Contacts of the strand formed by residues 34 - 40 (chain E) in PDB entry 1AXC
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 GLY 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29E ASP 4.0 0.5 - - - +
30E ILE* 3.8 1.2 - - - -
31E SER* 3.0 30.4 + - - -
32E SER 3.3 0.4 - - - -
33E SER* 1.3 81.6 + - - +
35E VAL* 1.3 60.5 + - - -
36E ASN* 4.2 5.7 + - - -
52E LEU 3.3 10.5 - - - -
53E ARG* 4.4 0.2 - - - -
54E SER 3.7 6.3 - - - -
60E TYR* 3.1 20.8 + - - -
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Residues in contact with VAL 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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2E PHE* 4.5 11.0 - - + -
28E TRP* 3.3 39.5 - - + -
29E ASP 3.6 4.3 - - - +
30E ILE* 3.4 25.8 - - + -
34E GLY* 1.3 74.2 - - - -
36E ASN* 1.3 69.5 + - - +
50E LEU* 3.9 2.7 - - + +
51E THR* 3.6 1.2 - - - -
52E LEU* 2.9 47.4 + - + +
57E PHE* 4.4 17.9 - - + -
60E TYR* 4.2 7.2 - - + +
90E LEU* 5.7 5.2 - - + -
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Residues in contact with ASN 36 (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 CYS 3.9 0.9 - - - +
28E TRP* 3.9 2.1 - - - -
29E ASP* 3.0 47.9 + - + +
31E SER* 5.5 3.4 - - - -
33E SER* 4.3 16.4 + - - -
34E GLY 4.5 6.1 + - - -
35E VAL* 1.3 82.9 - - - +
37E LEU* 1.3 62.2 + - - +
49E GLN* 4.8 4.0 - - - +
50E LEU* 3.2 4.9 - - - +
51E THR* 2.9 32.2 + - - +
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Residues in contact with LEU 37 (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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19E LEU* 4.5 7.9 - - + -
23E ILE* 3.9 20.4 - - + -
26E ALA* 3.7 23.1 - - + -
27E CYS 3.9 11.7 - - - +
28E TRP* 3.7 37.7 - - + +
29E ASP* 5.4 1.6 - - - -
36E ASN* 1.3 76.2 - - - +
38E GLN* 1.3 70.7 + - - +
39E SER* 4.4 0.2 - - - -
48E VAL* 4.3 12.3 - - + +
49E GLN* 3.1 7.3 + - - -
50E LEU* 2.7 57.7 + - + +
72E LEU* 4.3 7.2 - - + -
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Residues in contact with GLN 38 (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 CYS 4.5 5.8 + - - +
29E ASP* 5.5 1.4 + - - -
37E LEU* 1.3 75.5 - - - +
39E SER* 1.3 65.8 + - - +
47E LEU* 3.9 21.9 - - + +
48E VAL 3.2 13.2 - - - +
49E GLN* 4.2 14.8 - - + +
123E VAL* 4.8 2.9 - - - +
124E GLU 4.8 0.2 - - - +
125E GLN* 3.3 44.4 + - - +
126E LEU 3.0 45.0 + - - -
128E ILE* 4.3 15.4 - - - +
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Residues in contact with SER 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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23E ILE* 3.8 28.9 - - - +
25E GLU 3.7 17.5 + - - -
26E ALA* 4.0 12.2 - - - -
37E LEU* 4.4 0.9 - - - -
38E GLN* 1.3 81.2 - - - +
40E MET* 1.3 72.6 + - - +
41E ASP 4.3 0.2 + - - -
47E LEU* 3.4 3.4 - - - -
48E VAL* 2.9 33.9 + - - +
123E VAL* 5.9 3.0 - - - +
124E GLU 5.8 2.9 - - - -
125E GLN* 5.9 0.2 - - - -
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Residues in contact with MET 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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23E ILE* 3.9 5.0 - - - +
39E SER* 1.3 84.7 + - - +
41E ASP* 1.3 64.3 + - - +
44E HIS* 3.3 65.2 - - + +
46E SER 3.5 9.0 - - - +
47E LEU* 3.6 21.5 - - + -
124E GLU* 4.6 18.4 + - - +
126E LEU* 4.3 10.3 - - + -
147F MET* 3.3 20.2 - - + -
148F THR* 3.5 26.9 - - + +
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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