Contacts of the strand formed by residues 9 - 14 (chain F) in PDB entry 5EEY
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E ASP* 3.4 42.0 - - + -
9E PHE 5.6 2.2 - - - -
10E VAL* 5.8 0.4 - - + -
48E PHE* 4.2 8.5 - + + -
65E THR* 3.7 27.6 - - - -
66E ARG* 4.1 12.1 - - + -
67E HIS* 3.0 59.0 + + - -
7F SER 4.5 1.3 - - - -
8F ASP* 1.3 81.9 + - - +
10F VAL* 1.3 70.1 + - - +
11F VAL* 3.8 7.2 - - + -
45F ILE* 3.5 21.8 - - + -
46F ALA 3.2 19.5 - - - +
47F GLN* 3.9 10.8 - - + +
48F PHE 4.6 0.2 - - - +
65F THR* 4.4 5.0 - - - -
66F ARG 4.9 0.2 + - - -
9G PHE* 5.5 1.4 - - - -
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Residues in contact with VAL 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F PHE* 1.3 80.0 - - - +
11F VAL* 1.3 62.9 + - - +
12F ILE* 3.4 27.1 - - + -
44F LEU 3.8 0.5 - - - +
45F ILE* 3.4 2.9 - - - +
46F ALA* 2.9 40.4 + - + +
48F PHE* 4.1 16.2 - - + -
55F ILE* 4.1 28.7 - - + -
63F ILE* 5.0 1.3 - - + -
64F GLN 3.5 9.9 - - - +
65F THR* 4.1 17.5 - - + -
9G PHE* 5.9 0.9 - - + -
45G ILE* 4.2 15.9 - - + -
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Residues in contact with VAL 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 4.0 17.0 - - + +
67E HIS* 4.2 5.8 - - + -
70E ILE* 4.1 18.4 - - + -
9F PHE* 3.8 27.1 - - + -
10F VAL* 1.3 74.8 - - - +
12F ILE* 1.4 65.5 + - - +
43F VAL* 4.0 22.7 - - + -
44F LEU 3.5 4.0 - - - +
45F ILE* 4.3 6.5 - - + -
62F TYR 3.8 0.4 - - - +
63F ILE* 3.2 9.0 - - - +
64F GLN* 2.9 59.3 + - + +
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Residues in contact with ILE 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.4 31.6 - - + +
11F VAL* 1.4 78.4 - - - +
13F LYS* 1.3 60.6 + - - +
19F VAL* 4.8 0.9 - - + -
21F VAL* 3.8 44.9 - - + -
38F LEU* 3.9 11.4 - - + +
42F GLU 3.8 1.0 - - - +
43F VAL* 3.2 3.1 - - - -
44F LEU* 2.8 53.2 + - + +
46F ALA* 4.8 1.8 - - + -
55F ILE* 5.0 0.2 - - + -
57F VAL* 4.2 21.3 - - + -
61F ALA* 3.8 23.6 - - + -
62F TYR 3.7 2.7 - - - -
63F ILE* 4.3 8.3 - - + -
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ILE* 4.1 21.5 - - + +
71E GLU* 2.9 27.3 + - - +
73E GLU* 2.8 37.9 + - - -
11F VAL* 4.3 0.4 - - - +
12F ILE* 1.3 72.8 - - - +
14F ALA* 1.4 71.2 + - - +
15F LEU* 4.0 18.9 - - + +
41F GLY* 4.3 9.0 - - - +
42F GLU 3.4 5.8 - - - +
43F VAL* 3.8 17.3 - - + -
61F ALA* 3.2 4.2 - - - -
62F TYR* 2.9 43.2 + - + +
51P HIS* 5.7 0.2 + - - -
28Q ALA* 3.5 18.6 - - - +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE 4.1 1.6 + - - -
13F LYS* 1.4 74.9 - - - +
15F LEU* 1.3 59.0 + - - +
16F GLU 3.7 13.9 - - - +
19F VAL* 3.9 7.9 - - + -
38F LEU* 3.7 24.2 - - + +
39F ASP 3.2 26.2 - - - +
40F LYS* 4.4 0.2 - - - +
41F GLY* 2.8 28.8 + - - -
42F GLU 2.9 9.8 + - - +
60F LYS 4.0 4.7 - - - -
61F ALA* 4.5 2.0 - - - -
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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