Contacts of the strand formed by residues 61 - 65 (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 ALA 61 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 3.8 23.8 - - + -
13F LYS 3.2 14.8 - - - +
14F ALA* 4.5 2.2 - - - -
15F LEU* 3.8 9.4 - - - -
19F VAL* 4.5 3.8 - - + -
57F VAL* 4.1 8.1 - - + -
59F GLY 4.4 0.2 - - - +
60F LYS* 1.3 74.7 - - - +
62F TYR* 1.3 59.3 - - - +
63F ILE* 4.0 3.3 + - + -
71F GLU* 3.4 8.5 - - - +
72F SER* 3.1 43.3 + - - +
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Residues in contact with TYR 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ILE* 3.6 28.9 - - + +
11F VAL 3.8 0.9 - - - +
12F ILE* 3.7 1.9 - - - -
13F LYS* 2.9 42.6 + - + +
15F LEU* 3.9 17.4 - - + +
61F ALA* 1.3 73.7 - - - +
63F ILE* 1.3 60.7 + - - +
64F GLN* 4.2 14.5 + - + -
69F VAL* 3.4 34.7 - - + +
70F ILE 4.1 1.1 - - - -
71F GLU* 3.9 27.8 - - + -
26P ARG 5.9 1.1 - - - -
50P GLU* 2.9 36.7 + - - +
51P HIS* 4.8 18.0 + + - -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F VAL* 5.0 1.6 - - + -
11F VAL 3.2 11.4 - - - +
12F ILE* 4.3 20.6 - - + -
57F VAL* 4.1 20.6 - - + -
61F ALA* 4.3 1.8 - - + -
62F TYR* 1.3 81.5 - - - +
64F GLN* 1.3 66.7 + - - +
65F THR* 4.1 18.8 - - + -
69F VAL* 3.3 7.4 - - - +
70F ILE* 2.8 57.9 + - + +
72F SER* 3.8 34.5 - - - +
43G VAL* 4.3 8.5 - - + -
45G ILE* 4.8 9.9 - - + -
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Residues in contact with GLN 64 (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* 4.7 0.7 + - - -
67E HIS* 3.9 33.8 + - + +
68E GLY* 4.7 4.4 - - - +
69E VAL 3.2 24.9 + - - +
70E ILE* 3.8 21.6 - - + +
10F VAL* 3.5 1.4 - - - -
11F VAL* 2.9 59.2 + - + +
62F TYR* 4.2 18.4 - - + -
63F ILE* 1.3 76.9 - - - +
65F THR* 1.3 68.8 + - - +
68F GLY 3.6 6.1 - - - +
69F VAL* 4.5 9.3 - - + +
50P GLU* 4.5 5.3 + - - -
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Residues in contact with THR 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E HIS* 3.8 21.7 - - - +
9F PHE 4.4 3.1 - - - -
10F VAL* 4.1 20.0 - - + -
63F ILE* 4.1 15.9 - - + -
64F GLN* 1.3 80.7 - - - +
66F ARG* 1.3 59.4 + - - +
67F HIS* 2.9 19.9 + - - +
68F GLY* 2.8 29.3 + - - +
70F ILE* 5.5 2.5 - - + -
9G PHE* 3.7 21.0 - - + -
11G VAL* 4.0 18.2 - - + +
45G ILE* 4.7 4.5 - - + -
64G GLN* 4.8 1.2 + - - -
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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