Contacts of the strand formed by residues 58 - 64 (chain C) in PDB entry 4J4D
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 3.0 28.3 + - + +
55C ILE* 3.5 16.6 - - - +
56C GLU 4.7 0.7 - - - -
57C THR* 1.3 81.4 + - - +
59C ARG* 1.3 61.9 + - - +
61C THR* 5.0 4.6 - - + +
71C ALA* 4.3 9.0 - - + -
72C GLU 3.3 8.1 - - - +
73C CYS* 2.0 50.3 - - - -
80C PHE* 4.9 1.8 - - - -
42D ASN* 3.8 16.8 - - - -
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Residues in contact with ARG 59 (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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58C CYS* 1.3 76.2 - - - +
60C ASN* 1.3 79.6 + - + +
61C THR* 3.3 6.8 + - - -
71C ALA* 3.8 2.9 - - - +
72C GLU* 2.8 62.8 + - + +
80C PHE* 3.6 52.8 - - + +
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Residues in contact with ASN 60 (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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59C ARG* 1.3 85.0 - - + +
61C THR* 1.3 62.7 + - - +
62C GLN* 3.0 37.7 + - - +
70C ALA 3.5 6.8 - - - +
71C ALA* 3.8 3.7 - - - -
72C GLU* 3.3 30.1 + - + +
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Residues in contact with THR 61 (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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54C PHE* 4.2 22.0 - - + +
55C ILE* 6.1 1.6 - - - -
58C CYS* 5.0 2.5 - - + +
59C ARG* 4.2 11.0 - - - +
60C ASN* 1.3 74.5 + - - +
62C GLN* 1.3 63.3 + - - +
69C LEU* 4.3 8.1 - - + -
70C ALA 3.5 4.9 - - - -
71C ALA* 4.0 17.9 - - + -
13D ILE* 3.8 12.8 - - - +
15D GLY* 2.8 41.7 + - - +
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Residues in contact with GLN 62 (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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60C ASN* 3.0 38.8 + - - +
61C THR* 1.3 78.6 - - - +
63C LEU* 1.3 70.9 + - - +
69C LEU* 3.4 12.0 - - - +
70C ALA* 3.0 35.0 + - + +
13D ILE* 3.7 12.2 - - - +
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Residues in contact with LEU 63 (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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62C GLN* 1.3 88.5 + - - +
64C ALA* 1.3 63.5 + - - +
65C GLY 3.4 20.4 - - - +
66C SER* 4.3 7.9 - - - +
67C SER* 4.6 4.3 - - - +
68C GLU 3.4 23.3 - - - +
70C ALA* 5.0 1.0 - - - +
87C LEU* 4.4 8.5 - - + -
11D SER* 3.5 36.1 - - - +
12D ALA* 5.2 0.7 - - - -
13D ILE* 3.8 31.3 - - + +
18D LEU* 4.5 8.5 - - + -
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Residues in contact with ALA 64 (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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63C LEU* 1.3 75.9 - - - +
65C GLY* 1.3 65.6 + - - +
66C SER 3.5 0.3 + - - -
67C SER 3.8 0.2 + - - -
68C GLU* 3.0 54.1 + - + +
70C ALA* 4.2 17.3 - - + -
84C LYS* 4.6 6.7 - - + -
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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