Contacts of the strand formed by residues 28 - 36 (chain E) in PDB entry 3IT8
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 GLN 28 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E HIS* 3.4 3.4 - - - -
25E TYR* 2.8 40.1 + - + +
26E ASN 3.2 0.4 - - - -
27E ASP* 1.3 104.6 - - - +
29E LEU* 1.3 66.8 + - - +
30E VAL* 3.3 1.9 + - - +
50E TRP* 4.2 21.4 - - + +
177E LYS 4.8 2.4 + - - -
178E ILE* 3.6 38.3 - - + +
179E PRO* 4.1 14.5 - - - +
208E TYR* 4.1 3.8 + - - +
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Residues in contact with LEU 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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22E TYR* 3.9 19.7 - - + -
23E ASP 3.6 6.1 - - - +
24E HIS* 3.4 27.3 + - + +
27E ASP 3.8 2.4 + - - -
28E GLN* 1.3 74.0 - - - +
30E VAL* 1.3 61.6 + - - +
31E THR 3.5 24.5 - - - +
32E LYS* 4.6 7.2 - - + -
46E PHE* 3.6 44.9 - - + -
48E ALA* 3.6 15.4 - - - +
50E TRP* 5.1 0.7 + - - -
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ASP* 2.7 27.3 + - - +
25E TYR* 3.8 23.1 - - + +
28E GLN 3.5 14.6 - - - +
29E LEU* 1.3 75.7 - - - +
31E THR* 1.3 66.6 + - - +
46E PHE* 4.3 2.7 - - - -
47E ARG* 3.3 4.5 - - - -
48E ALA* 2.9 28.4 + - - -
50E TRP* 4.0 14.1 - - + -
51E PHE* 3.5 43.3 - - + -
170E TYR* 4.0 11.7 - - + -
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Residues in contact with THR 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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21E PHE* 3.7 3.3 - - + +
22E TYR* 3.4 4.5 - - - -
23E ASP* 2.9 32.6 + - - -
29E LEU* 3.5 8.1 - - - +
30E VAL* 1.3 86.1 + - - +
32E LYS* 1.3 64.5 + - - +
33E ILE* 3.9 21.5 - - + -
44E VAL* 4.4 2.7 - - + -
46E PHE 3.3 8.7 - - - +
47E ARG* 2.3 40.6 + - - +
64E TYR* 3.0 29.2 + - + -
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Residues in contact with LYS 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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20E VAL* 4.5 13.5 - - + -
21E PHE 3.3 4.7 - - - +
22E TYR* 3.7 43.7 + - + -
29E LEU* 4.6 5.8 - - + -
31E THR* 1.3 76.1 - - - +
33E ILE* 1.3 72.5 + - - +
34E SER* 5.0 1.1 - - - -
44E VAL* 3.4 2.8 - - - +
45E ASN* 2.8 49.9 + - + +
46E PHE* 3.1 25.1 + - + +
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Residues in contact with ILE 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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20E VAL* 3.1 5.7 - - - +
21E PHE* 2.8 44.0 + - + +
31E THR* 3.9 12.6 - - + -
32E LYS* 1.3 81.1 - - - +
34E SER* 1.3 64.1 + - - +
42E GLY* 4.2 1.6 - - - -
43E ASN 3.2 18.8 - - - +
44E VAL* 3.9 15.5 - - + -
45E ASN* 3.7 2.2 - - - +
63E ASP* 3.6 38.6 - - + +
64E TYR* 3.9 17.3 - - + -
66E PHE* 3.6 31.6 - - + -
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Residues in contact with SER 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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19E GLY 3.2 11.0 - - - -
20E VAL* 4.0 11.4 - - - -
32E LYS* 5.0 1.1 - - - -
33E ILE* 1.3 76.5 - - - +
35E TYR* 1.3 65.7 + - - +
36E ASN 3.4 1.2 + - - -
42E GLY* 3.4 0.2 - - - -
43E ASN* 3.0 30.6 + - - +
45E ASN* 2.5 32.0 + - - -
66E PHE* 4.1 5.2 - - - -
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Residues in contact with TYR 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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18E ASP* 4.7 3.3 - - - +
19E GLY 2.9 19.7 + - - +
34E SER* 1.3 72.4 - - - +
36E ASN* 1.3 66.6 + - - +
37E HIS* 3.5 41.5 + + - +
40E ARG* 3.1 56.2 + - - +
41E HIS* 3.5 13.5 - - - -
66E PHE* 3.8 12.2 - + + -
67E ASN* 5.3 1.8 - - + -
70E TYR* 3.5 64.2 - + + -
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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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34E SER 3.4 1.6 + - - -
35E TYR* 1.3 72.5 - - - +
37E HIS* 1.3 52.5 + - - +
38E GLU* 2.8 16.2 + - - +
39E THR* 2.7 41.8 + - - -
40E ARG* 2.6 37.1 + - - -
41E HIS 2.9 16.7 + - - +
43E ASN* 2.9 32.4 - - - +
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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