Contacts of the strand formed by residues 10 - 17 (chain T) in PDB entry 4IBL
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 TYR 10 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7T VAL* 6.2 0.2 - - + -
8T ALA 3.8 13.5 - - - +
9T ALA* 1.3 76.0 - - - +
11T ASN* 1.3 89.4 + - - +
12T LEU* 3.2 7.0 + - - -
25T TRP* 3.7 1.6 - - - +
26T GLU* 2.9 51.3 + - + +
27T PRO* 3.9 29.4 - - + +
95T GLU* 4.7 4.7 - - + -
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Residues in contact with ASN 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T TYR* 1.3 98.5 - - + +
12T LEU* 1.3 66.3 + - - +
13T THR* 3.1 14.1 + - - +
24T GLU 3.5 5.6 - - - +
25T TRP* 3.8 4.3 - - - -
26T GLU* 4.4 13.2 - - + +
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Residues in contact with LEU 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T ALA* 3.9 7.2 - - + -
10T TYR 3.8 24.5 - - - +
11T ASN* 1.3 75.6 - - - +
13T THR* 1.3 60.5 + - - +
23T LEU* 4.3 6.5 - - + -
24T GLU 3.2 7.0 - - - +
25T TRP* 3.8 15.9 - - + -
74T ARG* 4.6 0.7 - - - -
75T VAL* 3.7 19.7 - - + +
95T GLU* 3.5 33.4 - - + +
96T ASN 3.5 3.8 - - - +
97T SER* 3.5 43.7 - - - +
98T PRO* 3.5 20.6 - - + +
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Residues in contact with THR 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T ASN* 3.1 17.1 + - - +
12T LEU* 1.3 73.2 + - - +
14T TRP* 1.3 67.0 + - - +
15T LYS* 3.5 36.1 + - + +
23T LEU* 3.6 7.2 - - - +
24T GLU* 2.9 38.8 + - - +
98T PRO* 5.2 0.9 - - - -
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Residues in contact with TRP 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T THR* 1.3 75.4 - - - +
15T LYS* 1.3 65.8 + - - +
16T SER* 4.0 2.3 + - - -
21T THR* 3.6 31.0 - - + -
22T ILE 3.9 0.9 - - - -
23T LEU* 3.9 14.6 - - + -
38T ILE* 4.4 11.9 - - + -
59T LEU* 3.9 31.2 - - + -
63T ILE* 5.0 1.6 - - + -
71T TYR* 4.5 8.1 - - + -
73T ALA* 3.8 16.8 - - + -
97T SER* 3.4 21.8 + - - -
98T PRO* 2.8 44.0 + - + +
99T GLU 4.4 1.3 - - - -
100T PHE* 3.4 49.3 - + + +
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Residues in contact with LYS 15 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79L ARG* 5.7 2.9 - - - +
13T THR* 3.5 23.7 - - + +
14T TRP* 1.3 77.7 - - - +
16T SER* 1.3 58.4 + - - +
20T LYS 3.6 1.8 - - - +
21T THR* 3.4 1.8 - - - -
22T ILE* 2.8 49.9 + - + +
24T GLU* 3.4 41.1 - - + +
107T ASN* 6.1 0.2 - - - +
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Residues in contact with SER 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T TRP 4.0 2.3 + - - -
15T LYS* 1.3 75.3 - - - +
17T THR* 1.3 62.2 + - - +
19T PHE* 4.1 0.5 - - - -
20T LYS 3.0 6.3 + - - -
21T THR* 2.9 24.7 + - - -
100T PHE* 3.4 29.5 - - - -
105T GLU 4.9 0.4 - - - +
106T THR* 2.6 27.4 + - - -
107T ASN* 2.8 35.5 + - - +
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Residues in contact with THR 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L GLN* 4.3 5.4 - - + +
69L ILE* 3.8 23.5 - - + +
16T SER* 1.3 76.8 + - - +
18T ASN* 1.3 73.5 + - - +
19T PHE 3.0 0.2 - - - -
20T LYS* 2.9 25.1 + - - +
106T THR* 3.4 0.4 + - - -
107T ASN* 3.4 26.0 + - + +
108T LEU 4.2 0.7 - - - +
109T GLY* 3.6 28.9 - - - +
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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