Contacts of the strand formed by residues 43 - 50 (chain E) in PDB entry 2ESV
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 ILE 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLN* 3.8 22.9 - - - +
42D PRO* 3.8 28.0 - - + -
88D TYR* 4.5 5.4 - - + +
103D LEU 5.1 0.2 - - - +
104D ILE* 5.5 0.2 - - - -
105D PHE* 3.6 55.2 + - + +
35E TYR* 3.8 23.3 - - + -
36E ARG 3.4 14.6 - - - +
37E ARG* 3.7 26.5 - - + +
42E GLU* 1.3 76.4 - - - +
44E LYS* 1.3 63.1 + - - +
91E PHE* 4.7 11.9 - - + -
108E PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 44 (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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103D LEU 5.4 0.9 - - - -
35E TYR* 3.4 6.4 - - - -
36E ARG* 2.8 39.2 + - + +
42E GLU 4.1 6.3 - - - +
43E ILE* 1.3 77.2 - - - +
45E PHE* 1.3 75.1 + - + +
46E LEU* 3.6 4.1 + - + +
59E GLY* 5.6 7.0 - - - -
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Residues in contact with PHE 45 (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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97D THR* 4.1 7.9 - - + -
102D LYS* 3.8 33.9 - - + -
103D LEU 4.5 4.8 + - - +
33E TYR* 4.0 9.4 - + - -
34E TRP 4.5 1.1 - - - -
35E TYR* 3.4 32.3 - + + -
44E LYS* 1.3 84.5 - - + +
46E LEU* 1.3 75.3 + - - +
47E LEU* 3.3 34.3 - - - -
48E HIS* 3.4 18.8 - - + -
56E ASP* 3.5 32.5 - - + -
58E SER* 3.8 13.2 - - - -
59E GLY* 3.2 20.7 - - - +
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Residues in contact with LEU 46 (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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34E TRP* 2.9 30.5 + - + +
35E TYR 4.0 9.2 - - - +
36E ARG* 3.8 48.2 - - + +
44E LYS* 4.1 6.1 - - + +
45E PHE* 1.3 83.6 - - - +
47E LEU* 1.3 60.5 + - - +
57E GLU* 3.7 7.3 - - - +
59E GLY 3.2 40.0 + - - +
60E MET* 3.3 27.7 + - + +
61E PRO* 4.0 11.7 - - + -
65E PHE* 5.8 0.7 - - + -
77E LEU* 4.5 3.8 - - + -
90E TYR* 4.4 12.1 - - + -
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Residues in contact with LEU 47 (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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32E LEU 4.6 0.2 - - - -
33E TYR* 3.3 4.9 - - - -
34E TRP* 3.0 34.3 + - + +
45E PHE* 3.3 12.4 - - - -
46E LEU* 1.3 82.5 - - + +
48E HIS* 1.3 90.5 + - - +
49E PHE* 3.6 19.7 - - + -
54E LYS* 3.8 30.1 - - + -
56E ASP 3.4 12.1 - - - +
57E GLU* 4.2 9.6 - - + +
60E MET* 3.6 25.8 - - + -
67E ALA* 3.7 24.0 - - + -
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Residues in contact with HIS 48 (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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96D ASN 3.5 17.3 - - - -
97D THR* 3.2 39.1 + - + +
31E ASN* 3.0 29.9 + - + +
32E LEU 3.5 7.2 - - - -
33E TYR* 3.5 24.3 + + + -
45E PHE* 3.7 7.4 - - + -
47E LEU* 1.3 82.2 - - - +
49E PHE* 1.3 76.7 + - - +
50E VAL* 3.4 22.4 - - + -
55E GLN* 2.8 31.8 + - + +
56E ASP* 2.9 14.6 + - + +
98E ARG* 4.3 0.2 - - - -
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Residues in contact with PHE 49 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E ASP 3.5 1.0 - - - +
31E ASN* 3.1 7.4 - - - -
32E LEU* 2.8 46.2 + - + +
34E TRP* 4.4 6.3 - + - -
47E LEU* 3.6 19.1 - - + -
48E HIS* 1.3 76.5 - - - +
50E VAL* 1.3 59.7 + - - +
51E LYS 3.5 11.4 - - - +
52E GLU 4.1 8.5 - - - -
53E SER 3.2 20.4 - - - -
54E LYS* 3.7 18.8 - - + -
67E ALA* 3.8 30.7 - - + -
68E GLU* 3.8 11.0 - - - -
69E ARG* 3.9 32.5 - - + +
75E SER* 3.7 20.2 - - - -
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Residues in contact with VAL 50 (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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73A ILE* 3.5 29.4 - - + -
76A VAL* 3.9 24.7 - - + +
30E ASP* 3.7 3.8 - - + +
31E ASN* 3.6 9.4 - - - +
48E HIS* 3.4 29.8 + - + -
49E PHE* 1.3 68.8 - - - +
51E LYS* 1.3 70.8 + - + +
53E SER* 2.9 29.1 + - - +
55E GLN* 3.8 9.6 - - + +
8P ILE* 3.9 26.0 - - + -
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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