Contacts of the strand formed by residues 28 - 36 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L HIS* 3.4 3.9 - - - -
25L TYR* 2.8 38.5 + - + +
26L ASN 3.3 0.6 + - - -
27L ASP* 1.3 102.7 - - - +
29L LEU* 1.3 65.5 + - - +
30L VAL* 3.3 2.3 + - - +
50L TRP* 4.2 21.4 - - + +
177L LYS 4.7 2.2 + - - -
178L ILE* 3.6 38.5 - - + +
179L PRO* 4.1 16.8 - - - +
208L TYR* 4.3 3.4 - - - +
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Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L TYR* 3.9 17.7 - - + -
23L ASP 3.7 4.3 - - - +
24L HIS* 3.4 31.3 + - + +
27L ASP 3.8 2.6 + - - -
28L GLN* 1.3 73.9 - - - +
30L VAL* 1.3 61.1 + - - +
31L THR 3.5 24.7 - - - +
32L LYS* 4.6 7.2 - - + -
46L PHE* 3.6 45.1 - - + -
48L ALA* 3.6 15.1 - - - +
50L TRP* 5.0 0.7 + - - -
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Residues in contact with VAL 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ASP* 2.7 27.5 + - - +
25L TYR* 3.8 24.2 - - + +
28L GLN 3.5 13.9 - - - +
29L LEU* 1.3 75.2 - - - +
31L THR* 1.3 66.1 + - - +
46L PHE* 4.3 2.2 - - - -
47L ARG* 3.3 4.3 - - - -
48L ALA* 2.9 27.9 + - + -
50L TRP* 3.9 15.0 - - + -
51L PHE* 3.5 41.3 - - + -
170L TYR* 4.0 11.4 - - + -
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Residues in contact with THR 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L PHE* 4.4 2.9 - - + -
22L TYR* 3.4 5.0 - - - -
23L ASP* 2.9 31.6 + - - -
29L LEU* 3.5 8.1 - - - +
30L VAL* 1.3 86.1 + - - +
32L LYS* 1.3 64.4 + - - +
33L ILE* 3.8 21.5 - - + -
44L VAL* 4.4 2.2 - - + -
46L PHE 3.3 9.4 - - - +
47L ARG* 2.3 41.1 + - - +
64L TYR* 3.0 28.8 + - + -
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Residues in contact with LYS 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L VAL* 4.5 12.5 - - - +
21L PHE 3.3 5.2 - - - +
22L TYR* 3.6 41.7 + - + -
29L LEU* 4.6 7.4 - - + -
31L THR* 1.3 75.7 - - - +
33L ILE* 1.3 72.1 + - - +
34L SER* 5.0 1.1 - - - -
44L VAL* 3.5 1.6 - - - -
45L ASN* 2.8 51.4 + - + +
46L PHE* 3.1 27.0 + - + +
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Residues in contact with ILE 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L VAL* 3.1 5.7 - - - +
21L PHE* 2.7 49.1 + - + +
31L THR* 3.8 12.3 - - + -
32L LYS* 1.3 82.1 - - - +
34L SER* 1.3 65.6 + - - +
42L GLY* 4.2 1.6 - - - -
43L ASN 3.3 18.2 - - - +
44L VAL* 3.9 14.8 - - + -
45L ASN* 3.8 1.8 - - - +
63L ASP* 3.6 38.8 - - + +
64L TYR* 3.8 18.2 - - + -
66L PHE* 3.6 31.4 - - + -
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Residues in contact with SER 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L GLY 3.1 10.5 - - - -
20L VAL* 4.0 11.4 - - - -
32L LYS* 5.0 1.6 - - - -
33L ILE* 1.3 76.3 - - - +
35L TYR* 1.3 66.6 + - - +
36L ASN 3.4 1.0 + - - -
42L GLY* 3.3 0.2 - - - -
43L ASN* 3.0 28.8 + - - +
45L ASN* 2.5 34.3 + - - -
66L PHE* 4.1 4.9 - - - -
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Residues in contact with TYR 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ASP* 4.7 3.5 - - - +
19L GLY 2.9 18.5 + - - +
34L SER* 1.3 73.1 - - - +
36L ASN* 1.3 66.6 + - - +
37L HIS* 3.5 40.6 + + - -
40L ARG* 3.1 55.5 + - - +
41L HIS* 3.5 13.0 - - - -
66L PHE* 3.8 10.9 - + + -
67L ASN* 5.4 2.0 - - - -
70L TYR* 3.5 65.9 - + + -
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Residues in contact with ASN 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L SER 3.4 1.6 + - - -
35L TYR* 1.3 71.1 - - - +
37L HIS* 1.3 55.3 + - - +
38L GLU* 2.8 22.6 + - - +
39L THR* 2.6 42.6 + - - -
40L ARG* 2.6 36.7 + - - -
41L HIS 2.9 16.8 + - - +
43L ASN* 2.9 32.7 - - - +
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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