Contacts of the strand formed by residues 58 - 66 (chain A) in PDB entry 1Z0F
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 5.6 6.3 - - - -
53A ILE 3.6 0.2 - - - +
54A GLU* 3.3 6.1 - - - -
55A VAL 2.7 46.4 + - - +
56A SER* 3.3 2.4 - - - +
57A GLY* 1.3 74.1 - - - +
59A LYS* 1.3 61.8 + - - +
60A ILE* 3.7 17.2 + - + +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASN* 3.6 24.2 - - + +
8A TYR* 3.9 6.3 - - - -
9A SER* 2.9 34.9 + - - +
10A TYR 3.7 1.6 + - - -
52A ILE* 4.6 5.4 - - + -
53A ILE 3.6 6.5 - - - +
54A GLU* 4.7 2.5 - - + +
57A GLY 4.4 0.4 + - - -
58A GLN* 1.3 70.5 - - - +
60A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 4.3 2.9 - - - -
9A SER* 6.2 0.2 - - - -
10A TYR* 3.6 20.0 - - + +
12A PHE* 3.7 55.2 - - + -
52A ILE* 3.4 2.6 - - - +
53A ILE* 2.8 50.4 + - + +
55A VAL* 3.8 28.9 - - + -
58A GLN* 4.1 17.7 - - + +
59A LYS* 1.3 79.3 - - - +
61A LYS* 1.3 67.7 + - - +
62A LEU* 4.2 4.5 - - + -
173A TYR 4.5 5.6 - - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 3.6 55.6 + - + +
10A TYR 3.0 8.2 + - - +
11A ILE* 3.4 12.3 - - + +
12A PHE 2.9 26.9 + - - +
50A THR* 4.2 28.6 - - - +
51A ARG 3.7 4.7 - - - +
52A ILE* 4.2 11.9 - - + -
60A ILE* 1.3 70.7 - - - +
62A LEU* 1.3 67.6 + - - +
63A GLN* 4.0 18.8 + - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.5 35.9 - - + +
14A TYR* 3.9 26.5 - - + +
31A PHE* 3.9 25.4 - - + -
50A THR* 3.1 10.4 - - - -
51A ARG 2.8 39.2 + - - +
53A ILE* 3.8 33.9 - - + -
60A ILE* 4.2 3.1 - - + -
61A LYS* 1.3 74.2 - - - +
63A GLN* 1.3 61.2 + - - +
64A ILE* 4.5 11.5 - - + +
165A PHE* 4.4 12.6 - - + -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.7 20.7 - - + +
12A PHE 2.9 10.0 + - - +
13A LYS* 3.4 32.2 - - - +
14A TYR* 2.7 36.6 + - - +
48A PHE* 3.9 18.1 - - + -
49A GLY 3.6 4.0 - - - -
50A THR* 4.1 13.9 - - + +
61A LYS* 4.4 20.8 - - + +
62A LEU* 1.3 74.4 - - - +
64A ILE* 1.3 60.2 + - - +
80A TYR* 3.4 15.2 - - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 3.6 15.9 - - + +
16A ILE* 4.3 15.9 - - + -
28A LEU* 3.8 25.8 - - + +
31A PHE* 4.0 16.2 - - + -
32A THR* 3.9 27.8 - - + -
48A PHE* 3.2 9.3 - - - -
49A GLY 2.8 36.6 + - - +
50A THR* 4.8 1.3 - - - -
62A LEU* 4.5 13.5 - - + +
63A GLN* 1.3 79.8 - - - +
65A TRP* 1.3 62.5 + - - +
66A ASP 4.2 0.4 - - - -
88A LEU* 6.1 0.2 - - + -
165A PHE* 3.9 36.3 - - + -
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Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR 3.1 8.7 + - - +
15A ILE* 3.7 3.3 - - - -
16A ILE* 3.1 22.6 + - - -
47A GLU* 2.9 45.4 + - + +
48A PHE* 3.7 19.1 - + + +
64A ILE* 1.3 75.0 - - - +
66A ASP* 1.3 70.0 + - - +
67A THR* 2.8 25.0 + - - +
70A GLN* 4.8 7.3 - - - +
76A VAL* 4.8 9.2 - - + -
77A THR* 3.2 36.6 - - + -
80A TYR* 3.5 59.9 - + + -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.6 16.5 - - + +
24A LYS* 3.4 30.1 - - + -
25A SER* 3.1 10.7 + - - +
28A LEU* 4.1 5.6 - - + +
46A VAL 4.1 9.3 - - - +
47A GLU* 2.8 28.4 + - - +
65A TRP* 1.3 74.6 + - - +
67A THR* 1.3 63.4 + - - +
68A ALA* 3.4 16.2 + - - +
70A GLN* 4.5 0.7 + - - -
200A GDP 3.6 2.8 + - - -
201A MG 2.4 30.6 - - - -
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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