Contacts of the strand formed by residues 25 - 30 (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 GLU 25 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E ILE* 4.6 2.9 - - - +
24E ASN* 1.3 89.2 - - + +
26E ALA* 1.3 63.4 + - - +
39E SER* 3.7 11.3 + - - -
70E VAL 3.4 7.2 - - - +
71E ASN* 5.1 2.5 - - - +
72E LEU* 4.6 0.9 - - - -
119E MET* 4.3 19.0 - - + +
121E LEU* 3.7 28.4 - - + +
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Residues in contact with ALA 26 (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* 4.3 0.4 - - + -
25E GLU* 1.3 76.6 - - - +
27E CYS* 1.3 62.3 + - - +
28E TRP* 3.7 4.4 - - - -
37E LEU* 3.7 26.5 - - + -
39E SER* 4.0 19.5 - - - +
70E VAL* 2.9 33.8 + - - +
72E LEU* 3.8 16.9 - - + +
121E LEU* 3.6 8.9 - - - +
123E VAL* 5.6 2.0 - - - -
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Residues in contact with CYS 27 (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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26E ALA* 1.3 75.1 - - - +
28E TRP* 1.3 62.3 + - - +
29E ASP* 3.7 27.1 + - - +
36E ASN 3.9 6.6 - - - +
37E LEU* 3.9 16.5 - - - +
38E GLN 4.5 6.1 + - - +
67E ALA* 3.8 15.7 - - - -
68E MET 3.6 4.0 - - - -
121E LEU* 4.1 1.7 - - + +
123E VAL* 4.1 22.4 - - + +
125E GLN* 4.2 11.6 + - - +
156F ARG* 4.1 4.7 - - - -
158F ILE* 3.6 31.6 - - + -
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Residues in contact with TRP 28 (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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12E LEU* 4.8 11.2 - - + -
15E VAL* 4.8 0.9 - - + -
16E LEU* 4.0 23.8 - - + -
19E LEU* 4.9 2.7 - - + -
26E ALA 3.7 7.2 + - - -
27E CYS* 1.3 75.0 - - - +
29E ASP* 1.3 63.8 + - - +
30E ILE* 3.5 10.1 + - + +
35E VAL* 3.3 29.6 - - + -
36E ASN 3.9 3.6 - - - -
37E LEU* 3.7 17.6 - - + +
50E LEU* 3.9 24.5 - - + -
52E LEU* 4.9 1.8 - - + -
66E LEU 3.4 2.8 - - - +
67E ALA* 4.4 0.7 - - - -
68E MET* 2.9 50.5 + - + +
70E VAL* 3.5 26.9 - - + +
72E LEU* 3.1 35.1 - - + +
75E MET* 4.0 22.7 - - + -
90E LEU* 6.2 4.0 - - + -
99E LEU* 6.5 1.1 - - + -
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Residues in contact with ASP 29 (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* 3.7 9.5 + - - +
28E TRP* 1.3 72.0 - - - +
30E ILE* 1.3 63.8 + - - +
31E SER* 5.6 0.7 - - - -
34E GLY 4.0 0.3 - - - +
35E VAL* 3.6 0.3 - - - -
36E ASN* 3.0 51.9 + - + +
37E LEU* 5.4 1.0 - - - -
38E GLN 5.5 0.7 + - - -
66E LEU 3.1 5.7 - - - +
67E ALA* 3.9 5.0 - - - +
125E GLN* 4.2 9.0 + - - +
156F ARG* 2.8 44.4 + - - -
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Residues in contact with ILE 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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2E PHE* 3.4 33.9 - - + -
28E TRP* 3.7 8.7 - - + +
29E ASP* 1.3 81.0 - - - +
31E SER* 1.3 63.4 + - - +
34E GLY 3.8 1.3 - - - -
35E VAL* 3.4 30.7 - - + -
60E TYR* 3.3 20.6 - - - +
62E CYS* 4.1 7.2 - - - -
65E ASN* 3.3 9.7 - - - +
66E LEU* 2.7 45.5 + - + +
68E MET* 3.5 33.2 - - + -
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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