Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 5EN1
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 LEU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.3 66.2 + - + +
41A TYR* 4.0 12.3 - - + -
42A GLU* 3.8 19.1 + - + +
45A GLY 3.7 0.8 + - - +
46A LYS* 1.3 74.6 - - - +
48A THR* 1.3 60.6 + - - +
49A ASP 3.5 3.6 - - - +
50A CYS* 4.5 5.2 - - + -
67A VAL* 4.2 22.2 - - + -
68A THR 3.5 9.4 - - - +
69A PHE* 3.6 42.6 - - + -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 4.9 6.3 - - - +
21A ARG* 4.0 13.7 + - - +
38A ARG* 4.8 3.6 + - - -
46A LYS 3.8 0.2 + - - -
47A LEU* 1.3 73.5 - - - +
49A ASP* 1.3 63.1 + - + +
68A THR* 2.9 34.5 + - + -
69A PHE 4.4 5.4 - - - -
70A SER* 4.5 13.0 - - - -
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 4.3 1.7 + - - -
38A ARG* 3.8 8.2 + - - +
47A LEU* 3.5 3.2 - - - +
48A THR* 1.3 86.0 + - + +
50A CYS* 1.3 74.4 + - - +
51A VAL* 4.5 1.7 - - - +
66A PHE 4.5 0.8 - - - +
67A VAL* 3.6 1.7 - - - +
68A THR* 3.0 43.1 + - + +
3B G 2.7 52.1 + - - +
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.5 41.5 - - + +
37A LEU* 3.7 29.4 - - - -
38A ARG* 3.6 36.1 + - + +
47A LEU* 4.5 4.7 - - + -
49A ASP* 1.3 83.9 + - - +
51A VAL* 1.3 66.4 + - - +
66A PHE 3.4 6.5 - - - +
67A VAL* 4.0 9.0 - - + -
3B G 4.5 1.4 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.6 13.5 - - - +
37A LEU* 4.3 1.5 - - - +
49A ASP* 4.5 2.5 - - - +
50A CYS* 1.3 77.2 - - - +
52A VAL* 1.3 68.3 + - - +
53A MET* 3.9 22.5 - - + +
65A GLY* 3.0 4.9 - - - -
66A PHE* 2.9 53.9 + - + +
3B G 3.5 52.0 - - + +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.1 11.7 - - + -
32A THR* 4.0 13.2 - - + +
33A THR* 3.6 30.5 - - - +
34A GLU* 3.4 19.7 + - + +
37A LEU* 3.8 19.7 - - + -
51A VAL* 1.3 79.1 - - - +
53A MET* 1.3 67.8 + - - +
54A ARG* 3.6 20.3 + - - +
61A SER* 3.6 25.6 - - - +
64A PHE 3.7 11.0 - - - +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.9 28.0 - - + -
52A VAL* 1.3 72.5 - - - +
54A ARG* 1.3 54.9 + - - +
61A SER* 3.6 5.7 + - - -
62A ARG* 2.7 46.1 + - - +
64A PHE* 3.2 53.6 + - + +
65A GLY* 4.7 3.4 - - - -
66A PHE* 4.7 2.9 - - + -
2B G 4.0 25.6 - - - +
3B G 3.4 41.5 - - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 4.8 5.9 + - - -
31A GLU 5.8 0.2 - - - -
32A THR 3.7 22.2 + - - -
33A THR* 4.5 14.3 - - - +
52A VAL* 3.6 18.1 + - - +
53A MET* 1.3 82.5 - - - +
55A ASP* 1.3 71.1 + - - +
56A PRO* 3.3 9.5 - - - +
59A LYS* 2.8 44.2 + - + +
60A ARG 3.1 7.9 - - - +
61A SER* 3.2 25.3 - - - +
62A ARG* 3.6 17.3 + - - +
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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