Contacts of the strand formed by residues 70 - 77 (chain C) in PDB entry 3DEG
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 THR 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ASN* 2.9 25.3 + - - +
62C ASP* 4.0 33.0 - - + +
63C TYR 3.6 7.6 - - - +
64C LYS* 3.4 21.4 - - + +
68C GLY 5.3 0.2 + - - -
69C GLU* 1.3 75.7 - - - +
71C TYR* 1.3 64.0 + - - +
72C GLN 4.1 0.9 + - - +
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Residues in contact with TYR 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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2C LYS 4.3 0.9 - - - -
3C ASN* 3.2 49.0 + - + +
5C ARG* 3.9 14.6 + - + -
62C ASP* 3.4 3.5 - - - -
63C TYR* 2.8 41.1 + - + +
65C ALA* 3.5 29.6 - - + -
67C ASP* 2.8 23.4 + - - -
69C GLU* 3.7 23.7 + - + -
70C THR* 1.3 73.8 - - - +
72C GLN* 1.3 58.7 + - - +
73C LEU* 3.2 23.8 + - + +
177C VAL* 3.6 34.3 - - + +
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Residues in contact with GLN 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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3C ASN* 3.0 7.2 + - + +
4C ILE* 3.2 19.2 - - + +
5C ARG 2.9 26.2 + - - -
60C THR* 3.9 22.1 - - + +
61C LEU 3.4 5.6 - - - +
62C ASP* 3.8 11.4 + - - +
70C THR 4.1 1.6 + - - -
71C TYR* 1.3 68.5 - - - +
73C LEU* 1.3 60.5 + - - +
74C ASN* 3.0 24.6 + - - +
239C ILE* 4.5 13.5 - - - +
254C GLU* 2.8 53.9 + - - +
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Residues in contact with LEU 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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5C ARG* 3.6 32.1 - - + -
7C PHE* 4.2 17.5 - - + -
24C ILE* 5.1 4.3 - - + -
28C CYS* 4.6 5.8 - - - -
59C VAL 3.6 1.7 - - - +
60C THR* 3.3 2.6 - - - -
61C LEU* 2.7 49.0 + - + +
63C TYR* 3.9 14.4 - - + -
71C TYR* 3.9 13.2 - - + +
72C GLN* 1.3 72.5 - - - +
74C ASN* 1.3 61.2 + - - +
75C PHE* 4.0 2.3 - - + -
173C LEU* 3.9 35.7 - - + -
176C LEU* 4.2 9.0 - - + -
177C VAL* 4.1 15.5 - - + -
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Residues in contact with ASN 74 (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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4C ILE* 3.5 15.6 - - - +
5C ARG 3.1 7.6 + - - +
6C ASN* 3.2 11.9 + - - +
7C PHE 3.2 22.0 + - - +
59C VAL 3.5 3.4 - - - -
60C THR* 2.7 31.5 + - - +
72C GLN* 3.0 33.3 + - - +
73C LEU* 1.3 71.2 - - - +
75C PHE* 1.3 60.6 + - - +
76C ILE* 4.6 3.6 - - - +
255C VAL* 2.7 45.6 + - + +
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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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7C PHE* 3.1 44.6 - + + +
9C ILE* 3.9 21.5 - - + -
21C SER* 3.2 41.5 - - - -
24C ILE* 5.0 6.7 - - + -
25C ILE* 4.8 4.3 - - + -
58C SER* 3.3 5.1 - - - -
59C VAL* 2.9 69.1 + - + -
61C LEU* 4.9 10.5 - - + -
73C LEU* 4.0 2.4 - - + -
74C ASN* 1.3 73.9 - - - +
76C ILE* 1.3 77.5 + - - +
77C ASP* 4.5 10.1 - - + -
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Residues in contact with ILE 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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6C ASN* 5.6 1.1 - - + -
7C PHE 3.0 6.8 + - - +
8C SER* 3.1 32.9 - - - -
9C ILE 3.6 3.8 + - - -
55C LYS* 5.3 2.5 - - - -
58C SER* 4.1 16.2 - - - -
74C ASN 4.6 6.3 - - - +
75C PHE* 1.3 86.1 - - - +
77C ASP* 1.3 72.0 + - - +
91C SER* 3.4 33.4 - - - +
94C ALA* 4.6 15.7 - - + +
95C CYS* 3.9 23.1 - - - -
196C ILE* 4.9 23.6 - - + -
209C LEU* 5.6 0.2 - - + -
211C ARG* 6.1 0.2 - - + -
255C VAL* 5.3 11.0 - - + -
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Residues in contact with ASP 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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9C ILE* 5.2 2.2 - - - +
17C LYS* 2.9 28.4 + - - -
18C SER* 4.7 5.9 + - - -
21C SER* 4.8 7.5 + - - -
42C ASP* 4.4 2.3 - - - +
53C THR* 3.2 25.8 + - - +
55C LYS* 3.7 9.8 - - - +
56C ALA* 3.6 37.5 + - + +
58C SER* 4.7 6.0 - - - +
75C PHE* 4.3 11.6 + - + -
76C ILE* 1.3 84.1 - - - +
78C THR* 1.3 72.0 + - - +
79C PRO* 3.3 12.5 - - - +
91C SER* 4.7 0.2 + - - -
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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