Contacts of the strand formed by residues 21 - 26 (chain J) in PDB entry 4EMG
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 21 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLU* 1.3 76.8 + - - +
22J VAL* 1.3 63.6 + - - +
33J ASN* 5.0 8.5 - - + +
34J GLY* 3.2 23.3 - - - +
35J ARG* 3.8 36.3 - - + +
90J PRO 4.3 0.3 - - - -
91J PRO* 3.3 30.3 - - + +
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J SER* 3.6 33.2 - - - +
20J GLU 4.3 2.7 - - - +
21J ILE* 1.3 78.3 - - - +
23J TYR* 1.3 59.8 + - - +
24J VAL* 3.9 20.2 + - + +
32J LEU 4.5 0.2 - - - -
33J ASN* 3.3 8.5 - - - +
34J GLY 2.8 33.7 + - - +
36J LEU* 4.3 20.0 - - + -
45J MSE 5.1 1.1 - - - -
47J LEU* 4.2 16.2 - - + -
88J ILE* 4.3 14.6 - - + -
89J ALA 3.4 11.2 - - - +
90J PRO* 4.4 3.1 - - + -
91J PRO* 4.7 0.2 - - + -
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Residues in contact with TYR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I GLU* 4.7 2.9 + - - -
73I LYS* 3.8 15.1 + - - +
75I TYR* 3.3 41.1 + + - -
21J ILE 4.3 0.4 + - - -
22J VAL* 1.3 73.6 - - - +
24J VAL* 1.3 64.5 + - - +
25J LYS* 3.6 29.5 - - + +
31J GLU* 2.7 47.8 + - + +
32J LEU 3.5 9.6 - - - -
33J ASN* 3.8 18.6 - - - +
87J LEU* 4.8 6.5 - - + +
88J ILE* 3.2 6.1 - - - +
89J ALA* 2.8 45.9 + - + +
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Residues in contact with VAL 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J VAL* 3.9 21.8 - - + +
23J TYR* 1.3 84.3 - - - +
25J LYS* 1.3 62.6 + - - +
26J LEU* 3.6 25.9 + - + -
31J GLU* 3.3 5.0 - - - +
32J LEU* 2.8 46.8 + - + +
45J MSE 3.8 31.9 - - + -
47J LEU* 4.2 13.9 - - + -
85J VAL* 4.0 5.4 - - + -
87J LEU 3.4 11.2 - - - +
88J ILE* 4.5 3.6 - - + -
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Residues in contact with LYS 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG* 3.2 38.5 - - - +
23J TYR* 3.6 18.7 - - + +
24J VAL* 1.3 73.2 - - - +
26J LEU* 1.3 76.4 + - - +
28J GLY 4.4 0.6 - - - +
29J ASP* 3.1 34.6 - - - +
30J ARG 3.5 14.8 + - - +
31J GLU* 4.0 12.0 - - + +
85J VAL* 3.9 0.7 - - - -
86J ILE* 2.9 35.0 + - + -
87J LEU* 3.0 39.2 + - + +
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Residues in contact with LEU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J VAL* 3.6 24.9 + - + -
25J LYS* 1.3 98.5 + - - +
27J ARG* 1.3 71.0 + - - +
30J ARG* 2.9 40.8 + - + +
32J LEU* 3.9 26.0 - - + -
80J VAL* 3.9 15.3 - - + -
84J SER* 3.1 19.1 - - - +
85J VAL* 3.9 15.5 - - + -
86J ILE* 3.6 4.8 - - - +
86K ILE* 4.3 11.4 - - + -
87K LEU* 4.3 9.2 - - + -
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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