Contacts of the strand formed by residues 28 - 35 (chain E) in PDB entry 1IBL
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 PHE 28 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C ARG* 5.2 12.8 - - - -
13E ILE* 6.0 1.8 - - + -
14E ARG 3.2 13.9 - - - -
15E ARG* 3.7 31.9 - - + -
16E THR* 5.7 1.1 - - - -
26E PHE* 4.8 5.6 - + + -
27E ARG* 1.3 87.5 - - - +
29E GLY* 1.3 61.7 + - - +
47E LYS* 2.9 28.8 - - - +
48E ALA 3.0 12.5 + - - +
49E PRO 3.0 26.7 - - - -
50E GLU* 4.8 0.9 - - - -
51E VAL* 3.1 44.9 - - + -
54E ALA* 3.7 4.5 - - + +
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Residues in contact with GLY 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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1080A A 5.6 0.4 - - - -
12E LEU* 5.0 0.4 - - - +
13E ILE* 3.0 9.1 - - - +
14E ARG* 2.8 39.2 + - - +
16E THR* 5.2 1.6 - - - +
28E PHE* 1.3 75.1 - - - +
30E ALA* 1.3 60.2 + - - +
45E PHE* 3.8 20.9 - - - -
46E GLY 3.6 4.9 - - - -
47E LYS* 4.2 5.4 - - - -
54E ALA* 4.9 0.2 - - - -
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Residues in contact with ALA 30 (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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10E MET* 5.4 0.4 - - + -
12E LEU 3.4 4.9 - - - +
13E ILE* 3.9 14.8 - - + -
29E GLY* 1.3 74.3 - - - +
31E LEU* 1.3 60.6 + - - +
32E VAL* 4.9 0.9 - - + -
45E PHE* 3.1 10.3 - - - -
46E GLY 2.9 34.9 + - - +
51E VAL* 6.1 0.2 - - + -
54E ALA* 4.0 3.8 - - + +
55E VAL* 3.8 36.8 - - + +
58E ALA* 3.3 6.7 - - + +
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Residues in contact with LEU 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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10E MET* 3.4 5.9 - - - +
11E ILE* 2.7 61.6 + - + -
12E LEU* 2.9 24.3 + - + +
30E ALA* 1.3 71.0 - - - +
32E VAL* 1.3 56.7 + - - +
43E LEU* 3.4 24.5 - - + -
44E GLY 3.2 15.3 - - - +
45E PHE* 3.6 28.1 - - + -
128E PRO 4.4 0.4 - - - +
129E ILE* 4.1 19.1 - - + +
132E ALA* 3.7 24.5 - - + -
133E TYR* 4.6 4.3 - - + -
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Residues in contact with VAL 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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8E GLU* 4.5 8.7 - - + +
9E LYS 3.3 9.2 - - - +
10E MET* 4.5 5.6 - - + -
30E ALA* 4.7 2.0 - - + +
31E LEU* 1.3 79.3 - - - +
33E VAL* 1.3 77.0 + - - +
34E VAL* 3.8 9.2 - - + -
43E LEU* 3.2 4.8 - - - +
44E GLY 2.5 45.0 + - - +
55E VAL* 3.9 24.9 - - + +
58E ALA* 3.4 28.0 - - + -
59E GLY* 3.7 21.3 - - - +
62E ALA* 3.6 2.0 - - + +
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Residues in contact with VAL 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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8E GLU* 3.2 4.5 - - - -
9E LYS* 2.6 49.3 + - + +
11E ILE* 3.2 39.7 - - + -
32E VAL* 1.3 75.6 - - - +
34E VAL* 1.3 68.4 + - - +
41E VAL* 4.6 5.4 - - + -
42E GLY 3.4 8.3 - - - +
43E LEU* 4.6 3.6 - - + -
108E ALA* 3.6 26.7 - - + +
109E ILE* 3.8 24.2 - - + -
112E LEU* 4.3 10.1 - - + -
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Residues in contact with VAL 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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6E PHE* 3.6 40.8 - - + -
7E GLU 3.1 4.3 - - - +
8E GLU* 3.6 21.5 - - + -
32E VAL* 3.8 12.1 - - + -
33E VAL* 1.3 81.8 - - - +
35E GLY* 1.3 60.4 + - - +
41E VAL* 3.1 4.2 - - - -
42E GLY* 2.5 44.5 + - - +
62E ALA* 3.9 13.2 - - + -
63E ARG* 3.8 21.8 - - + +
66E MET* 4.5 4.0 - - - +
112E LEU* 4.5 1.1 - - - -
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Residues in contact with GLY 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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6E PHE* 3.4 7.2 - - - -
7E GLU* 2.7 42.1 + - - +
34E VAL* 1.3 75.8 - - - +
36E ASP* 1.3 59.7 + - - -
37E ARG 3.5 1.3 - - - -
40E ARG 2.9 13.0 - - - -
41E VAL* 4.0 0.9 - - - -
112E LEU* 3.3 23.5 - - - +
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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