Contacts of the strand formed by residues 18 - 24 (chain I) in PDB entry 4EUP
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 ALA 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I LEU* 4.6 1.6 - - + -
12I VAL* 3.6 29.8 - - + +
16I ALA 4.1 0.4 + - - -
17I ILE* 1.3 73.7 - - - +
19I SER* 1.3 61.5 + - - +
20I LEU* 4.0 2.4 - - + +
73I LEU 3.5 1.7 - - - +
74I LEU* 3.4 7.4 - - - -
75I ILE* 3.4 47.4 + - + +
78I ALA* 5.0 2.9 - - + +
106I VAL* 4.3 19.5 - - + -
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Residues in contact with SER 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ASN* 2.9 20.4 + - - -
10I LEU* 3.6 15.7 - - - +
17I ILE* 3.9 8.5 + - - +
18I ALA* 1.3 71.1 - - - +
20I LEU* 1.3 62.4 + - - +
21I ASN* 4.4 12.0 - - - +
73I LEU 3.7 3.4 - - - -
74I LEU* 3.2 23.4 - - - +
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ASN* 3.8 3.1 - - - +
10I LEU* 4.6 1.8 - - + -
18I ALA* 4.7 2.7 - - + +
19I SER* 1.3 79.2 - - - +
21I ASN* 1.3 67.4 + - - +
34I TRP* 3.9 19.5 - - + -
72I SER* 3.4 0.7 - - - -
73I LEU* 2.9 48.0 + - + +
75I ILE* 4.0 23.1 - - + -
86I TYR* 3.9 30.1 - - + -
104I THR* 3.4 38.4 - - + +
106I VAL* 3.8 19.7 - - + -
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Residues in contact with ASN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLN* 3.3 23.5 + - - +
6I ASN* 2.9 38.9 + - + +
19I SER* 4.4 10.8 - - - +
20I LEU* 1.3 81.9 + - - +
22I CYS* 1.3 61.9 + - - +
23I THR* 6.1 0.2 - - + -
34I TRP* 3.9 2.3 - - - -
70I TYR* 3.0 31.8 + - + +
71I VAL 3.7 3.4 - - - -
72I SER* 2.8 27.7 + - - -
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Residues in contact with CYS 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 3.6 21.8 - - - -
4I GLU 3.3 5.8 - - - -
5I GLN* 4.3 0.4 - - - -
21I ASN* 1.3 78.7 - - - +
23I THR* 1.3 65.3 + - - +
24I TYR* 4.7 1.3 - - - -
34I TRP* 3.9 3.4 - - + -
70I TYR* 3.3 6.5 - - - -
71I VAL* 2.8 48.4 + - + +
88I CYS* 2.1 51.4 - - + -
90I VAL* 4.9 4.0 - - - -
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Residues in contact with THR 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU 4.0 0.9 - - - +
3I VAL* 3.5 3.3 - - - +
4I GLU* 2.7 67.6 + - - +
21I ASN* 6.1 0.2 - - + -
22I CYS* 1.3 75.0 - - - +
24I TYR* 1.3 62.7 + - - +
68I SER 5.4 1.3 - - - +
69I GLN 3.4 9.0 - - - +
70I TYR* 3.4 37.7 - - + -
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Residues in contact with TYR 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I GLU 3.7 4.9 - - - -
3I VAL* 4.4 8.5 - - + -
22I CYS* 4.7 1.6 - - - -
23I THR* 1.3 81.0 - - - +
25I SER* 1.3 63.2 + - - +
26I ASP 3.4 23.3 - - - +
27I ARG* 4.9 4.1 + - - -
29I SER* 4.1 5.6 + - - -
32I PHE* 3.4 44.8 - + - -
64I LEU* 4.0 2.0 - - + +
66I LYS* 3.5 23.2 + - - +
69I GLN* 3.2 72.0 + - + +
70I TYR 3.5 3.4 - - - -
71I VAL* 3.9 16.6 - - + -
90I VAL* 4.2 18.4 - - + -
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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