Contacts of the strand formed by residues 68 - 73 (chain C) in PDB entry 5JMO
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 PHE 68 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 4.4 0.4 - - - -
48C VAL* 3.6 20.9 - - + -
60C TYR* 3.4 20.1 - - + -
64C VAL* 3.2 41.0 + - + +
66C GLY* 5.0 3.5 + - - -
67C ARG* 1.3 113.2 + - + +
69C THR* 1.3 64.7 + - - +
81C LEU* 4.0 18.8 - - + -
82C GLN 3.2 4.5 - - - +
83C MET* 3.4 49.6 - - + -
84C ASN 4.1 1.8 - - - -
86C LEU* 4.0 5.6 - - + -
90C ASP* 4.0 17.9 - - - -
94C TYR* 4.3 5.4 - - - -
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Residues in contact with THR 69 (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 TYR* 3.5 8.3 - - - +
67C ARG 5.1 1.0 + - - -
68C PHE* 1.3 77.5 + - - +
70C ILE* 1.3 72.3 + - - +
71C SER* 4.1 6.4 + - - -
80C TYR 4.5 0.3 - - - -
81C LEU* 3.5 4.2 - - - -
82C GLN* 2.7 62.7 + - + +
84C ASN* 5.2 2.1 + - - -
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Residues in contact with ILE 70 (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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34C MET 4.3 3.1 - - - +
36C TRP* 3.5 23.6 - - + +
49C SER* 3.2 26.2 - - - +
50C SER* 3.7 39.3 - - - +
51C ILE* 3.7 18.4 - - + +
58C THR* 3.8 16.0 - - + +
60C TYR* 3.0 22.8 + - + +
69C THR* 1.3 78.4 - - - +
71C SER* 1.3 66.7 + - - +
79C LEU* 4.0 9.6 - - + -
80C TYR 3.5 14.4 - - - +
81C LEU* 4.1 2.7 - - + -
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Residues in contact with SER 71 (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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51C ILE* 3.8 11.4 - - - -
69C THR* 4.9 6.5 + - - +
70C ILE* 1.3 77.8 - - - +
72C ARG* 1.3 59.2 + - - +
79C LEU* 3.4 6.4 - - - +
80C TYR* 2.7 55.3 + - - +
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Residues in contact with ARG 72 (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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29C PHE* 3.0 48.6 + - + -
30C SER* 4.0 1.0 - - - +
32C TYR 2.9 21.8 + - - -
34C MET* 3.6 22.3 - - - +
51C ILE* 3.9 17.9 + - + +
52C ASN 2.8 34.3 + - - -
53C ARG* 3.2 20.7 + - - +
54C VAL 4.5 4.7 - - - +
55C GLY* 4.2 7.6 - - - +
71C SER* 1.3 79.6 - - - +
73C ASP* 1.3 60.1 + - - +
74C ASN* 2.9 20.2 + - - +
78C THR 3.4 11.4 - - - +
79C LEU* 4.0 10.8 - - + +
80C TYR* 4.5 4.3 - - - -
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Residues in contact with ASP 73 (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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72C ARG* 1.3 72.8 - - - +
74C ASN* 1.3 58.3 + - - +
75C ALA* 3.2 13.3 + - - +
76C LYS* 3.1 45.9 + - + +
77C ASN 3.0 22.3 + - - -
78C THR 2.8 18.5 + - - +
80C TYR* 4.2 18.0 + - + +
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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