Contacts of the strand formed by residues 35 - 41 (chain E) in PDB entry 2XN9
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 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E ILE* 3.6 3.6 - - - +
32E TYR* 2.8 39.0 + - + +
33E ASN 2.9 6.8 + - - +
34E GLN* 1.3 73.0 - - - +
36E GLU* 1.3 67.8 + - - +
37E SER* 3.3 4.7 + - - -
51E THR* 3.9 20.9 + - + +
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Residues in contact with GLU 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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143D HIS* 4.3 9.4 + - - +
29E ARG* 3.1 57.5 + - + +
30E CYS 3.4 12.8 - - - +
31E ILE* 3.8 15.8 - - + +
34E GLN 3.8 2.4 + - - -
35E GLU* 1.3 71.3 - - - +
37E SER* 1.3 60.9 + - - +
38E VAL 4.2 2.9 - - - +
39E ARG* 3.2 30.5 + - - +
50E VAL* 3.3 37.5 - - + +
51E THR* 3.4 11.3 - - - +
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Residues in contact with SER 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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73D MET* 4.5 12.9 - - - +
9E TRP* 4.4 9.9 - - - -
30E CYS* 2.8 18.6 + - - +
32E TYR* 5.2 1.1 - - - -
35E GLU 3.3 6.5 + - - -
36E GLU* 1.3 73.0 - - - +
38E VAL* 1.3 68.7 + - - +
50E VAL* 2.8 26.4 + - - -
51E THR* 3.3 18.8 + - - +
53E LEU* 4.6 3.8 - - - -
54E GLY* 3.2 27.3 - - - -
57E ASP* 5.1 1.0 + - - -
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Residues in contact with VAL 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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9E TRP* 5.6 0.2 - - + -
29E ARG* 3.8 0.3 - - - -
30E CYS* 3.0 41.7 + - + +
36E GLU* 4.0 1.6 - - - +
37E SER* 1.3 90.2 + - - +
39E ARG* 1.3 70.1 + - - +
47E TYR* 4.3 3.4 - - + -
48E ARG 3.5 21.8 - - - +
49E ALA* 4.3 0.2 - - - -
50E VAL* 3.5 5.6 - - - +
54E GLY* 4.0 7.4 - - - +
57E ASP* 4.3 14.1 - - + +
58E ALA* 4.0 26.7 - - + +
61E TRP* 3.9 23.6 - - + -
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Residues in contact with ARG 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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25E ARG* 5.6 1.8 - - - +
27E LEU* 3.6 22.0 - - - +
28E GLU 3.0 17.3 - - - +
29E ARG* 2.7 34.8 - - + +
36E GLU* 3.2 28.1 + - - +
38E VAL* 1.3 72.4 - - - +
40E PHE* 1.3 60.3 + - - +
41E ASP* 4.8 8.1 - - + -
46E GLU 4.1 0.3 - - - +
47E TYR* 3.2 11.1 - - - -
48E ARG* 2.9 45.2 + - + +
50E VAL* 4.1 19.1 - - + +
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Residues in contact with PHE 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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26E LEU* 4.6 12.8 - - + -
27E LEU* 3.3 6.9 - - - +
28E GLU* 2.7 45.4 + - + +
39E ARG* 1.3 71.6 - - - +
41E ASP* 1.3 59.1 + - - +
42E SER* 3.7 25.4 - - - -
45E GLY* 3.3 41.1 - - - -
46E GLU* 3.4 21.8 - - - -
47E TYR* 3.4 37.1 - + + +
68E LEU* 4.5 4.0 - - + -
71E ARG* 3.9 37.9 - - + -
72E ARG* 4.0 13.7 - - + -
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Residues in contact with ASP 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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25E ARG* 2.7 45.6 + - - -
26E LEU 3.5 4.2 - - - +
27E LEU* 3.8 9.4 - - + +
39E ARG* 4.2 8.9 - - + -
40E PHE* 1.3 79.4 - - - +
42E SER* 1.3 54.9 + - - +
43E ASP* 3.1 16.8 + - - +
44E VAL* 2.7 46.9 + - + +
45E GLY* 2.8 11.4 + - - -
46E GLU 4.2 3.5 + - - +
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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