Contacts of the strand formed by residues 74 - 79 (chain C) in PDB entry 3DGG
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 ASP 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C SER* 4.7 8.3 + - - +
23C CYS 3.7 2.3 - - - +
24C ARG* 3.9 25.6 + - - +
70C GLY* 3.2 21.7 - - - -
71C SER 3.3 11.0 + - - +
72C GLY 3.7 0.2 - - - -
73C THR* 1.3 99.8 + - - +
75C PHE* 1.3 63.3 + - - +
76C THR* 5.6 1.8 - - + -
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Residues in contact with PHE 75 (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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22C SER* 3.4 2.0 + - - -
23C CYS* 2.8 47.7 + - + +
25C ALA* 5.2 2.5 - - + -
29C VAL* 3.6 26.7 - - + -
35C SER* 3.5 22.0 - - - -
37C MET* 3.7 24.5 - - + -
39C TRP* 4.1 11.8 - - + +
55C ALA* 3.8 13.5 - - + -
69C SER 3.4 8.3 - - - +
70C GLY* 3.4 27.6 - - - -
71C SER* 3.6 15.3 - - - -
72C GLY 3.4 21.8 - - - -
73C THR 4.0 6.7 - - - -
74C ASP* 1.3 76.3 - - - +
76C THR* 1.3 69.1 + - - +
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Residues in contact with THR 76 (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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20C THR* 4.4 13.0 - - + -
21C ILE 3.2 10.1 - - - +
22C SER* 4.5 9.9 - - - +
39C TRP* 4.0 7.1 + - - -
68C GLY* 3.3 4.7 - - - -
69C SER* 2.6 59.2 + - - +
70C GLY* 5.5 0.2 - - - -
74C ASP* 5.6 1.6 - - + -
75C PHE* 1.3 81.9 - - - +
77C LEU* 1.3 59.3 - - - +
78C ASN* 3.7 16.6 + - - -
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Residues in contact with LEU 77 (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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19C ALA 3.7 0.9 - - - +
20C THR* 3.5 3.3 - - - +
21C ILE* 2.8 46.9 + - + +
39C TRP* 3.7 43.8 - - + -
51C LEU* 4.8 3.8 - - + -
52C ILE* 3.9 25.4 - - + -
66C PHE* 4.6 10.5 - - + -
67C SER 3.7 14.6 - - - +
76C THR* 1.3 73.2 - - - +
78C ASN* 1.3 67.1 + - - +
79C ILE* 4.6 9.0 - - + +
90C TYR* 3.7 36.6 - - + -
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Residues in contact with ASN 78 (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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18C ARG* 3.4 28.6 + - - +
19C ALA 3.3 1.5 - - - +
20C THR* 2.9 28.6 + - - +
65C ARG 3.6 1.4 - - - +
66C PHE* 3.5 4.5 - - - +
67C SER* 2.8 51.5 + - - +
68C GLY* 6.1 0.2 - - - -
69C SER* 4.7 3.8 + - - +
76C THR* 3.7 24.7 + - - -
77C LEU* 1.3 75.0 - - - +
79C ILE* 1.3 65.1 + - - +
80C HIS* 4.2 1.3 - - + +
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Residues in contact with ILE 79 (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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18C ARG* 3.4 1.6 - - - -
19C ALA* 2.8 45.3 + - + +
21C ILE* 4.9 4.5 - - + -
65C ARG* 3.5 13.9 - - + +
66C PHE* 3.7 36.6 - - + -
77C LEU* 4.6 11.2 - - + +
78C ASN* 1.3 78.1 - - - +
80C HIS* 1.3 65.1 + - - +
82C VAL* 3.5 9.1 - - + +
86C ASP* 3.6 24.2 - - + +
90C TYR* 3.8 15.9 - - + +
107C LEU* 3.6 29.2 - - + -
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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