Contacts of the strand formed by residues 38 - 45 (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 MET 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E ILE* 3.4 7.0 - - - +
35E MET 3.0 32.6 + - - +
36E ASN* 3.1 13.4 - - + +
37E ASP* 1.3 87.7 - - - +
39E PRO* 1.3 73.2 - - + +
40E ILE* 3.5 7.6 + - + +
15I GLY* 3.5 26.2 - - - +
82I SER* 3.4 33.4 - - - -
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Residues in contact with PRO 39 (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* 4.8 14.6 - - - +
33E ASN 3.4 7.0 - - - +
34E ILE* 4.6 7.8 - - + -
37E ASP 4.7 0.2 - - - +
38E MET* 1.3 88.5 - - + +
40E ILE* 1.3 65.0 + - - +
41E TYR* 4.3 20.9 - - + +
14I PRO* 3.8 29.4 - - + +
15I GLY* 3.9 19.7 - - - +
82I LEU 5.7 0.2 - - + -
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Residues in contact with ILE 40 (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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11E ALA* 6.4 1.8 - - + -
32E GLN* 3.5 2.0 - - - +
33E ASN* 2.6 42.4 + - - +
35E MET* 3.4 53.4 - - + +
36E ASN* 5.3 2.2 - - - +
38E MET* 3.8 7.9 - - + +
39E PRO* 1.3 79.7 - - - +
41E TYR* 1.3 74.9 + - - +
42E MET* 4.1 16.0 - - + +
168E LEU* 4.7 15.3 - - + +
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Residues in contact with TYR 41 (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* 3.8 18.3 - - + -
11E ALA* 5.9 0.5 - - - -
14E GLY* 3.4 27.8 + - - -
15E GLY* 3.5 31.6 - - - +
30E LEU* 4.5 19.3 - - + -
31E MET 3.3 8.7 - - - +
32E GLN* 3.0 42.1 + - + -
39E PRO* 4.5 19.9 - - + +
40E ILE* 1.3 88.0 - - - +
42E MET* 1.3 63.6 + - - +
168E LEU* 4.0 6.9 - - - +
113I SER* 5.8 4.0 - - - -
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Residues in contact with MET 42 (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* 4.3 3.1 - - - -
29E ASP 3.5 0.7 - - - +
30E LEU* 3.4 6.0 - - - +
31E MET* 2.8 56.1 + - + +
33E ASN* 3.8 28.5 - - + +
35E MET* 5.2 6.7 - - - -
40E ILE* 4.1 21.5 - - + +
41E TYR* 1.3 76.1 - - - +
43E TYR* 1.3 64.4 + - - +
44E SER* 5.0 0.7 - - - -
166E ALA* 4.1 6.7 - - + -
167E LEU 3.3 16.6 - - - +
168E LEU* 3.7 29.4 - - + -
100H VAL* 3.9 26.2 - - - -
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Residues in contact with TYR 43 (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* 3.8 23.1 - + - -
17E LEU 4.1 2.8 + - - -
18E GLY* 3.8 6.9 - - - -
19E TRP* 2.9 46.9 + + + -
21E THR* 4.2 11.7 - - + -
28E TRP* 3.4 11.2 - - + -
29E ASP* 3.4 11.0 - - - -
30E LEU* 3.5 47.2 - - + +
42E MET* 1.3 72.0 - - - +
44E SER* 1.3 59.8 + - - +
57E LEU* 3.4 44.6 - - + -
166E ALA* 3.6 0.5 - - - -
167E LEU* 2.8 41.8 + - + +
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Residues in contact with SER 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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27E GLY 3.8 0.9 - - - +
28E TRP* 3.3 9.0 - - - -
29E ASP* 2.8 37.3 + - - +
31E MET* 3.7 31.1 - - - +
42E MET* 4.7 0.9 - - - -
43E TYR* 1.3 76.8 - - - +
45E VAL* 1.3 60.7 + - - +
165E VAL 3.3 11.9 + - - -
166E ALA* 4.0 5.3 - - - +
100H ALA* 3.4 20.1 + - - +
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Residues in contact with VAL 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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27E GLY* 3.6 33.9 - - - +
28E TRP* 4.0 20.0 - - + +
44E SER* 1.3 78.6 - - - +
46E CYS* 1.3 64.1 + - - +
47E ASN* 3.8 16.8 - - - +
55E ASN* 4.1 2.0 - - - +
160E ASP* 3.3 45.3 - - + +
163E ALA 3.2 3.0 - - - +
165E VAL* 3.0 33.6 + - + +
100H ALA* 4.8 0.3 - - - +
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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