Contacts of the strand formed by residues 59 - 66 (chain E) in PDB entry 1EFX
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 VAL 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E TRP* 3.9 21.3 - - + -
30E SER 3.6 13.7 - - - +
31E ASP* 5.1 9.2 - - - +
54E GLU 3.5 1.4 - - - +
55E HIS* 3.4 2.6 - - - +
56E HIS* 3.1 32.2 + - + +
57E ASP* 2.9 15.1 + - + +
58E GLY* 1.3 82.5 - - - +
60E SER* 1.3 76.7 + - - +
61E LYS* 3.7 35.0 - - + -
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Residues in contact with SER 60 (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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29E TRP* 3.1 21.7 - - - -
30E SER 3.0 6.8 + - - -
31E ASP 4.6 1.0 + - - -
32E VAL 3.2 26.3 + - - -
33E ARG* 3.2 15.4 - - - +
34E PHE 4.1 10.3 - - - -
37E PHE* 3.2 10.3 - - - -
54E GLU 3.3 6.5 - - - -
55E HIS* 3.4 21.9 - - - +
59E VAL* 1.3 77.7 - - - +
61E LYS* 1.3 60.8 + - - +
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Residues in contact with LYS 61 (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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27E GLN* 3.6 34.4 + - + +
28E CYS 3.2 7.6 - - - +
29E TRP* 3.4 19.7 - - + -
37E PHE* 3.7 1.3 - - - -
53E GLY* 3.3 3.1 - - - -
54E GLU* 2.4 50.7 + - + +
56E HIS* 5.5 13.5 - - + +
59E VAL* 3.7 24.5 - - + -
60E SER* 1.3 71.7 - - - +
62E ALA* 1.3 64.7 + - - +
63E ASN* 4.7 6.5 - - - +
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Residues in contact with ALA 62 (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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27E GLN* 3.5 1.4 - - - -
28E CYS 3.0 25.5 + - - -
37E PHE* 3.2 35.4 - - + -
51E LEU* 4.6 7.6 - - + -
52E ILE 3.9 14.6 - - - +
54E GLU* 4.6 4.7 - - - -
61E LYS* 1.3 81.4 - - - +
63E ASN* 1.3 65.7 + - - +
64E PHE* 3.7 10.5 + - + -
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Residues in contact with ASN 63 (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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25E ILE* 3.8 21.9 - - + +
26E LEU 3.8 2.9 - - - -
27E GLN* 2.9 34.2 + - - +
51E LEU* 3.4 14.5 - - - +
54E GLU* 5.2 6.5 - - - +
61E LYS* 4.7 5.7 - - - +
62E ALA* 1.3 77.7 + - - +
64E PHE* 1.3 62.5 + - - +
65E SER* 3.7 3.5 + - - -
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Residues in contact with PHE 64 (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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25E ILE* 3.3 5.4 - - - +
26E LEU* 2.7 47.3 + - + +
28E CYS* 4.5 13.0 - - + -
37E PHE* 3.2 42.6 - - + -
38E LEU 4.6 0.2 - - - -
39E LEU* 3.4 38.8 - - + -
49E LEU* 3.2 40.8 - - + -
50E HIS 3.6 3.8 - - - -
51E LEU* 3.2 35.0 - - + -
62E ALA* 4.1 9.2 - - + -
63E ASN* 1.3 71.3 - - - +
65E SER* 1.3 61.9 + - - +
66E ILE* 3.6 2.1 + - + +
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Residues in contact with SER 65 (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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23E THR* 5.3 5.4 - - - +
24E VAL 3.9 5.4 + - - -
25E ILE* 4.3 16.6 - - - +
49E LEU* 4.9 8.2 - - - +
63E ASN 3.7 4.1 + - - -
64E PHE* 1.3 71.5 - - - +
66E ILE* 1.3 64.8 + - - +
67E GLY* 3.1 10.2 + - - -
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Residues in contact with ILE 66 (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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23E THR* 3.7 2.8 - - - -
24E VAL* 2.9 37.7 + - + +
26E LEU* 3.9 26.2 - - + -
39E LEU* 4.8 4.3 - - + -
41E ARG* 5.0 5.4 - - - +
49E LEU* 4.5 19.5 - - + -
64E PHE* 3.6 2.4 + - + +
65E SER* 1.3 71.8 - - - +
67E GLY* 1.3 67.5 + - - +
69E MET* 3.4 31.4 - - + +
73E LEU* 3.6 20.2 - - + -
77E TYR* 3.4 33.4 - - + +
99E ILE* 5.5 0.7 - - + -
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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