Contacts of the strand formed by residues 45 - 53 (chain E) in PDB entry 4IHB
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 VAL 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E LEU 3.7 11.2 - - - +
8E TYR* 4.0 14.6 - - + -
36E LYS* 5.0 0.7 + - - -
38E ILE* 3.4 21.4 - - - +
43E ASN 3.4 9.4 + - - +
44E PRO* 1.3 76.5 - - - +
46E TRP* 1.3 63.2 + - - +
47E ASN* 4.4 13.9 - - + +
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Residues in contact with TRP 46 (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 ILE* 3.6 23.1 - - + +
7E LEU 2.8 7.9 + - - -
8E TYR* 3.9 14.4 - - - -
9E ALA* 3.6 28.9 - - + -
22E ALA* 3.1 34.6 + - + -
23E TYR* 3.9 7.2 - - - -
24E CYS* 4.2 7.4 - - + -
35E THR* 3.3 25.6 + - + -
36E LYS* 3.1 47.4 + - + +
38E ILE* 3.4 17.2 - - + +
44E PRO* 3.6 20.6 - - + -
45E VAL* 1.3 74.3 - - - +
47E ASN* 1.3 71.5 + - - +
48E GLU* 3.3 5.1 + - - +
69E VAL* 4.5 9.6 - - + -
117E LEU* 3.6 26.9 - - + -
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Residues in contact with ASN 47 (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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5E PHE* 5.6 3.4 - - - -
6E ILE 3.1 6.4 + - - -
7E LEU* 3.0 34.7 + - + +
45E VAL* 4.5 13.0 - - + -
46E TRP* 1.3 79.8 - - - +
48E GLU* 1.3 59.7 + - - +
49E GLY 4.4 0.2 + - - -
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Residues in contact with GLU 48 (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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4E VAL 3.7 0.5 - - - +
5E PHE* 3.3 6.9 - - - -
6E ILE 2.9 31.5 + - - +
7E LEU* 5.2 0.2 - - - +
35E THR* 3.4 9.5 - - + -
36E LYS* 2.6 62.3 + - - +
46E TRP* 3.6 5.7 - - + +
47E ASN* 1.3 77.3 - - - +
49E GLY* 1.3 59.8 + - - +
50E PHE* 3.6 23.1 - - + -
204E FMT 2.5 32.3 + - - -
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Residues in contact with GLY 49 (chain E).
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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3E ARG* 6.0 0.2 - - - -
4E VAL 3.4 5.6 - - - -
5E PHE* 3.6 22.0 - - - -
47E ASN 4.4 0.4 + - - -
48E GLU* 1.3 73.1 - - - +
50E PHE* 1.3 77.1 + - - -
51E GLU* 5.8 0.4 - - - -
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Residues in contact with PHE 50 (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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2E LEU 3.7 0.7 - - - +
3E ARG* 3.4 4.6 - - - +
4E VAL* 2.8 41.6 + - + +
6E ILE* 3.5 32.1 - - + -
26E ALA* 5.5 0.9 - - + -
33E LYS* 3.6 34.3 - - + -
34E ARG* 3.5 26.5 - - - -
35E THR* 3.7 13.0 - - + -
48E GLU* 3.6 37.2 - - + -
49E GLY* 1.3 79.7 - - - -
51E GLU* 1.3 65.9 + - - +
52E TRP* 3.8 13.5 - + + -
202E FMT 3.6 14.1 - - - -
204E FMT 4.1 1.8 - - - -
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Residues in contact with GLU 51 (chain E).
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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1E MET* 3.3 38.5 - - + +
2E LEU 3.3 2.2 - - - -
3E ARG* 3.7 31.1 + - + +
33E LYS* 3.2 24.0 + - - +
49E GLY 5.8 0.2 - - - -
50E PHE* 1.3 80.5 - - - +
52E TRP* 1.3 60.0 + - - +
53E ASP 3.9 1.6 + - - -
124E THR* 4.0 6.2 - - - +
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Residues in contact with TRP 52 (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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1E MET* 3.7 4.0 - - - -
2E LEU* 2.9 54.5 + - + +
4E VAL* 3.5 30.1 - - + -
26E ALA* 3.7 40.4 - - + -
28E PHE* 3.4 49.2 + + + +
29E ALA* 5.7 0.2 - - + -
31E VAL* 3.0 37.6 + - + +
33E LYS* 3.5 26.4 - - + +
50E PHE* 3.8 14.6 - + + -
51E GLU* 1.3 72.9 - - - +
53E ASP* 1.3 66.0 + - - +
54E LEU* 3.2 2.4 + - - -
65E LEU* 3.9 8.5 - - + -
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Residues in contact with ASP 53 (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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0E PHE 4.7 1.0 - - - +
1E MET* 3.7 22.1 - - + +
28E PHE* 6.0 0.7 - - - -
51E GLU 3.9 3.6 + - - -
52E TRP* 1.3 69.9 - - - +
54E LEU* 1.3 73.0 + - - +
55E LYS* 3.4 47.0 + - - +
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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