Contacts of the strand formed by residues 28 - 35 (chain A) in PDB entry 5TSQ
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 ILE 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PRO* 4.2 3.6 - - - +
3A ARG 3.5 5.2 - - - +
5A ILE* 3.7 33.9 - - + -
22A ALA* 3.5 28.2 - - + +
23A TYR 5.6 0.7 - - - +
25A ASN* 3.3 12.8 + - + +
26A PRO* 3.2 4.9 - - - +
27A GLU* 1.3 84.6 - - - +
29A GLU* 1.3 66.6 + - - +
30A LEU 3.9 2.7 + - - +
245A VAL* 4.3 9.6 - - + +
248A VAL* 3.6 33.4 - - + -
249A ILE* 3.6 34.8 - - + +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 4.1 19.0 - - + +
3A ARG 2.9 12.4 + - - +
4A LYS* 3.2 30.7 - - + +
5A ILE 3.0 25.5 + - - -
28A ILE* 1.3 73.6 - - - +
30A LEU* 1.3 63.0 + - - +
31A LEU* 3.3 21.4 + - + +
116A HIS* 5.5 1.4 - - - -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.9 24.7 - - + -
7A LEU* 3.9 15.7 - - + +
19A ILE* 4.6 4.5 - - + +
22A ALA* 4.2 18.2 - - + +
23A TYR* 4.4 29.4 - - + +
28A ILE* 3.8 4.3 + - + -
29A GLU* 1.3 72.4 - - - +
31A LEU* 1.3 60.3 + - - +
32A ALA 3.5 21.5 - - - +
33A ILE* 4.1 15.9 - - + -
58A ILE* 5.1 1.8 - - + -
61A VAL* 3.7 40.1 - - + +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.9 10.8 - - + -
5A ILE 2.9 20.0 + - - +
6A ILE* 4.5 0.9 - - + -
29A GLU* 3.8 35.7 - - + +
30A LEU* 1.3 74.6 - - - +
32A ALA* 1.3 62.9 + - - +
60A GLY 5.3 0.2 - - - +
61A VAL* 4.2 2.0 - - - -
62A PRO* 3.3 20.8 - - - +
112A LEU* 4.2 22.5 - - + +
116A HIS* 3.9 27.4 - - + +
121A ILE* 3.6 39.7 - - + -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE 4.0 1.6 + - - -
6A ILE* 3.8 12.9 - - + -
7A LEU 3.1 24.4 + - - -
30A LEU* 3.5 9.7 + - - +
31A LEU* 1.3 81.7 - - - +
33A ILE* 1.3 63.8 + - - +
34A THR* 4.0 2.2 - - + -
61A VAL* 3.8 4.5 - - - +
62A PRO* 3.5 8.5 - - + +
108A LEU* 3.8 22.9 - - + -
112A LEU* 3.8 21.1 - - + -
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.4 6.7 - - + +
9A CYS* 3.9 24.5 - - - -
19A ILE* 3.8 33.2 - - + -
30A LEU* 4.1 22.7 - - + -
32A ALA* 1.3 75.1 - - - +
34A THR* 1.3 62.8 + - - +
35A THR* 4.6 1.1 - - + -
49A ALA* 4.3 21.3 - - + +
53A ALA* 5.3 2.2 - - + -
58A ILE* 4.5 11.7 - - + -
61A VAL* 4.1 9.4 - - + +
62A PRO 2.9 8.9 + - - +
63A ILE* 3.2 24.6 - - + +
64A ALA 3.0 23.7 + - - +
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.8 13.9 - - + +
7A LEU 2.9 6.1 + - - +
8A ASP* 2.6 35.8 + - - +
9A CYS* 2.8 27.0 + - - +
32A ALA* 4.5 1.1 - - + -
33A ILE* 1.3 78.2 - - - +
35A THR* 1.3 63.9 + - - +
64A ALA 3.3 4.9 - - - +
105A ALA* 3.6 29.2 - - + +
108A LEU* 4.3 17.3 - - + -
109A ILE* 4.1 17.3 - - + +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A CYS* 3.1 9.6 - - - +
11A PRO* 4.4 3.6 - - + -
33A ILE* 4.6 3.6 - - + -
34A THR* 1.3 80.1 - - - +
36A VAL* 1.3 62.4 + - - +
42A LEU* 3.6 1.8 - - - +
45A VAL* 4.2 10.8 - - - +
46A THR* 2.9 32.3 + - - +
49A ALA* 3.9 28.5 - - + -
63A ILE* 4.6 7.6 - - + -
64A ALA 3.0 7.7 + - - +
65A ALA* 3.3 14.4 + - - -
66A GLY* 2.8 23.6 + - - -
131A ASN* 2.9 10.5 + - - -
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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