + - - -
59V ASN 4.2 1.9 - - - +
60V PHE* 3.6 22.4 - - + -
65V PHE* 3.6 26.2 - - + -
77V MET* 4.6 7.6 - - + -
90V TYR* 4.6 6.7 - - + -
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Residues in contact with PHE 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V VAL 3.9 0.9 - - - +
33V SER* 3.2 2.4 - - - -
34V TRP* 2.9 33.7 + + + -
45V PHE* 3.4 9.4 - - - -
46V LEU* 1.3 114.9 - - + +
48V GLU* 1.3 60.8 + - - +
49V TYR* 3.6 34.1 - + + +
54V GLN* 4.2 11.7 - - + +
56V ASN 3.2 16.2 - - - +
57V LYS* 4.1 7.2 - - + -
59V ASN 5.6 0.4 - - - -
60V PHE* 6.0 1.1 - - + -
65V PHE* 4.2 16.6 - - + -
66V SER* 3.1 34.8 - - - -
67V GLY* 4.6 0.4 - - - -
77V MET* 3.7 23.1 - - + -
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Residues in contact with GLU 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U TYR* 3.6 33.6 - - + +
31V SER* 2.6 23.0 + - - +
32V VAL 3.4 2.7 - - - -
33V SER* 3.7 17.0 - - - +
45V PHE* 4.1 6.3 - - + -
47V PHE* 1.3 75.9 - - - +
49V TYR* 1.3 67.8 + - - +
54V GLN* 2.9 25.3 - - - +
55V ARG* 2.4 59.5 + - - +
56V ASN 3.2 8.8 + - - +
102V THR* 5.6 4.9 - - + +
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Residues in contact with TYR 49 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31V SER* 2.8 9.9 + - - -
32V VAL* 2.7 49.0 + - + +
34V TRP* 5.1 2.9 - + - -
47V PHE* 3.6 40.2 - + + -
48V GLU* 1.3 77.1 + - - +
50V PHE* 1.3 59.5 + - - +
52V GLU 5.1 0.7 - - - -
53V THR 4.4 1.6 - - - -
54V GLN* 3.0 52.9 + - + +
67V GLY* 3.3 30.0 + - - -
68V ARG* 4.0 16.6 - - - -
69V GLN* 2.8 37.8 + - + +
75V SER* 4.3 14.8 - - - -
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Residues in contact with PHE 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J ALA* 3.8 14.7 - - + +
65J VAL* 3.6 33.2 - - + -
8L VAL* 4.0 17.0 - - + -
10L PRO* 4.0 28.3 - - + -
30V ARG* 3.8 20.9 - - + +
31V SER* 4.3 1.3 - - - -
48V GLU* 4.0 0.8 + - - -
49V TYR* 1.3 72.0 - - - +
51V ASN* 1.3 81.7 + - + +
52V GLU 2.9 1.8 - - - -
53V THR* 2.6 21.3 + - - +
54V GLN 4.3 2.0 + - - +
55V ARG* 2.9 51.5 - - - +
69V GLN* 2.8 4.8 - - - +
97V ALA* 3.9 17.5 - - + -
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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