Contacts of the strand formed by residues 3 - 7 (chain C) in PDB entry 3O9Z
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 ARG 3 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.7 12.6 - - + +
2C THR* 1.3 72.3 - - - +
4C PHE* 1.3 61.8 + - - +
27C VAL* 3.6 17.4 - - + +
29C VAL* 3.7 37.7 - - + +
64C LEU* 4.0 7.7 - - - +
69C GLU* 2.8 39.1 + - - +
70C GLY 3.4 11.4 + - - -
71C VAL* 3.6 8.7 - - - +
72C ASP* 2.8 44.4 + - - +
73C TYR* 3.1 8.5 + - - +
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Residues in contact with PHE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C THR* 3.5 40.2 - - + -
3C ARG* 1.3 75.0 - - - +
5C ALA* 1.3 61.7 + - - +
21C ILE* 3.8 36.3 - - + -
24C VAL* 4.5 4.5 - - + -
26C GLY* 4.1 9.2 - - - -
27C VAL 2.8 11.0 + - - +
28C LEU* 3.5 4.3 - - + -
29C VAL* 2.7 35.2 + - - +
71C VAL* 4.1 4.0 - - - -
73C TYR* 3.3 32.3 - + + -
75C SER* 3.4 18.8 - - - -
98C LEU* 5.3 1.3 - - + -
268C TYR* 3.6 32.1 - + - -
272C LEU* 4.2 14.8 - - + -
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Residues in contact with ALA 5 (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 PHE* 1.3 75.8 - - - +
6C LEU* 1.3 61.3 + - - +
28C LEU* 4.0 2.0 - - - -
30C ALA* 3.1 15.5 - - + +
57C PHE* 3.9 13.2 - - + -
61C LEU* 4.2 20.4 - - + -
71C VAL* 4.2 6.9 - - + +
73C TYR 3.0 8.4 + - - +
74C LEU* 3.4 20.1 - - + +
75C SER* 2.8 27.7 + - - -
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Residues in contact with LEU 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ALA* 1.3 76.2 - - - +
7C THR* 1.3 78.9 + - - +
9C LEU* 3.9 18.2 - - + +
14C ALA* 4.5 8.7 - - + -
17C HIS* 4.0 26.5 - - + -
18C LEU* 3.7 31.9 - - + +
21C ILE* 5.0 3.6 - - + -
28C LEU* 3.8 14.6 - - + -
30C ALA 3.0 7.1 + - - -
31C SER* 3.1 6.9 - - - +
32C LEU 2.9 24.9 + - - +
57C PHE* 4.1 1.2 - - - -
75C SER* 3.3 34.5 - - - +
77C ALA* 4.5 5.6 - - + -
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Residues in contact with THR 7 (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 LEU* 1.3 80.1 - - - +
8C GLY* 1.3 61.3 + - - +
9C LEU 3.6 0.4 - - - -
32C LEU* 3.5 6.7 - - + -
57C PHE* 3.9 24.9 - - + -
74C LEU* 4.0 16.6 - - + -
75C SER 2.9 9.2 + - - +
76C ILE* 3.4 14.7 - - - +
77C ALA* 2.8 31.1 + - - +
78C SER* 3.8 2.1 + - - -
86C GLN* 2.8 38.1 + - - +
89C MET* 6.1 0.4 - - - -
311C NAD 3.7 11.4 - - - -
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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