Contacts of the strand formed by residues 29 - 35 (chain E) in PDB entry 3SKJ
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 ASP 29 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E THR* 5.9 0.5 - - - +
27E GLY 4.4 4.0 - - - +
28E TRP* 1.3 77.4 - - - +
30E LEU* 1.3 83.3 + - - +
31E MET* 3.5 2.6 + - + +
42E MET 3.5 0.2 - - - +
43E TYR* 3.4 8.8 - - - -
44E SER* 2.8 38.7 + - - +
31L THR* 5.3 6.1 - - - +
50L LYS* 4.2 24.4 + - - +
52L SER* 5.5 1.6 + - - -
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Residues in contact with LEU 30 (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 PHE* 4.0 14.8 - - + -
15E GLY* 4.3 19.5 - - - +
17E LEU 5.1 5.8 - - - +
18E GLY* 5.9 2.0 - - - -
29E ASP* 1.3 93.8 + - - +
31E MET* 1.3 67.0 + - - +
41E TYR* 4.5 15.0 - - + -
42E MET 3.4 16.4 - - - +
43E TYR* 3.5 43.4 - - + +
31L THR* 5.0 6.9 - - - +
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Residues in contact with MET 31 (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 ASP* 4.2 0.9 - - + +
30E LEU* 1.3 79.1 - - - +
32E GLN* 1.3 64.0 + - - +
33E ASN* 5.6 1.1 - - - +
41E TYR* 3.3 7.5 - - - +
42E MET* 2.8 62.6 + - + +
44E SER* 3.7 28.5 - - - +
100H VAL* 4.9 24.9 - - + +
31L THR* 4.3 17.5 - - + +
32L TRP* 4.4 26.9 - - + -
50L LYS* 4.5 25.6 - - + +
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Residues in contact with GLN 32 (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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31E MET* 1.3 79.3 - - - +
33E ASN* 1.3 76.6 + - - +
34E ILE* 6.3 0.7 - - + -
39E PRO* 4.8 13.4 - - + +
40E ILE 3.5 7.0 - - - +
41E TYR* 3.0 45.1 + - + +
42E MET* 5.4 0.2 - - - -
14I PRO* 6.0 1.9 - - - +
28L SER* 5.2 4.4 + - - -
30L SER* 4.1 32.7 + - - +
31L THR* 5.8 0.2 + - - -
32L TRP* 4.2 14.4 + - - -
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Residues in contact with ASN 33 (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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31E MET* 5.7 0.9 - - - -
32E GLN* 1.3 79.2 - - - +
34E ILE* 1.3 87.4 + - - +
35E MET* 4.0 7.9 - - - +
39E PRO* 3.4 2.9 - - - +
40E ILE* 2.6 39.7 + - + +
42E MET* 3.8 22.8 - - + +
100H VAL* 3.8 36.6 + - - +
32L TRP* 3.7 24.4 + - + +
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Residues in contact with ILE 34 (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 GLN* 6.3 0.7 - - + -
33E ASN* 1.3 92.6 + - - +
35E MET* 1.3 62.4 + - - +
36E ASN 4.9 0.2 - - - +
37E ASP* 4.1 15.0 - - - +
38E MET 3.4 11.2 - - - +
39E PRO* 4.6 9.4 - - + -
100H PRO* 6.4 2.5 - - + -
83I ARG* 3.4 47.8 - - + +
85I GLU* 5.8 1.3 - - - +
92L ASN* 6.0 4.3 - - - +
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Residues in contact with MET 35 (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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33E ASN* 4.0 8.1 + - - +
34E ILE* 1.3 74.8 - - - +
36E ASN* 1.3 87.4 + - - +
37E ASP 3.4 1.1 - - - -
38E MET* 3.0 19.4 + - - +
40E ILE* 3.4 31.7 - - + +
42E MET* 5.2 6.1 - - + -
135E ARG 6.2 0.2 - - - +
137E VAL* 3.6 42.4 - - + -
139E LEU* 4.8 13.2 - - + -
168E LEU* 4.0 27.8 - - + -
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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