Contacts of the strand formed by residues 58 - 64 (chain A) in PDB entry 2Z21
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 CYS 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASN* 3.9 11.0 - - - -
47A LEU* 4.1 0.2 - - - -
54A PHE* 3.0 42.3 + - + +
55A ILE* 3.5 14.7 + - - +
57A THR* 1.3 80.9 - - - +
59A ARG* 1.3 63.6 + - - +
61A THR* 5.4 2.7 - - + -
71A ALA* 4.5 5.8 - - + -
72A GLU 3.0 6.7 - - - +
73A CYS* 2.1 48.2 - - - -
80A PHE* 4.4 3.1 - - - -
52B SER* 5.2 3.1 + - - -
53B ASN* 4.8 6.6 + - - +
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Residues in contact with ARG 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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58A CYS* 1.3 77.7 - - - +
60A ASN* 1.3 84.4 + - - +
61A THR* 3.3 5.9 + - - -
71A ALA* 3.7 2.8 - - - +
72A GLU* 2.7 51.7 + - - +
80A PHE* 3.4 64.2 - - + +
52B SER* 5.7 3.6 - - - -
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Residues in contact with ASN 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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59A ARG* 1.3 91.2 - - - +
61A THR* 1.3 66.2 + - - +
62A GLN* 3.6 16.3 + - + +
70A ALA 3.8 5.0 - - - +
71A ALA* 3.8 4.7 - - - -
72A GLU* 2.8 35.5 + - - +
52B SER* 5.9 0.4 + - - -
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Residues in contact with THR 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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13A ILE* 3.8 12.8 - - - +
14A GLN* 5.9 0.2 - - - -
15A GLY* 2.6 44.1 + - - +
54A PHE* 3.9 27.1 - - + -
55A ILE* 5.6 1.3 - - + -
58A CYS* 5.4 2.9 - - + -
59A ARG* 4.6 5.2 - - - +
60A ASN* 1.3 77.5 - - - +
62A GLN* 1.3 66.4 + - - +
69A LEU* 4.0 5.8 - - + -
70A ALA 3.3 5.6 - - - -
71A ALA* 3.9 11.9 - - + -
52B SER* 4.9 6.1 + - - +
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Residues in contact with GLN 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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13A ILE* 3.9 11.6 - - - +
60A ASN* 3.7 12.7 - - + +
61A THR* 1.3 82.0 - - - +
63A LEU* 1.3 66.1 + - - +
64A ALA* 6.0 0.4 - - + -
68A GLU 3.6 0.9 - - - +
69A LEU* 3.6 4.9 - - - +
70A ALA* 2.8 45.8 + - + +
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Residues in contact with LEU 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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4A PHE* 5.4 0.2 - - + -
11A SER* 3.7 42.2 - - - +
12A ALA* 4.1 2.5 - - - +
13A ILE* 3.6 32.8 + - + +
18A LEU* 4.6 5.4 - - + -
62A GLN* 1.3 78.2 - - - +
64A ALA* 1.3 60.2 + - - +
65A GLY 3.6 17.6 + - - +
66A SER* 4.0 8.7 - - - +
67A SER* 4.0 7.4 - - - -
68A GLU 3.4 26.9 - - - +
87A LEU* 4.4 8.1 - - + -
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Residues in contact with ALA 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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62A GLN* 3.8 1.1 + - + -
63A LEU* 1.3 72.1 - - - +
65A GLY* 1.3 66.0 + - - +
66A SER 3.6 0.2 + - - -
67A SER 3.7 0.2 + - - -
68A GLU* 2.8 53.3 + - + +
70A ALA* 4.5 15.3 - - + -
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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