Contacts of the strand formed by residues 9 - 14 (chain V) in PDB entry 5EF3
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 9 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8L ASP* 3.4 31.6 - - + -
9L PHE 5.4 1.1 - - - -
10L VAL* 5.2 2.5 - - + -
48L PHE* 4.2 16.8 - + + -
65L THR* 3.9 26.2 - - + -
66L ARG* 4.0 11.7 - - + -
67L HIS* 3.2 51.3 + + - -
9U PHE* 5.6 1.2 - - - -
7V SER 4.6 6.1 - - - -
8V ASP* 1.3 83.9 + - - +
10V VAL* 1.3 70.2 + - - +
11V VAL* 3.9 2.9 - - + -
45V ILE* 3.4 26.9 - - + -
46V ALA 3.1 21.3 - - - +
47V GLN* 3.9 9.0 - - + -
48V PHE* 4.7 1.6 - - - +
65V THR* 4.6 2.8 - - - -
66V ARG* 4.9 1.6 + - - -
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Residues in contact with VAL 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U PHE* 5.4 1.8 - - + -
45U ILE* 4.0 27.4 - - + -
9V PHE* 1.3 79.2 - - - +
11V VAL* 1.3 64.0 + - - +
12V ILE* 3.5 26.5 - - + -
44V LEU 3.8 0.5 - - - +
45V ILE* 3.3 5.2 - - - +
46V ALA* 2.8 41.1 + - + +
48V PHE* 4.6 11.0 - - + -
55V ILE* 4.0 16.4 - - + -
63V ILE* 4.8 1.1 - - + -
64V GLN 3.6 8.5 - - - +
65V THR* 3.8 23.3 - - + -
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Residues in contact with VAL 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L ILE* 6.1 0.2 - - + -
65L THR* 3.9 23.1 - - + +
67L HIS* 4.6 1.1 - - + -
70L ILE* 4.3 19.7 - - + -
9V PHE* 3.9 15.0 - - + -
10V VAL* 1.3 76.3 - - - +
12V ILE* 1.3 63.4 + - - +
43V VAL* 4.0 22.4 - - + -
44V LEU 3.6 2.7 - - - +
45V ILE* 4.2 10.5 - - + +
62V TYR 3.7 0.9 - - - +
63V ILE* 3.2 6.9 - - - +
64V GLN* 2.9 64.5 + - + +
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Residues in contact with ILE 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U ILE* 5.5 0.4 - - + -
10V VAL* 3.5 28.9 - - + -
11V VAL* 1.3 80.8 - - - +
13V LYS* 1.3 60.0 + - - +
19V VAL* 4.6 0.7 - - + -
21V VAL* 3.6 48.5 - - + -
38V LEU* 4.1 9.9 - - + +
42V GLU 3.8 1.0 - - - +
43V VAL* 3.2 3.9 - - - +
44V LEU* 2.7 46.6 + - + +
46V ALA* 5.1 1.8 - - + -
55V ILE* 4.6 1.1 - - + -
57V VAL* 4.2 16.4 - - + -
61V ALA* 3.9 23.8 - - + -
62V TYR 3.6 2.7 - - - +
63V ILE* 4.1 15.0 - - + -
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Residues in contact with LYS 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ILE* 3.8 25.2 - - + +
71L GLU* 2.8 32.6 + - - +
73L GLU* 3.0 28.7 + - - +
11V VAL 4.2 0.2 - - - -
12V ILE* 1.3 72.9 - - - +
14V ALA* 1.3 68.4 + - - +
15V LEU* 3.9 20.5 - - + +
41V GLY* 4.2 16.6 - - - +
42V GLU 3.5 5.8 - - - +
43V VAL* 3.8 16.2 - - + -
61V ALA* 3.3 3.9 - - - -
62V TYR* 2.8 45.3 + - + +
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Residues in contact with ALA 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V ILE 4.1 1.2 - - - -
13V LYS* 1.3 76.6 - - - +
15V LEU* 1.3 60.0 + - - +
16V GLU 3.5 14.8 - - - +
19V VAL* 3.6 15.9 - - + -
38V LEU* 3.8 20.7 - - + +
39V ASP 3.4 22.9 - - - +
41V GLY* 2.8 27.0 + - - -
42V GLU 3.0 8.8 + - - +
60V LYS 3.9 4.3 - - - -
61V ALA* 4.3 1.8 - - - -
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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