Contacts of the strand formed by residues 10 - 17 (chain e) in PDB entry 4B2Q
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 THR 10 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8e PRO* 3.9 9.3 + - - +
9e ILE* 1.3 79.5 + - - +
11e GLY* 1.3 71.4 + - - +
12e LYS* 5.4 6.7 - - - +
25e PHE* 3.8 18.0 - - - +
26e GLU* 4.4 14.9 - - - +
75e LYS* 4.0 29.6 - - + -
76e VAL 3.6 7.6 - - - +
77e LEU* 5.6 1.8 - - - +
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Residues in contact with GLY 11 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10e THR* 1.3 78.9 - - - +
12e LYS* 1.3 67.8 + - - +
23e VAL* 3.9 9.0 - - - -
24e HIS 3.1 16.4 - - - -
25e PHE* 4.2 4.0 - - - -
26e GLU* 5.7 2.0 - - - -
75e LYS* 3.3 7.4 - - - -
76e VAL 2.9 31.5 + - - -
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Residues in contact with LYS 12 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10e THR* 5.4 6.9 - - - +
11e GLY* 1.3 81.2 + - - +
13e VAL* 1.3 65.9 + - - +
14e THR* 3.3 8.0 + - + +
23e VAL* 3.5 4.3 - - - +
24e HIS* 2.8 38.8 + - + +
26e GLU* 5.3 6.7 + - - -
73e GLY* 3.4 29.6 - - - +
74e GLU 3.4 3.6 - - - -
75e LYS* 4.9 10.0 - - + +
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Residues in contact with VAL 13 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12e LYS* 1.3 72.0 - - - +
14e THR* 1.3 61.8 + - - +
15e ALA 3.8 3.6 - - - +
16e VAL* 3.7 22.9 - - + -
21e VAL* 3.5 33.7 - - + -
22e ASP 3.4 6.5 - - - +
23e VAL* 4.2 2.9 - - + +
39e ILE* 4.2 10.5 - - + -
70e LEU* 5.3 3.8 - - + -
71e VAL 4.4 10.3 - - - +
72e ARG* 3.3 8.4 - - - +
73e GLY* 2.8 27.1 + - - +
74e GLU* 3.2 17.6 + - + +
76e VAL* 3.5 24.9 - - + -
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Residues in contact with THR 14 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70a PRO* 3.3 30.5 - - - +
12e LYS* 3.4 16.8 - - + +
13e VAL* 1.3 74.5 - - - +
15e ALA* 1.3 57.2 + - - +
22e ASP* 2.6 29.2 + - - +
24e HIS* 3.6 23.3 - - + -
58e THR* 4.0 10.7 - - + +
72e ARG* 3.2 25.0 - - - +
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Residues in contact with ALA 15 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68a LEU 3.0 9.6 - - - +
69a GLU* 4.5 1.1 - - - -
70a PRO* 3.9 15.9 - - + -
13e VAL* 3.7 1.4 - - - +
14e THR* 1.3 84.3 + - - +
16e VAL* 1.3 68.4 + - - +
17e ILE* 4.1 7.2 - - + -
21e VAL* 3.3 6.8 - - - +
22e ASP* 2.7 57.7 + - + +
72e ARG* 4.8 0.7 - - - +
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Residues in contact with VAL 16 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51a ALA* 4.3 20.6 - - + -
66a LEU 3.7 8.0 - - - +
68a LEU* 2.8 57.0 + - + +
13e VAL* 3.7 19.7 - - + -
15e ALA* 1.3 80.6 - - - +
17e ILE* 1.3 62.2 + - - +
18e GLY 4.5 4.9 - - - +
20e ILE 3.9 1.8 - - - -
21e VAL* 4.4 6.5 - - + +
67e THR* 4.4 19.5 - - - +
70e LEU* 4.0 22.9 - - + -
71e VAL 5.2 0.4 - - - +
72e ARG* 5.2 3.4 - - + -
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Residues in contact with ILE 17 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66a LEU 4.5 0.7 - - - -
67a ASN* 3.1 28.5 - - - +
68a LEU 4.4 7.9 - - - +
69a GLU* 4.7 17.9 - - + -
289a ARG* 4.1 17.5 - - + +
15e ALA* 5.2 7.6 - - + -
16e VAL* 1.3 81.2 - - - +
18e GLY* 1.3 60.6 + - - +
19e ALA 3.5 0.2 + - - -
20e ILE* 2.9 43.9 + - + +
22e ASP* 5.4 3.8 - - - +
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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