Contacts of the strand formed by residues 9 - 14 (chain Q) in PDB entry 5EEV
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9P PHE* 5.5 1.4 - - - -
7Q SER 4.6 4.9 - - - -
8Q ASP* 1.3 82.3 + - - +
10Q VAL* 1.3 71.3 + - - +
11Q VAL* 3.8 15.3 - - + -
45Q ILE* 3.5 19.7 - - + -
46Q ALA 3.2 21.1 - - - +
47Q GLN* 3.9 9.2 - - + -
48Q PHE* 5.3 0.7 - - - -
64Q GLN 4.7 0.2 - - - +
65Q THR* 4.7 2.9 - - - -
66Q ARG* 5.1 0.6 + - - -
8R ASP* 3.3 33.7 - - + -
9R PHE 5.5 1.1 - - - -
10R VAL* 5.2 2.2 - - + -
48R PHE* 4.0 20.9 - + + -
65R THR* 3.8 22.2 - - + -
66R ARG* 4.2 6.7 - - + -
67R HIS* 3.4 46.2 + + - -
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Residues in contact with VAL 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P PHE* 5.3 1.8 - - + -
45P ILE* 4.1 28.5 - - + -
9Q PHE* 1.3 79.3 - - - +
11Q VAL* 1.3 62.6 + - - +
12Q ILE* 3.7 26.2 - - + -
44Q LEU 3.8 0.5 - - - +
45Q ILE* 3.3 3.3 - - - -
46Q ALA* 2.8 43.3 + - + +
48Q PHE* 4.4 12.1 - - + -
55Q ILE* 4.0 15.7 - - + -
63Q ILE* 4.8 0.7 - - + -
64Q GLN 3.6 8.3 - - - +
65Q THR* 3.7 21.5 - - + -
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Residues in contact with VAL 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q PHE* 3.8 24.7 - - + -
10Q VAL* 1.3 74.0 - - - +
12Q ILE* 1.3 68.4 + - - +
43Q VAL* 3.9 22.0 - - + -
44Q LEU 3.6 3.1 - - - +
45Q ILE* 4.2 6.5 - - + +
62Q TYR 3.7 0.5 - - - +
63Q ILE* 3.3 6.2 - - - +
64Q GLN* 2.9 61.0 + - + +
63R ILE* 5.9 0.2 - - + -
65R THR* 3.9 22.2 - - + +
67R HIS* 4.8 1.3 - - + -
70R ILE* 4.2 19.1 - - + -
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Residues in contact with ILE 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P ILE* 5.5 0.4 - - + -
10Q VAL* 3.7 25.8 - - + -
11Q VAL* 1.3 81.1 - - - +
13Q LYS* 1.3 64.1 + - - +
14Q ALA 4.1 0.2 + - - -
19Q VAL* 4.8 0.4 - - + -
21Q VAL* 3.6 47.3 - - + -
38Q LEU* 4.1 8.1 - - + +
42Q GLU 3.7 1.2 - - - +
43Q VAL* 3.2 5.1 - - - -
44Q LEU* 2.8 47.8 + - + +
46Q ALA* 5.3 1.3 - - + -
55Q ILE* 4.6 1.6 - - + -
57Q VAL* 4.2 12.8 - - + -
61Q ALA* 3.9 23.8 - - + -
62Q TYR 3.5 3.1 - - - +
63Q ILE* 4.2 15.5 - - + -
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Residues in contact with LYS 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q VAL 4.4 0.2 - - - -
12Q ILE* 1.3 74.4 - - - +
14Q ALA* 1.3 68.6 + - - +
15Q LEU* 3.4 19.0 + - + +
41Q GLY* 4.1 14.1 - - - +
42Q GLU 3.4 5.8 - - - +
43Q VAL* 3.9 12.3 - - + +
61Q ALA* 3.2 4.9 - - - -
62Q TYR* 2.8 45.4 + - + +
70R ILE* 3.6 29.3 - - + +
71R GLU* 2.7 32.2 + - - +
73R GLU* 3.1 28.9 + - - -
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Residues in contact with ALA 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q ILE 4.1 0.8 + - - -
13Q LYS* 1.3 76.9 - - - +
15Q LEU* 1.3 60.5 + - - +
16Q GLU 3.4 14.8 - - - +
19Q VAL* 3.7 19.1 - - + -
38Q LEU* 3.8 19.1 - - + +
39Q ASP 3.3 24.7 - - - +
40Q LYS* 4.3 0.2 - - - +
41Q GLY* 2.8 24.1 + - - -
42Q GLU 3.0 9.6 + - - +
60Q LYS 4.0 0.2 - - - -
61Q ALA* 4.5 1.1 - - - +
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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